https://launchpad.net/ubuntu/+archive/test-rebuild-20240502-noble/+build/28246702
RUN: /usr/share/launchpad-buildd/bin/builder-prep 
Kernel version: Linux bos02-arm64-065 5.4.0-182-generic #202-Ubuntu SMP Fri Apr 26 16:08:13 UTC 2024 aarch64
Buildd toolchain package versions: launchpad-buildd_237~660~ubuntu20.04.1 python3-lpbuildd_237~660~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1.
Syncing the system clock with the buildd NTP service...
19 May 13:40:44 ntpdate[1804]: adjust time server 10.211.37.1 offset 0.001879 sec
RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-28246702 --image-type chroot /home/buildd/filecache-default/0aaa0d191106d33e51979a9c6a062e50b7f5b3b2
Creating target for build PACKAGEBUILD-28246702
RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-28246702
Starting target for build PACKAGEBUILD-28246702
RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-28246702 'deb http://ftpmaster.internal/ubuntu noble main universe'
Overriding sources.list in build-PACKAGEBUILD-28246702
RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-28246702
Updating target for build PACKAGEBUILD-28246702
Get:1 http://ftpmaster.internal/ubuntu noble InRelease [256 kB]
Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 Packages [1377 kB]
Get:3 http://ftpmaster.internal/ubuntu noble/main Translation-en [513 kB]
Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 Packages [15.3 MB]
Get:5 http://ftpmaster.internal/ubuntu noble/universe Translation-en [5982 kB]
Fetched 23.4 MB in 8s (3092 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages were automatically installed and are no longer required:
  libnsl-dev libperl5.36 libtirpc-dev libunistring2 perl-modules-5.36
Use 'sudo apt autoremove' to remove them.
The following packages will be REMOVED:
  libapt-pkg6.0* libdb5.3* libext2fs2* libgdbm-compat4* libgdbm6* libgnutls30*
  libhogweed6* libnettle8* libnpth0* libpng16-16* libreadline8* libssl3*
  libtirpc3* usrmerge*
The following NEW packages will be installed:
  cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu g++-13-aarch64-linux-gnu
  g++-aarch64-linux-gnu gcc-13-aarch64-linux-gnu gcc-14-base
  gcc-aarch64-linux-gnu libapt-pkg6.0t64 libdb5.3t64 libext2fs2t64
  libgdbm-compat4t64 libgdbm6t64 libgnutls30t64 libhogweed6t64 libnettle8t64
  libnpth0t64 libperl5.38t64 libpng16-16t64 libreadline8t64 libssl3t64
  libtirpc3t64 libunistring5 perl-modules-5.38
The following packages will be upgraded:
  advancecomp apt apt-utils base-files base-passwd bash bash-completion
  binutils binutils-aarch64-linux-gnu binutils-common bsdextrautils bsdutils
  bzip2 ca-certificates coreutils cpp cpp-13 dash debconf debconf-i18n
  debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot findutils g++ g++-13
  gcc gcc-13 gcc-13-base gpg gpg-agent gpgconf gpgv grep gzip hostname init
  init-system-helpers krb5-locales libacl1 libapparmor1 libargon2-1 libasan8
  libassuan0 libatomic1 libattr1 libaudit-common libaudit1 libbinutils
  libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0
  libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12
  libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl
  libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgmp10
  libgomp1 libgpg-error-l10n libgpg-error0 libgpm2 libgprofng0
  libgssapi-krb5-2 libhwasan0 libidn2-0 libip4tc2 libisl23 libitm1 libjansson4
  libjson-c5 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0
  liblocale-gettext-perl liblockfile-bin liblockfile1 liblsan0 liblz4-1
  liblzma5 libmd0 libmount1 libmpc3 libmpfr6 libncursesw6 libnsl-dev libnsl2
  libnss-nis libnss-nisplus libp11-kit0 libpam-modules libpam-modules-bin
  libpam-runtime libpam0g libpcre2-8-0 libproc2-0 libseccomp2 libselinux1
  libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1
  libsqlite3-0 libss2 libstdc++-13-dev libstdc++6 libsystemd-shared
  libsystemd0 libtasn1-6 libtext-charwidth-perl libtext-iconv-perl libtinfo6
  libtirpc-common libtirpc-dev libtsan2 libubsan1 libudev1 libuuid1 libxxhash0
  libzstd1 linux-libc-dev lockfile-progs login logsave lto-disabled-list make
  mawk mount ncurses-base ncurses-bin openssl optipng passwd patch perl
  perl-base pinentry-curses procps psmisc readline-common rpcsvc-proto sed
  sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata
  ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g
176 upgraded, 23 newly installed, 14 to remove and 0 not upgraded.
Need to get 116 MB of archives.
After this operation, 77.5 MB of additional disk space will be used.
Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 libtirpc-common all 1.3.4+ds-1.1build1 [8094 B]
Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libtirpc-dev arm64 1.3.4+ds-1.1build1 [201 kB]
Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl-dev arm64 1.3.0-3build3 [72.5 kB]
Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl2 arm64 1.3.0-3build3 [41.6 kB]
Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.1build1 [83.6 kB]
Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libgssapi-krb5-2 arm64 1.20.1-6ubuntu2 [141 kB]
Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libkrb5-3 arm64 1.20.1-6ubuntu2 [349 kB]
Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libk5crypto3 arm64 1.20.1-6ubuntu2 [85.6 kB]
Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libkrb5support0 arm64 1.20.1-6ubuntu2 [33.9 kB]
Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libacl1 arm64 2.3.2-1build1 [17.0 kB]
Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libapparmor1 arm64 4.0.0-beta3-0ubuntu3 [50.0 kB]
Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libaudit-common all 1:3.1.2-2.1build1 [5736 B]
Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libcap-ng0 arm64 0.8.4-2build2 [14.8 kB]
Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libaudit1 arm64 1:3.1.2-2.1build1 [47.6 kB]
Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libblkid1 arm64 2.39.3-9ubuntu6 [123 kB]
Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libcap2 arm64 1:2.66-5ubuntu2 [30.2 kB]
Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4build1 [118 kB]
Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt1 arm64 1:4.4.36-4build1 [85.9 kB]
Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libgpg-error-l10n all 1.47-3build2 [8064 B]
Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libgpg-error0 arm64 1.47-3build2 [70.0 kB]
Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libgcrypt20 arm64 1.10.3-2build1 [472 kB]
Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 liblzma5 arm64 5.6.1+really5.4.5-1 [125 kB]
Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libzstd1 arm64 1.5.5+dfsg2-2build1 [271 kB]
Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libkmod2 arm64 31+20240202-2ubuntu7 [51.8 kB]
Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 liblz4-1 arm64 1.9.4-1build1 [64.1 kB]
Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-8-0 arm64 10.42-4ubuntu2 [212 kB]
Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libselinux1 arm64 3.5-2ubuntu2 [79.9 kB]
Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libmount1 arm64 2.39.3-9ubuntu6 [133 kB]
Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 perl-modules-5.38 all 5.38.2-3.2build2 [3110 kB]
Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-7 [732 kB]
Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libgdbm6t64 arm64 1.23-5.1build1 [34.4 kB]
Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libgdbm-compat4t64 arm64 1.23-5.1build1 [6578 B]
Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libperl5.38t64 arm64 5.38.2-3.2build2 [4774 kB]
Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 perl arm64 5.38.2-3.2build2 [231 kB]
Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 perl-base arm64 5.38.2-3.2build2 [1777 kB]
Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 liblocale-gettext-perl arm64 1.07-6ubuntu5 [15.3 kB]
Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libtext-iconv-perl arm64 1.7-8build3 [13.1 kB]
Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libtext-charwidth-perl arm64 0.04-11build3 [9406 B]
Get:39 http://ftpmaster.internal/ubuntu noble/universe arm64 libnss-nisplus arm64 1.3-5build1 [22.5 kB]
Get:40 http://ftpmaster.internal/ubuntu noble/universe arm64 libnss-nis arm64 3.1-0ubuntu7 [26.6 kB]
Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libc-dev-bin arm64 2.39-0ubuntu8 [19.7 kB]
Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 rpcsvc-proto arm64 1.4.2-0ubuntu7 [64.8 kB]
Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libc6-dev arm64 2.39-0ubuntu8 [1596 kB]
Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libc6 arm64 2.39-0ubuntu8 [2774 kB]
Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libc-bin arm64 2.39-0ubuntu8 [591 kB]
Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 openssl arm64 3.0.13-0ubuntu3 [984 kB]
Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libsystemd-shared arm64 255.4-1ubuntu8 [2016 kB]
Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libcryptsetup12 arm64 2:2.7.0-1ubuntu4 [262 kB]
Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libssl3t64 arm64 3.0.13-0ubuntu3 [1793 kB]
Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 systemd-dev all 255.4-1ubuntu8 [104 kB]
Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 systemd-sysv arm64 255.4-1ubuntu8 [11.9 kB]
Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 systemd arm64 255.4-1ubuntu8 [3403 kB]
Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libsystemd0 arm64 255.4-1ubuntu8 [424 kB]
Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libpam-modules-bin arm64 1.5.3-5ubuntu5 [50.4 kB]
Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libpam-modules arm64 1.5.3-5ubuntu5 [278 kB]
Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libnettle8t64 arm64 3.9.1-2.2build1 [192 kB]
Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libhogweed6t64 arm64 3.9.1-2.2build1 [199 kB]
Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libp11-kit0 arm64 0.25.3-4ubuntu2 [276 kB]
Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libunistring5 arm64 1.1-2build1 [530 kB]
Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 libgnutls30t64 arm64 3.8.3-1.1ubuntu3 [942 kB]
Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 libapt-pkg6.0t64 arm64 2.7.14build2 [935 kB]
Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 bzip2 arm64 1.0.8-5.1 [34.0 kB]
Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 libbz2-1.0 arm64 1.0.8-5.1 [35.7 kB]
Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-14-base arm64 14-20240412-0ubuntu1 [47.6 kB]
Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-s1 arm64 14-20240412-0ubuntu1 [61.7 kB]
Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++6 arm64 14-20240412-0ubuntu1 [748 kB]
Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 libudev1 arm64 255.4-1ubuntu8 [173 kB]
Get:68 http://ftpmaster.internal/ubuntu noble/main arm64 libxxhash0 arm64 0.8.2-2build1 [21.7 kB]
Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 zlib1g arm64 1:1.3.dfsg-3.1ubuntu2 [61.7 kB]
Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 libgmp10 arm64 2:6.3.0+dfsg-2ubuntu6 [243 kB]
Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 libffi8 arm64 3.4.6-1build1 [22.7 kB]
Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 libidn2-0 arm64 2.3.7-2build1 [67.2 kB]
Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 libtasn1-6 arm64 4.19.0-3build1 [43.1 kB]
Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 libdebconfclient0 arm64 0.271ubuntu3 [11.3 kB]
Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 base-passwd arm64 3.6.3build1 [51.1 kB]
Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 libassuan0 arm64 2.5.6-1build1 [36.8 kB]
Get:77 http://ftpmaster.internal/ubuntu noble/main arm64 libsqlite3-0 arm64 3.45.1-1ubuntu2 [703 kB]
Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 gpg arm64 2.4.4-2ubuntu17 [548 kB]
Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 libreadline8t64 arm64 8.2-4build1 [153 kB]
Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 readline-common all 8.2-4build1 [56.5 kB]
Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 libncursesw6 arm64 6.4+20240113-1ubuntu2 [145 kB]
Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 libtinfo6 arm64 6.4+20240113-1ubuntu2 [104 kB]
Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 gpg-agent arm64 2.4.4-2ubuntu17 [221 kB]
Get:84 http://ftpmaster.internal/ubuntu noble/main arm64 gpgconf arm64 2.4.4-2ubuntu17 [103 kB]
Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 pinentry-curses arm64 1.2.1-3ubuntu5 [34.3 kB]
Get:86 http://ftpmaster.internal/ubuntu noble/main arm64 init-system-helpers all 1.66ubuntu1 [39.4 kB]
Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 libnpth0t64 arm64 1.6-3.1build1 [8144 B]
Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 gpgv arm64 2.4.4-2ubuntu17 [150 kB]
Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-keyring all 2023.11.28.1 [11.1 kB]
Get:90 http://ftpmaster.internal/ubuntu noble/main arm64 libseccomp2 arm64 2.5.5-1ubuntu3 [51.1 kB]
Get:91 http://ftpmaster.internal/ubuntu noble/main arm64 apt-utils arm64 2.7.14build2 [205 kB]
Get:92 http://ftpmaster.internal/ubuntu noble/main arm64 apt arm64 2.7.14build2 [1336 kB]
Get:93 http://ftpmaster.internal/ubuntu noble/main arm64 debconf-i18n all 1.5.86ubuntu1 [205 kB]
Get:94 http://ftpmaster.internal/ubuntu noble/main arm64 debconf all 1.5.86ubuntu1 [124 kB]
Get:95 http://ftpmaster.internal/ubuntu noble/main arm64 libpam0g arm64 1.5.3-5ubuntu5 [67.8 kB]
Get:96 http://ftpmaster.internal/ubuntu noble/main arm64 libargon2-1 arm64 0~20190702+dfsg-4build1 [20.5 kB]
Get:97 http://ftpmaster.internal/ubuntu noble/main arm64 libdevmapper1.02.1 arm64 2:1.02.185-3ubuntu3 [128 kB]
Get:98 http://ftpmaster.internal/ubuntu noble/main arm64 libjson-c5 arm64 0.17-1build1 [36.4 kB]
Get:99 http://ftpmaster.internal/ubuntu noble/main arm64 libuuid1 arm64 2.39.3-9ubuntu6 [35.4 kB]
Get:100 http://ftpmaster.internal/ubuntu noble/main arm64 libfdisk1 arm64 2.39.3-9ubuntu6 [142 kB]
Get:101 http://ftpmaster.internal/ubuntu noble/main arm64 mount arm64 2.39.3-9ubuntu6 [116 kB]
Get:102 http://ftpmaster.internal/ubuntu noble/main arm64 libcom-err2 arm64 1.47.0-2.4~exp1ubuntu4 [22.4 kB]
Get:103 http://ftpmaster.internal/ubuntu noble/main arm64 libkeyutils1 arm64 1.6.3-3build1 [9654 B]
Get:104 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.8.0-31.31 [1572 kB]
Get:105 http://ftpmaster.internal/ubuntu noble/main arm64 base-files arm64 13ubuntu10 [73.8 kB]
Get:106 http://ftpmaster.internal/ubuntu noble/main arm64 debianutils arm64 5.17build1 [90.2 kB]
Get:107 http://ftpmaster.internal/ubuntu noble/main arm64 bash arm64 5.2.21-2ubuntu4 [780 kB]
Get:108 http://ftpmaster.internal/ubuntu noble/main arm64 bsdutils arm64 1:2.39.3-9ubuntu6 [97.7 kB]
Get:109 http://ftpmaster.internal/ubuntu noble/main arm64 coreutils arm64 9.4-3ubuntu6 [1363 kB]
Get:110 http://ftpmaster.internal/ubuntu noble/main arm64 tar arm64 1.35+dfsg-3build1 [248 kB]
Get:111 http://ftpmaster.internal/ubuntu noble/main arm64 dpkg arm64 1.22.6ubuntu6 [1265 kB]
Get:112 http://ftpmaster.internal/ubuntu noble/main arm64 dash arm64 0.5.12-6ubuntu5 [90.4 kB]
Get:113 http://ftpmaster.internal/ubuntu noble/main arm64 diffutils arm64 1:3.10-1build1 [175 kB]
Get:114 http://ftpmaster.internal/ubuntu noble/main arm64 findutils arm64 4.9.0-5build1 [300 kB]
Get:115 http://ftpmaster.internal/ubuntu noble/main arm64 grep arm64 3.11-4build1 [159 kB]
Get:116 http://ftpmaster.internal/ubuntu noble/main arm64 gzip arm64 1.12-1ubuntu3 [97.2 kB]
Get:117 http://ftpmaster.internal/ubuntu noble/main arm64 hostname arm64 3.23+nmu2ubuntu2 [11.0 kB]
Get:118 http://ftpmaster.internal/ubuntu noble/main arm64 login arm64 1:4.13+dfsg1-4ubuntu3 [200 kB]
Get:119 http://ftpmaster.internal/ubuntu noble/main arm64 ncurses-bin arm64 6.4+20240113-1ubuntu2 [186 kB]
Get:120 http://ftpmaster.internal/ubuntu noble/main arm64 sed arm64 4.9-2build1 [191 kB]
Get:121 http://ftpmaster.internal/ubuntu noble/main arm64 util-linux arm64 2.39.3-9ubuntu6 [1114 kB]
Get:122 http://ftpmaster.internal/ubuntu noble/main arm64 ncurses-base all 6.4+20240113-1ubuntu2 [25.5 kB]
Get:123 http://ftpmaster.internal/ubuntu noble/main arm64 sysvinit-utils arm64 3.08-6ubuntu3 [33.8 kB]
Get:124 http://ftpmaster.internal/ubuntu noble/main arm64 logsave arm64 1.47.0-2.4~exp1ubuntu4 [22.2 kB]
Get:125 http://ftpmaster.internal/ubuntu noble/main arm64 libext2fs2t64 arm64 1.47.0-2.4~exp1ubuntu4 [225 kB]
Get:126 http://ftpmaster.internal/ubuntu noble/main arm64 e2fsprogs arm64 1.47.0-2.4~exp1ubuntu4 [594 kB]
Get:127 http://ftpmaster.internal/ubuntu noble/main arm64 optipng arm64 0.7.8+ds-1build2 [109 kB]
Get:128 http://ftpmaster.internal/ubuntu noble/main arm64 libpng16-16t64 arm64 1.6.43-5build1 [185 kB]
Get:129 http://ftpmaster.internal/ubuntu noble/main arm64 init arm64 1.66ubuntu1 [6186 B]
Get:130 http://ftpmaster.internal/ubuntu noble/main arm64 libsmartcols1 arm64 2.39.3-9ubuntu6 [64.4 kB]
Get:131 http://ftpmaster.internal/ubuntu noble/main arm64 uuid-runtime arm64 2.39.3-9ubuntu6 [32.5 kB]
Get:132 http://ftpmaster.internal/ubuntu noble/main arm64 libattr1 arm64 1:2.5.2-1build1 [11.0 kB]
Get:133 http://ftpmaster.internal/ubuntu noble/main arm64 libmd0 arm64 1.1.0-2build1 [24.6 kB]
Get:134 http://ftpmaster.internal/ubuntu noble/main arm64 libpam-runtime all 1.5.3-5ubuntu5 [40.8 kB]
Get:135 http://ftpmaster.internal/ubuntu noble/main arm64 libsemanage-common all 3.5-1build5 [10.1 kB]
Get:136 http://ftpmaster.internal/ubuntu noble/main arm64 libsepol2 arm64 3.5-2build1 [291 kB]
Get:137 http://ftpmaster.internal/ubuntu noble/main arm64 libsemanage2 arm64 3.5-1build5 [90.8 kB]
Get:138 http://ftpmaster.internal/ubuntu noble/main arm64 passwd arm64 1:4.13+dfsg1-4ubuntu3 [839 kB]
Get:139 http://ftpmaster.internal/ubuntu noble/main arm64 libproc2-0 arm64 2:4.0.4-4ubuntu3 [58.5 kB]
Get:140 http://ftpmaster.internal/ubuntu noble/main arm64 libss2 arm64 1.47.0-2.4~exp1ubuntu4 [16.5 kB]
Get:141 http://ftpmaster.internal/ubuntu noble/main arm64 mawk arm64 1.3.4.20240123-1build1 [124 kB]
Get:142 http://ftpmaster.internal/ubuntu noble/main arm64 procps arm64 2:4.0.4-4ubuntu3 [708 kB]
Get:143 http://ftpmaster.internal/ubuntu noble/main arm64 sensible-utils all 0.0.22 [22.5 kB]
Get:144 http://ftpmaster.internal/ubuntu noble/main arm64 ca-certificates all 20240203 [159 kB]
Get:145 http://ftpmaster.internal/ubuntu noble/main arm64 krb5-locales all 1.20.1-6ubuntu2 [13.8 kB]
Get:146 http://ftpmaster.internal/ubuntu noble/main arm64 tzdata all 2024a-2ubuntu1 [273 kB]
Get:147 http://ftpmaster.internal/ubuntu noble/main arm64 bash-completion all 1:2.11-8 [180 kB]
Get:148 http://ftpmaster.internal/ubuntu noble/main arm64 bsdextrautils arm64 2.39.3-9ubuntu6 [71.5 kB]
Get:149 http://ftpmaster.internal/ubuntu noble/main arm64 libgpm2 arm64 1.20.7-11 [14.7 kB]
Get:150 http://ftpmaster.internal/ubuntu noble/main arm64 libip4tc2 arm64 1.8.10-3ubuntu2 [23.4 kB]
Get:151 http://ftpmaster.internal/ubuntu noble/main arm64 libjansson4 arm64 2.14-2build2 [34.4 kB]
Get:152 http://ftpmaster.internal/ubuntu noble/main arm64 psmisc arm64 23.7-1build1 [178 kB]
Get:153 http://ftpmaster.internal/ubuntu noble/main arm64 xz-utils arm64 5.6.1+really5.4.5-1 [268 kB]
Get:154 http://ftpmaster.internal/ubuntu noble/main arm64 advancecomp arm64 2.5-1build1 [177 kB]
Get:155 http://ftpmaster.internal/ubuntu noble/main arm64 libgprofng0 arm64 2.42-4ubuntu2 [777 kB]
Get:156 http://ftpmaster.internal/ubuntu noble/main arm64 libctf0 arm64 2.42-4ubuntu2 [95.7 kB]
Get:157 http://ftpmaster.internal/ubuntu noble/main arm64 libctf-nobfd0 arm64 2.42-4ubuntu2 [99.8 kB]
Get:158 http://ftpmaster.internal/ubuntu noble/main arm64 binutils-aarch64-linux-gnu arm64 2.42-4ubuntu2 [3291 kB]
Get:159 http://ftpmaster.internal/ubuntu noble/main arm64 libbinutils arm64 2.42-4ubuntu2 [767 kB]
Get:160 http://ftpmaster.internal/ubuntu noble/main arm64 binutils arm64 2.42-4ubuntu2 [18.1 kB]
Get:161 http://ftpmaster.internal/ubuntu noble/main arm64 binutils-common arm64 2.42-4ubuntu2 [239 kB]
Get:162 http://ftpmaster.internal/ubuntu noble/main arm64 libsframe1 arm64 2.42-4ubuntu2 [14.4 kB]
Get:163 http://ftpmaster.internal/ubuntu noble/main arm64 libubsan1 arm64 14-20240412-0ubuntu1 [1155 kB]
Get:164 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13 arm64 13.2.0-23ubuntu4 [14.5 kB]
Get:165 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++-13-dev arm64 13.2.0-23ubuntu4 [2379 kB]
Get:166 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240412-0ubuntu1 [144 kB]
Get:167 http://ftpmaster.internal/ubuntu noble/main arm64 libitm1 arm64 14-20240412-0ubuntu1 [27.9 kB]
Get:168 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240412-0ubuntu1 [11.4 kB]
Get:169 http://ftpmaster.internal/ubuntu noble/main arm64 libasan8 arm64 14-20240412-0ubuntu1 [2921 kB]
Get:170 http://ftpmaster.internal/ubuntu noble/main arm64 liblsan0 arm64 14-20240412-0ubuntu1 [1286 kB]
Get:171 http://ftpmaster.internal/ubuntu noble/main arm64 libhwasan0 arm64 14-20240412-0ubuntu1 [1604 kB]
Get:172 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13 arm64 13.2.0-23ubuntu4 [472 kB]
Get:173 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-13-dev arm64 13.2.0-23ubuntu4 [2470 kB]
Get:174 http://ftpmaster.internal/ubuntu noble/main arm64 libtsan2 arm64 14-20240412-0ubuntu1 [2692 kB]
Get:175 http://ftpmaster.internal/ubuntu noble/main arm64 libcc1-0 arm64 14-20240412-0ubuntu1 [44.7 kB]
Get:176 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13 arm64 13.2.0-23ubuntu4 [1032 B]
Get:177 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-base arm64 13.2.0-23ubuntu4 [49.0 kB]
Get:178 http://ftpmaster.internal/ubuntu noble/main arm64 libisl23 arm64 0.26-3build1 [669 kB]
Get:179 http://ftpmaster.internal/ubuntu noble/main arm64 libmpfr6 arm64 4.2.1-1build1 [329 kB]
Get:180 http://ftpmaster.internal/ubuntu noble/main arm64 libmpc3 arm64 1.3.1-1build1 [56.4 kB]
Get:181 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-23ubuntu4 [20.1 MB]
Get:182 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-23ubuntu4 [11.7 MB]
Get:183 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-23ubuntu4 [10.3 MB]
Get:184 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B]
Get:185 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B]
Get:186 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB]
Get:187 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B]
Get:188 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B]
Get:189 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B]
Get:190 http://ftpmaster.internal/ubuntu noble/main arm64 dpkg-dev all 1.22.6ubuntu6 [1074 kB]
Get:191 http://ftpmaster.internal/ubuntu noble/main arm64 libdpkg-perl all 1.22.6ubuntu6 [268 kB]
Get:192 http://ftpmaster.internal/ubuntu noble/main arm64 patch arm64 2.7.6-7build3 [101 kB]
Get:193 http://ftpmaster.internal/ubuntu noble/main arm64 make arm64 4.3-4.1build2 [178 kB]
Get:194 http://ftpmaster.internal/ubuntu noble/main arm64 lto-disabled-list all 47 [12.4 kB]
Get:195 http://ftpmaster.internal/ubuntu noble/main arm64 libfakeroot arm64 1.33-1 [32.5 kB]
Get:196 http://ftpmaster.internal/ubuntu noble/main arm64 fakeroot arm64 1.33-1 [66.9 kB]
Get:197 http://ftpmaster.internal/ubuntu noble/main arm64 liblockfile-bin arm64 1.17-1build3 [11.0 kB]
Get:198 http://ftpmaster.internal/ubuntu noble/main arm64 liblockfile1 arm64 1.17-1build3 [6874 B]
Get:199 http://ftpmaster.internal/ubuntu noble/main arm64 lockfile-progs arm64 0.1.19build2 [8440 B]
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dpkg: libtirpc3:arm64: dependency problems, but removing anyway as you requested:
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Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
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dpkg: libdb5.3:arm64: dependency problems, but removing anyway as you requested:
 libperl5.36:arm64 depends on libdb5.3.
 libpam-modules:arm64 depends on libdb5.3.
 apt-utils depends on libdb5.3.

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dpkg: libgdbm6:arm64: dependency problems, but removing anyway as you requested:
 libperl5.36:arm64 depends on libgdbm6 (>= 1.21).
 libgdbm-compat4:arm64 depends on libgdbm6 (>= 1.16).

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dpkg: libgdbm-compat4:arm64: dependency problems, but removing anyway as you requested:
 libperl5.36:arm64 depends on libgdbm-compat4 (>= 1.18-3).

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dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested:
 systemd depends on libssl3 (>= 3.0.0).

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dpkg: warning: unable to delete old directory '/lib/systemd/system-preset': Directory not empty
dpkg: warning: unable to delete old directory '/lib/systemd/system-generators': Directory not empty
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dpkg: warning: unable to delete old directory '/lib/aarch64-linux-gnu/security': Directory not empty
Setting up libpam-modules:arm64 (1.5.3-5ubuntu5) ...
Installing new version of config file /etc/security/namespace.init ...
dpkg: libhogweed6:arm64: dependency problems, but removing anyway as you requested:
 libgnutls30:arm64 depends on libhogweed6 (>= 3.6).

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dpkg: libnettle8:arm64: dependency problems, but removing anyway as you requested:
 libgnutls30:arm64 depends on libnettle8 (>= 3.7~).

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Current default time zone: 'Etc/UTC'
Local time is now:      Sun May 19 13:42:06 UTC 2024.
Universal Time is now:  Sun May 19 13:42:06 UTC 2024.
Run 'dpkg-reconfigure tzdata' if you wish to change it.

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Running in chroot, ignoring request.
invoke-rc.d: policy-rc.d denied execution of restart.
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Updating certificates in /etc/ssl/certs...
rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL
14 added, 5 removed; done.
Setting up perl (5.38.2-3.2build2) ...
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Setting up libc6-dev:arm64 (2.39-0ubuntu8) ...
Setting up gpg (2.4.4-2ubuntu17) ...
Setting up libstdc++-13-dev:arm64 (13.2.0-23ubuntu4) ...
Setting up gpg-agent (2.4.4-2ubuntu17) ...
Setting up cpp-13 (13.2.0-23ubuntu4) ...
Setting up libtirpc3t64:arm64 (1.3.4+ds-1.1build1) ...
Setting up binutils-aarch64-linux-gnu (2.42-4ubuntu2) ...
Setting up binutils (2.42-4ubuntu2) ...
Setting up gcc-13-aarch64-linux-gnu (13.2.0-23ubuntu4) ...
Setting up dpkg-dev (1.22.6ubuntu6) ...
Setting up libtirpc-dev:arm64 (1.3.4+ds-1.1build1) ...
Setting up gcc-13 (13.2.0-23ubuntu4) ...
Setting up cpp (4:13.2.0-7ubuntu1) ...
Setting up libnsl2:arm64 (1.3.0-3build3) ...
Setting up g++-13-aarch64-linux-gnu (13.2.0-23ubuntu4) ...
Setting up gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ...
Setting up g++-13 (13.2.0-23ubuntu4) ...
Setting up libnss-nisplus:arm64 (1.3-5build1) ...
Setting up gcc (4:13.2.0-7ubuntu1) ...
Setting up libnss-nis:arm64 (3.1-0ubuntu7) ...
Setting up libnsl-dev:arm64 (1.3.0-3build3) ...
Setting up g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ...
Setting up g++ (4:13.2.0-7ubuntu1) ...
Processing triggers for libc-bin (2.39-0ubuntu8) ...
Processing triggers for debianutils (5.17build1) ...
(Reading database ... 15845 files and directories currently installed.)
Purging configuration files for libssl3:arm64 (3.0.10-1ubuntu2) ...
Processing triggers for ca-certificates (20240203) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-28246702 arm64 noble -c chroot:build-PACKAGEBUILD-28246702 --arch=arm64 --dist=noble --nolog relion_3.1.3-3build3.dsc
Initiating build PACKAGEBUILD-28246702 with 4 jobs across 4 processor cores.
Kernel reported to sbuild: 5.4.0-182-generic #202-Ubuntu SMP Fri Apr 26 16:08:13 UTC 2024 aarch64
sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-arm64-065.buildd

+==============================================================================+
| relion 3.1.3-3build3 (arm64)                 Sun, 19 May 2024 13:42:20 +0000 |
+==============================================================================+

Package: relion
Version: 3.1.3-3build3
Source Version: 3.1.3-3build3
Distribution: noble
Machine Architecture: arm64
Host Architecture: arm64
Build Architecture: arm64
Build Type: any

I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-28246702/chroot-autobuild' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/relion-Gn9qGi/resolver-y79HcA' with '<<RESOLVERDIR>>'

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Local sources
-------------

relion_3.1.3-3build3.dsc exists in .; copying to chroot
I: NOTICE: Log filtering will replace 'build/relion-Gn9qGi/relion-3.1.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/relion-Gn9qGi' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: cmake, debhelper-compat (= 13), libfftw3-dev, libfltk1.3-dev, libopenmpi-dev, libtiff-dev, fluid, build-essential, fakeroot
Filtered Build-Depends: cmake, debhelper-compat (= 13), libfftw3-dev, libfltk1.3-dev, libopenmpi-dev, libtiff-dev, fluid, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [405 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [485 B]
Fetched 1847 B in 0s (51.3 kB/s)
Reading package lists...
Reading package lists...

Install main build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  apt-utils bash-completion ca-certificates debconf-i18n krb5-locales
  libgpg-error-l10n libgpm2 libip4tc2 liblocale-gettext-perl libnsl-dev
  libnsl2 libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl
  libtext-iconv-perl libtext-wrapi18n-perl libtirpc-common libtirpc-dev
  libtirpc3t64 libunistring2 openssl perl-modules-5.36 psmisc uuid-runtime
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev cmake cmake-data debhelper
  debugedit dh-autoreconf dh-strip-nondeterminism dwz file fluid
  fontconfig-config fonts-dejavu-core fonts-dejavu-mono gettext gettext-base
  gfortran-13 gfortran-13-aarch64-linux-gnu groff-base ibverbs-providers
  intltool-debian libarchive-zip-perl libarchive13t64 libbrotli1 libbsd0
  libcairo2 libcbor0.10 libcurl4t64 libdebhelper-perl libdeflate-dev
  libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-nouveau2 libdrm-radeon1
  libdrm2 libdw1t64 libedit2 libelf1t64 libevent-2.1-7t64
  libevent-core-2.1-7t64 libevent-dev libevent-extra-2.1-7t64
  libevent-openssl-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libfabric1
  libfftw3-bin libfftw3-dev libfftw3-double3 libfftw3-long3 libfftw3-single3
  libfido2-1 libfile-stripnondeterminism-perl libfltk-cairo1.3t64
  libfltk-forms1.3t64 libfltk-gl1.3t64 libfltk-images1.3t64 libfltk1.3-dev
  libfltk1.3t64 libfontconfig1 libfreetype6 libgfortran-13-dev libgfortran5
  libgl1 libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0
  libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu74
  libjbig-dev libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8
  libjpeg8-dev libjs-jquery libjs-jquery-ui libjsoncpp25 libldap2 liblerc-dev
  liblerc4 libllvm17t64 libltdl-dev libltdl7 liblzma-dev libmagic-mgc
  libmagic1t64 libmunge2 libnghttp2-14 libnl-3-200 libnl-3-dev
  libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev
  libopenmpi3t64 libpciaccess0 libpipeline1 libpixman-1-0 libpmix-dev
  libpmix2t64 libpsl5t64 libpthread-stubs0-dev librdmacm1t64 librhash0
  librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5
  libsharpyuv-dev libsharpyuv0 libssh-4 libsub-override-perl libtiff-dev
  libtiff6 libtiffxx6 libtool libuchardet0 libucx0 libuv1t64 libvulkan1
  libwebp-dev libwebp7 libwebpdecoder3 libwebpdemux2 libwebpmux3 libx11-6
  libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0
  libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0
  libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcb1-dev libxcursor1
  libxdmcp-dev libxdmcp6 libxext6 libxfixes3 libxft2 libxinerama1 libxml2
  libxnvctrl0 libxrender1 libxshmfence1 libxxf86vm1 libzstd-dev m4 man-db
  ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf
  x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc cmake-doc cmake-format
  elpa-cmake-mode ninja-build dh-make gettext-doc libasprintf-dev
  libgettextpo-dev gfortran-13-doc libcoarrays-dev groff lrzip libfftw3-doc
  fltk1.3-doc libcairo2-dev libpng-dev libxext-dev libxft-dev libxinerama-dev
  libjs-jquery-ui-docs libtool-doc liblzma-doc openmpi-doc pciutils lm-sensors
  gcj-jdk libx11-doc libxcb-doc m4-doc apparmor less www-browser opencl-icd
  gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass
  libmail-box-perl
Recommended packages:
  fltk1.3-doc curl | wget | lynx libarchive-cpio-perl libgl-dev
  libglu1-mesa-dev | libglu-dev libgl1-amber-dri javascript-common
  libldap-common libcoarrays-openmpi-dev publicsuffix libsasl2-modules
  mesa-vulkan-drivers | vulkan-icd xauth libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev cmake cmake-data debhelper
  debugedit dh-autoreconf dh-strip-nondeterminism dwz file fluid
  fontconfig-config fonts-dejavu-core fonts-dejavu-mono gettext gettext-base
  gfortran-13 gfortran-13-aarch64-linux-gnu groff-base ibverbs-providers
  intltool-debian libarchive-zip-perl libarchive13t64 libbrotli1 libbsd0
  libcairo2 libcbor0.10 libcurl4t64 libdebhelper-perl libdeflate-dev
  libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-nouveau2 libdrm-radeon1
  libdrm2 libdw1t64 libedit2 libelf1t64 libevent-2.1-7t64
  libevent-core-2.1-7t64 libevent-dev libevent-extra-2.1-7t64
  libevent-openssl-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libfabric1
  libfftw3-bin libfftw3-dev libfftw3-double3 libfftw3-long3 libfftw3-single3
  libfido2-1 libfile-stripnondeterminism-perl libfltk-cairo1.3t64
  libfltk-forms1.3t64 libfltk-gl1.3t64 libfltk-images1.3t64 libfltk1.3-dev
  libfltk1.3t64 libfontconfig1 libfreetype6 libgfortran-13-dev libgfortran5
  libgl1 libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0
  libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu74
  libjbig-dev libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8
  libjpeg8-dev libjs-jquery libjs-jquery-ui libjsoncpp25 libldap2 liblerc-dev
  liblerc4 libllvm17t64 libltdl-dev libltdl7 liblzma-dev libmagic-mgc
  libmagic1t64 libmunge2 libnghttp2-14 libnl-3-200 libnl-3-dev
  libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev
  libopenmpi3t64 libpciaccess0 libpipeline1 libpixman-1-0 libpmix-dev
  libpmix2t64 libpsl5t64 libpthread-stubs0-dev librdmacm1t64 librhash0
  librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5
  libsharpyuv-dev libsharpyuv0 libssh-4 libsub-override-perl libtiff-dev
  libtiff6 libtiffxx6 libtool libuchardet0 libucx0 libuv1t64 libvulkan1
  libwebp-dev libwebp7 libwebpdecoder3 libwebpdemux2 libwebpmux3 libx11-6
  libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0
  libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0
  libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcb1-dev libxcursor1
  libxdmcp-dev libxdmcp6 libxext6 libxfixes3 libxft2 libxinerama1 libxml2
  libxnvctrl0 libxrender1 libxshmfence1 libxxf86vm1 libzstd-dev m4 man-db
  ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf
  sbuild-build-depends-main-dummy x11proto-dev xorg-sgml-doctools xtrans-dev
  zlib1g-dev
0 upgraded, 180 newly installed, 0 to remove and 0 not upgraded.
Need to get 108 MB of archives.
After this operation, 430 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [702 B]
Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libbsd0 arm64 0.12.1-1build1 [40.9 kB]
Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libelf1t64 arm64 0.190-1.1build4 [58.0 kB]
Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libexpat1 arm64 2.6.1-2build1 [76.1 kB]
Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libicu74 arm64 74.2-1ubuntu3 [10.8 MB]
Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libxml2 arm64 2.9.14+dfsg-1.3ubuntu3 [735 kB]
Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libmagic-mgc arm64 1:5.45-3build1 [307 kB]
Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libmagic1t64 arm64 1:5.45-3build1 [85.7 kB]
Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 file arm64 1:5.45-3build1 [22.0 kB]
Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 gettext-base arm64 0.21-14ubuntu2 [37.6 kB]
Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libuchardet0 arm64 0.0.8-1build1 [75.4 kB]
Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 groff-base arm64 1.23.0-3build2 [993 kB]
Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libnl-3-200 arm64 3.7.0-0.3build1 [57.5 kB]
Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libnl-route-3-200 arm64 3.7.0-0.3build1 [183 kB]
Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libibverbs1 arm64 50.0-2build2 [67.3 kB]
Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 ibverbs-providers arm64 50.0-2build2 [367 kB]
Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libcbor0.10 arm64 0.10.2-1.2ubuntu2 [26.0 kB]
Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-common all 2.4.120-2build1 [8096 B]
Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm2 arm64 2.4.120-2build1 [42.1 kB]
Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libedit2 arm64 3.1-20230828-1build1 [97.5 kB]
Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libfido2-1 arm64 1.14.0-1build3 [82.5 kB]
Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libnghttp2-14 arm64 1.59.0-1build4 [74.1 kB]
Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libnuma1 arm64 2.0.18-1build1 [23.6 kB]
Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libpipeline1 arm64 1.5.7-2 [23.7 kB]
Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libpsl5t64 arm64 0.21.2-1.1build1 [57.4 kB]
Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libsensors-config all 1:3.6.0-9build1 [5546 B]
Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libsensors5 arm64 1:3.6.0-9build1 [27.0 kB]
Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libuv1t64 arm64 1.48.0-1.1build1 [95.3 kB]
Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libxau6 arm64 1:1.0.9-1build6 [7264 B]
Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libxdmcp6 arm64 1:1.1.3-0ubuntu6 [10.4 kB]
Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb1 arm64 1.15-1ubuntu2 [49.4 kB]
Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libx11-data all 2:1.8.7-1build1 [115 kB]
Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libx11-6 arm64 2:1.8.7-1build1 [649 kB]
Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libxext6 arm64 2:1.3.4-1build2 [30.4 kB]
Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 man-db arm64 2.12.0-4build2 [1232 kB]
Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 openssh-client arm64 1:9.6p1-3ubuntu13 [884 kB]
Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 m4 arm64 1.4.19-4build1 [240 kB]
Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 autoconf all 2.71-3 [339 kB]
Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 autotools-dev all 20220109.1 [44.9 kB]
Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 automake all 1:1.16.5-1.3ubuntu1 [558 kB]
Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 autopoint all 0.21-14ubuntu2 [422 kB]
Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libarchive13t64 arm64 3.7.2-2 [376 kB]
Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libbrotli1 arm64 1.1.0-2build2 [339 kB]
Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-5ubuntu3 [21.4 kB]
Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-5ubuntu3 [54.7 kB]
Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libldap2 arm64 2.6.7+dfsg-1~exp1ubuntu8 [193 kB]
Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2build7 [57.8 kB]
Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libssh-4 arm64 0.10.6-2build2 [189 kB]
Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libcurl4t64 arm64 8.5.0-2ubuntu10 [333 kB]
Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libjsoncpp25 arm64 1.9.5-6build1 [78.2 kB]
Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 librhash0 arm64 1.4.3-3build1 [126 kB]
Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 cmake-data all 3.28.3-1build7 [2155 kB]
Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 cmake arm64 3.28.3-1build7 [10.3 MB]
Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libdebhelper-perl all 13.14.1ubuntu5 [89.8 kB]
Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libtool all 2.4.7-7build1 [166 kB]
Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 dh-autoreconf all 20 [16.1 kB]
Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB]
Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libsub-override-perl all 0.10-1 [10.0 kB]
Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB]
Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 dh-strip-nondeterminism all 1.13.1-1 [5362 B]
Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 libdw1t64 arm64 0.190-1.1build4 [258 kB]
Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 debugedit arm64 1:5.0-5build2 [45.3 kB]
Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 dwz arm64 0.15-1build6 [113 kB]
Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 gettext arm64 0.21-14ubuntu2 [845 kB]
Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB]
Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 po-debconf all 1.0.21+nmu1 [233 kB]
Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 debhelper all 13.14.1ubuntu5 [869 kB]
Get:68 http://ftpmaster.internal/ubuntu noble/main arm64 libfreetype6 arm64 2.13.2+dfsg-1build3 [393 kB]
Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB]
Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB]
Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 libxfixes3 arm64 1:6.0.0-2build1 [11.2 kB]
Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB]
Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 libxcursor1 arm64 1:1.2.1-1build1 [21.1 kB]
Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB]
Get:77 http://ftpmaster.internal/ubuntu noble/main arm64 libxinerama1 arm64 2:1.1.4-3build1 [6394 B]
Get:78 http://ftpmaster.internal/ubuntu noble/universe arm64 libfltk1.3t64 arm64 1.3.8-6.1build2 [597 kB]
Get:79 http://ftpmaster.internal/ubuntu noble/universe arm64 libfltk-forms1.3t64 arm64 1.3.8-6.1build2 [13.8 kB]
Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB]
Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
Get:82 http://ftpmaster.internal/ubuntu noble/universe arm64 libfltk-images1.3t64 arm64 1.3.8-6.1build2 [27.5 kB]
Get:83 http://ftpmaster.internal/ubuntu noble/universe arm64 fluid arm64 1.3.8-6.1build2 [206 kB]
Get:84 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240412-0ubuntu1 [444 kB]
Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran-13-dev arm64 13.2.0-23ubuntu4 [478 kB]
Get:86 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13-aarch64-linux-gnu arm64 13.2.0-23ubuntu4 [10.8 MB]
Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13 arm64 13.2.0-23ubuntu4 [11.7 kB]
Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1build1 [204 kB]
Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1ubuntu2 [16.6 kB]
Get:90 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1ubuntu2 [5876 B]
Get:91 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-3build1 [555 kB]
Get:92 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1build1 [43.4 kB]
Get:93 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate-dev arm64 1.19-1build1 [51.2 kB]
Get:94 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-amdgpu1 arm64 2.4.120-2build1 [20.5 kB]
Get:95 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-nouveau2 arm64 2.4.120-2build1 [17.8 kB]
Get:96 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-radeon1 arm64 2.4.120-2build1 [20.9 kB]
Get:97 http://ftpmaster.internal/ubuntu noble/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-9ubuntu2 [140 kB]
Get:98 http://ftpmaster.internal/ubuntu noble/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-9ubuntu2 [90.3 kB]
Get:99 http://ftpmaster.internal/ubuntu noble/main arm64 libevent-extra-2.1-7t64 arm64 2.1.12-stable-9ubuntu2 [62.1 kB]
Get:100 http://ftpmaster.internal/ubuntu noble/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-9ubuntu2 [7932 B]
Get:101 http://ftpmaster.internal/ubuntu noble/main arm64 libevent-openssl-2.1-7t64 arm64 2.1.12-stable-9ubuntu2 [14.7 kB]
Get:102 http://ftpmaster.internal/ubuntu noble/main arm64 libevent-dev arm64 2.1.12-stable-9ubuntu2 [283 kB]
Get:103 http://ftpmaster.internal/ubuntu noble/main arm64 librdmacm1t64 arm64 50.0-2build2 [70.6 kB]
Get:104 http://ftpmaster.internal/ubuntu noble/universe arm64 libfabric1 arm64 1.17.0-3build2 [541 kB]
Get:105 http://ftpmaster.internal/ubuntu noble/main arm64 libfftw3-double3 arm64 3.3.10-1ubuntu3 [384 kB]
Get:106 http://ftpmaster.internal/ubuntu noble/main arm64 libfftw3-long3 arm64 3.3.10-1ubuntu3 [640 kB]
Get:107 http://ftpmaster.internal/ubuntu noble/main arm64 libfftw3-single3 arm64 3.3.10-1ubuntu3 [583 kB]
Get:108 http://ftpmaster.internal/ubuntu noble/main arm64 libfftw3-bin arm64 3.3.10-1ubuntu3 [34.2 kB]
Get:109 http://ftpmaster.internal/ubuntu noble/main arm64 libfftw3-dev arm64 3.3.10-1ubuntu3 [1453 kB]
Get:110 http://ftpmaster.internal/ubuntu noble/universe arm64 libfltk-cairo1.3t64 arm64 1.3.8-6.1build2 [6818 B]
Get:111 http://ftpmaster.internal/ubuntu noble/main arm64 libglvnd0 arm64 1.7.0-1build1 [60.6 kB]
Get:112 http://ftpmaster.internal/ubuntu noble/main arm64 libglapi-mesa arm64 24.0.5-1ubuntu1 [58.4 kB]
Get:113 http://ftpmaster.internal/ubuntu noble/main arm64 libx11-xcb1 arm64 2:1.8.7-1build1 [7870 B]
Get:114 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-dri2-0 arm64 1.15-1ubuntu2 [7418 B]
Get:115 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-dri3-0 arm64 1.15-1ubuntu2 [7196 B]
Get:116 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-glx0 arm64 1.15-1ubuntu2 [25.5 kB]
Get:117 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-present0 arm64 1.15-1ubuntu2 [5866 B]
Get:118 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-randr0 arm64 1.15-1ubuntu2 [18.4 kB]
Get:119 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-sync1 arm64 1.15-1ubuntu2 [9682 B]
Get:120 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-xfixes0 arm64 1.15-1ubuntu2 [10.6 kB]
Get:121 http://ftpmaster.internal/ubuntu noble/main arm64 libxshmfence1 arm64 1.3-1build5 [4938 B]
Get:122 http://ftpmaster.internal/ubuntu noble/main arm64 libxxf86vm1 arm64 1:1.1.4-1build4 [9130 B]
Get:123 http://ftpmaster.internal/ubuntu noble/main arm64 libvulkan1 arm64 1.3.275.0-1build1 [150 kB]
Get:124 http://ftpmaster.internal/ubuntu noble/main arm64 libllvm17t64 arm64 1:17.0.6-9ubuntu1 [25.0 MB]
Get:125 http://ftpmaster.internal/ubuntu noble/main arm64 libgl1-mesa-dri arm64 24.0.5-1ubuntu1 [8226 kB]
Get:126 http://ftpmaster.internal/ubuntu noble/main arm64 libglx-mesa0 arm64 24.0.5-1ubuntu1 [166 kB]
Get:127 http://ftpmaster.internal/ubuntu noble/main arm64 libglx0 arm64 1.7.0-1build1 [33.2 kB]
Get:128 http://ftpmaster.internal/ubuntu noble/main arm64 libgl1 arm64 1.7.0-1build1 [106 kB]
Get:129 http://ftpmaster.internal/ubuntu noble/universe arm64 libfltk-gl1.3t64 arm64 1.3.8-6.1build2 [42.1 kB]
Get:130 http://ftpmaster.internal/ubuntu noble/main arm64 xorg-sgml-doctools all 1:1.11-1.1 [10.9 kB]
Get:131 http://ftpmaster.internal/ubuntu noble/main arm64 x11proto-dev all 2023.2-1 [602 kB]
Get:132 http://ftpmaster.internal/ubuntu noble/main arm64 libxau-dev arm64 1:1.0.9-1build6 [10.0 kB]
Get:133 http://ftpmaster.internal/ubuntu noble/main arm64 libxdmcp-dev arm64 1:1.1.3-0ubuntu6 [26.3 kB]
Get:134 http://ftpmaster.internal/ubuntu noble/main arm64 xtrans-dev all 1.4.0-1 [68.9 kB]
Get:135 http://ftpmaster.internal/ubuntu noble/main arm64 libpthread-stubs0-dev arm64 0.4-1build3 [4734 B]
Get:136 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb1-dev arm64 1.15-1ubuntu2 [91.2 kB]
Get:137 http://ftpmaster.internal/ubuntu noble/main arm64 libx11-dev arm64 2:1.8.7-1build1 [742 kB]
Get:138 http://ftpmaster.internal/ubuntu noble/universe arm64 libfltk1.3-dev arm64 1.3.8-6.1build2 [907 kB]
Get:139 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc15 arm64 2.10.0-1build1 [159 kB]
Get:140 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8-dev arm64 2.1.5-2ubuntu2 [305 kB]
Get:141 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B]
Get:142 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B]
Get:143 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
Get:144 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB]
Get:145 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB]
Get:146 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc-dev arm64 4.0.0+ds-4ubuntu2 [168 kB]
Get:147 http://ftpmaster.internal/ubuntu noble/main arm64 libltdl7 arm64 2.4.7-7build1 [40.4 kB]
Get:148 http://ftpmaster.internal/ubuntu noble/main arm64 libltdl-dev arm64 2.4.7-7build1 [170 kB]
Get:149 http://ftpmaster.internal/ubuntu noble/main arm64 libnl-3-dev arm64 3.7.0-0.3build1 [105 kB]
Get:150 http://ftpmaster.internal/ubuntu noble/main arm64 libnl-route-3-dev arm64 3.7.0-0.3build1 [225 kB]
Get:151 http://ftpmaster.internal/ubuntu noble/universe arm64 libmunge2 arm64 0.5.15-4build1 [14.9 kB]
Get:152 http://ftpmaster.internal/ubuntu noble/main arm64 libpciaccess0 arm64 0.17-3build1 [18.9 kB]
Get:153 http://ftpmaster.internal/ubuntu noble/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu4 [12.4 kB]
Get:154 http://ftpmaster.internal/ubuntu noble/universe arm64 ocl-icd-libopencl1 arm64 2.3.2-1build1 [37.6 kB]
Get:155 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc-plugins arm64 2.10.0-1build1 [15.7 kB]
Get:156 http://ftpmaster.internal/ubuntu noble/universe arm64 libpmix2t64 arm64 5.0.1-4.1build1 [655 kB]
Get:157 http://ftpmaster.internal/ubuntu noble/universe arm64 libucx0 arm64 1.16.0+ds-5ubuntu1 [1074 kB]
Get:158 http://ftpmaster.internal/ubuntu noble/universe arm64 libopenmpi3t64 arm64 4.1.6-7ubuntu2 [2463 kB]
Get:159 http://ftpmaster.internal/ubuntu noble/main arm64 libnuma-dev arm64 2.0.18-1build1 [39.6 kB]
Get:160 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc-dev arm64 2.10.0-1build1 [261 kB]
Get:161 http://ftpmaster.internal/ubuntu noble/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3.1ubuntu2 [894 kB]
Get:162 http://ftpmaster.internal/ubuntu noble/universe arm64 libpmix-dev arm64 5.0.1-4.1build1 [4022 kB]
Get:163 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4build3 [14.5 kB]
Get:164 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv-dev arm64 1.3.2-0.4build3 [15.1 kB]
Get:165 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB]
Get:166 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig-dev arm64 2.1-6.1ubuntu2 [27.5 kB]
Get:167 http://ftpmaster.internal/ubuntu noble/main arm64 liblzma-dev arm64 5.6.1+really5.4.5-1 [178 kB]
Get:168 http://ftpmaster.internal/ubuntu noble/main arm64 libzstd-dev arm64 1.5.5+dfsg2-2build1 [344 kB]
Get:169 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4build3 [191 kB]
Get:170 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpdemux2 arm64 1.3.2-0.4build3 [12.3 kB]
Get:171 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpmux3 arm64 1.3.2-0.4build3 [25.0 kB]
Get:172 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpdecoder3 arm64 1.3.2-0.4build3 [88.7 kB]
Get:173 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp-dev arm64 1.3.2-0.4build3 [334 kB]
Get:174 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu2 [191 kB]
Get:175 http://ftpmaster.internal/ubuntu noble/main arm64 libtiffxx6 arm64 4.5.1+git230720-4ubuntu2 [5640 B]
Get:176 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff-dev arm64 4.5.1+git230720-4ubuntu2 [337 kB]
Get:177 http://ftpmaster.internal/ubuntu noble/universe arm64 openmpi-common all 4.1.6-7ubuntu2 [170 kB]
Get:178 http://ftpmaster.internal/ubuntu noble/universe arm64 openmpi-bin arm64 4.1.6-7ubuntu2 [113 kB]
Get:179 http://ftpmaster.internal/ubuntu noble/main arm64 libibverbs-dev arm64 50.0-2build2 [686 kB]
Get:180 http://ftpmaster.internal/ubuntu noble/universe arm64 libopenmpi-dev arm64 4.1.6-7ubuntu2 [865 kB]
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Setting up libbrotli1:arm64 (1.1.0-2build2) ...
Setting up libuv1t64:arm64 (1.48.0-1.1build1) ...
Setting up libmagic1t64:arm64 (1:5.45-3build1) ...
Setting up libsensors-config (1:3.6.0-9build1) ...
Setting up libpsl5t64:arm64 (0.21.2-1.1build1) ...
Setting up libnghttp2-14:arm64 (1.59.0-1build4) ...
Setting up libdeflate0:arm64 (1.19-1build1) ...
Setting up libwebpdecoder3:arm64 (1.3.2-0.4build3) ...
Setting up libfftw3-long3:arm64 (3.3.10-1ubuntu3) ...
Setting up gettext-base (0.21-14ubuntu2) ...
Setting up m4 (1.4.19-4build1) ...
Setting up libevent-2.1-7t64:arm64 (2.1.12-stable-9ubuntu2) ...
Setting up file (1:5.45-3build1) ...
Setting up libpthread-stubs0-dev:arm64 (0.4-1build3) ...
Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ...
Setting up libelf1t64:arm64 (0.190-1.1build4) ...
Setting up libdw1t64:arm64 (0.190-1.1build4) ...
Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-5ubuntu3) ...
Setting up xtrans-dev (1.4.0-1) ...
Setting up autotools-dev (20220109.1) ...
Setting up libmunge2:arm64 (0.5.15-4build1) ...
Setting up libfreetype6:arm64 (2.13.2+dfsg-1build3) ...
Setting up libx11-data (2:1.8.7-1build1) ...
Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2build7) ...
Setting up fonts-dejavu-mono (2.37-8) ...
Setting up libhwloc15:arm64 (2.10.0-1build1) ...
Setting up autopoint (0.21-14ubuntu2) ...
Setting up libjsoncpp25:arm64 (1.9.5-6build1) ...
Setting up fonts-dejavu-core (2.37-8) ...
Setting up libsensors5:arm64 (1:3.6.0-9build1) ...
Setting up liblerc-dev:arm64 (4.0.0+ds-4ubuntu2) ...
Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ...
Setting up libltdl7:arm64 (2.4.7-7build1) ...
Setting up libfftw3-double3:arm64 (3.3.10-1ubuntu3) ...
Setting up libglapi-mesa:arm64 (24.0.5-1ubuntu1) ...
Setting up libsasl2-2:arm64 (2.1.28+dfsg1-5ubuntu3) ...
Setting up libssh-4:arm64 (0.10.6-2build2) ...
Setting up libgfortran5:arm64 (14-20240412-0ubuntu1) ...
Setting up libvulkan1:arm64 (1.3.275.0-1build1) ...
Setting up autoconf (2.71-3) ...
Setting up libwebp7:arm64 (1.3.2-0.4build3) ...
Setting up liblzma-dev:arm64 (5.6.1+really5.4.5-1) ...
Setting up libicu74:arm64 (74.2-1ubuntu3) ...
Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3.1ubuntu2) ...
Setting up libnuma1:arm64 (2.0.18-1build1) ...
Setting up dwz (0.15-1build6) ...
Setting up ocl-icd-libopencl1:arm64 (2.3.2-1build1) ...
Setting up libxshmfence1:arm64 (1.3-1build5) ...
Setting up librhash0:arm64 (1.4.3-3build1) ...
Setting up libuchardet0:arm64 (0.0.8-1build1) ...
Setting up libnl-3-200:arm64 (3.7.0-0.3build1) ...
Setting up openmpi-common (4.1.6-7ubuntu2) ...
Setting up debugedit (1:5.0-5build2) ...
Setting up libsub-override-perl (0.10-1) ...
Setting up xorg-sgml-doctools (1:1.11-1.1) ...
Setting up cmake-data (3.28.3-1build7) ...
Setting up libevent-core-2.1-7t64:arm64 (2.1.12-stable-9ubuntu2) ...
Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Setting up libfido2-1:arm64 (1.14.0-1build3) ...
Setting up libsharpyuv-dev:arm64 (1.3.2-0.4build3) ...
Setting up libgfortran-13-dev:arm64 (13.2.0-23ubuntu4) ...
Setting up libwebpmux3:arm64 (1.3.2-0.4build3) ...
Setting up libbsd0:arm64 (0.12.1-1build1) ...
Setting up libdeflate-dev:arm64 (1.19-1build1) ...
Setting up libdrm-common (2.4.120-2build1) ...
Setting up libxml2:arm64 (2.9.14+dfsg-1.3ubuntu3) ...
Setting up libldap2:arm64 (2.6.7+dfsg-1~exp1ubuntu8) ...
Setting up libjpeg8:arm64 (8c-2ubuntu11) ...
Setting up automake (1:1.16.5-1.3ubuntu1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up x11proto-dev (2023.2-1) ...
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up libjpeg-turbo8-dev:arm64 (2.1.5-2ubuntu2) ...
Setting up libxdmcp6:arm64 (1:1.1.3-0ubuntu6) ...
Setting up libxcb1:arm64 (1.15-1ubuntu2) ...
Setting up gettext (0.21-14ubuntu2) ...
Setting up libxcb-xfixes0:arm64 (1.15-1ubuntu2) ...
Setting up libxau-dev:arm64 (1:1.0.9-1build6) ...
Setting up libcurl4t64:arm64 (8.5.0-2ubuntu10) ...
Setting up libtool (2.4.7-7build1) ...
Setting up libxcb-render0:arm64 (1.15-1ubuntu2) ...
Setting up libfftw3-bin (3.3.10-1ubuntu3) ...
Setting up libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-9ubuntu2) ...
Setting up fontconfig-config (2.15.0-1.1ubuntu2) ...
Setting up libxcb-glx0:arm64 (1.15-1ubuntu2) ...
Setting up libwebpdemux2:arm64 (1.3.2-0.4build3) ...
Setting up libedit2:arm64 (3.1-20230828-1build1) ...
Setting up libevent-openssl-2.1-7t64:arm64 (2.1.12-stable-9ubuntu2) ...
Setting up libjbig-dev:arm64 (2.1-6.1ubuntu2) ...
Setting up gfortran-13-aarch64-linux-gnu (13.2.0-23ubuntu4) ...
Setting up libxcb-shm0:arm64 (1.15-1ubuntu2) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libnuma-dev:arm64 (2.0.18-1build1) ...
Setting up libnl-route-3-200:arm64 (3.7.0-0.3build1) ...
Setting up libxcb-present0:arm64 (1.15-1ubuntu2) ...
Setting up dh-autoreconf (20) ...
Setting up libltdl-dev:arm64 (2.4.7-7build1) ...
Setting up libxdmcp-dev:arm64 (1:1.1.3-0ubuntu6) ...
Setting up libwebp-dev:arm64 (1.3.2-0.4build3) ...
Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
Setting up libllvm17t64:arm64 (1:17.0.6-9ubuntu1) ...
Setting up libxcb-sync1:arm64 (1.15-1ubuntu2) ...
Setting up gfortran-13 (13.2.0-23ubuntu4) ...
Setting up libevent-extra-2.1-7t64:arm64 (2.1.12-stable-9ubuntu2) ...
Setting up libxcb-dri2-0:arm64 (1.15-1ubuntu2) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up libdrm2:arm64 (2.4.120-2build1) ...
Setting up libnl-3-dev:arm64 (3.7.0-0.3build1) ...
Setting up groff-base (1.23.0-3build2) ...
Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu2) ...
Setting up libxcb-randr0:arm64 (1.15-1ubuntu2) ...
Setting up libx11-6:arm64 (2:1.8.7-1build1) ...
Setting up libhwloc-dev:arm64 (2.10.0-1build1) ...
Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ...
Setting up libjpeg8-dev:arm64 (8c-2ubuntu11) ...
Setting up libtiffxx6:arm64 (4.5.1+git230720-4ubuntu2) ...
Setting up libarchive13t64:arm64 (3.7.2-2) ...
Setting up libfftw3-dev:arm64 (3.3.10-1ubuntu3) ...
Setting up libdrm-amdgpu1:arm64 (2.4.120-2build1) ...
Setting up libxcb-dri3-0:arm64 (1.15-1ubuntu2) ...
Setting up libx11-xcb1:arm64 (2:1.8.7-1build1) ...
Setting up libibverbs1:arm64 (50.0-2build2) ...
Setting up libdrm-nouveau2:arm64 (2.4.120-2build1) ...
Setting up libxcb1-dev:arm64 (1.15-1ubuntu2) ...
Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ...
Setting up ibverbs-providers:arm64 (50.0-2build2) ...
Setting up libdrm-radeon1:arm64 (2.4.120-2build1) ...
Setting up openssh-client (1:9.6p1-3ubuntu13) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libgl1-mesa-dri:arm64 (24.0.5-1ubuntu1) ...
Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ...
Setting up libx11-dev:arm64 (2:1.8.7-1build1) ...
Setting up libxext6:arm64 (2:1.3.4-1build2) ...
Setting up man-db (2.12.0-4build2) ...
Not building database; man-db/auto-update is not 'true'.
Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /usr/lib/systemd/system/man-db.timer.
Setting up libcairo2:arm64 (1.18.0-3build1) ...
Setting up libxxf86vm1:arm64 (1:1.1.4-1build4) ...
Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu4) ...
Setting up libnl-route-3-dev:arm64 (3.7.0-0.3build1) ...
Setting up libtiff-dev:arm64 (4.5.1+git230720-4ubuntu2) ...
Setting up libxfixes3:arm64 (1:6.0.0-2build1) ...
Setting up libxinerama1:arm64 (2:1.1.4-3build1) ...
Setting up libevent-dev (2.1.12-stable-9ubuntu2) ...
Setting up cmake (3.28.3-1build7) ...
Setting up librdmacm1t64:arm64 (50.0-2build2) ...
Setting up libfabric1:arm64 (1.17.0-3build2) ...
Setting up libucx0:arm64 (1.16.0+ds-5ubuntu1) ...
Setting up libxft2:arm64 (2.3.6-1build1) ...
Setting up libglx-mesa0:arm64 (24.0.5-1ubuntu1) ...
Setting up libglx0:arm64 (1.7.0-1build1) ...
Setting up libxcursor1:arm64 (1:1.2.1-1build1) ...
Setting up debhelper (13.14.1ubuntu5) ...
Setting up libibverbs-dev:arm64 (50.0-2build2) ...
Setting up libhwloc-plugins:arm64 (2.10.0-1build1) ...
Setting up libgl1:arm64 (1.7.0-1build1) ...
Setting up libpmix2t64:arm64 (5.0.1-4.1build1) ...
Setting up libopenmpi3t64:arm64 (4.1.6-7ubuntu2) ...
Setting up libfltk1.3t64:arm64 (1.3.8-6.1build2) ...
Setting up libpmix-dev:arm64 (5.0.1-4.1build1) ...
Setting up libfltk-forms1.3t64:arm64 (1.3.8-6.1build2) ...
Setting up openmpi-bin (4.1.6-7ubuntu2) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
Setting up libfltk-images1.3t64:arm64 (1.3.8-6.1build2) ...
Setting up fluid (1.3.8-6.1build2) ...
Setting up libfltk-gl1.3t64:arm64 (1.3.8-6.1build2) ...
Setting up libfltk-cairo1.3t64:arm64 (1.3.8-6.1build2) ...
Setting up libopenmpi-dev:arm64 (4.1.6-7ubuntu2) ...
update-alternatives: using /usr/lib/aarch64-linux-gnu/openmpi/include to provide /usr/include/aarch64-linux-gnu/mpi (mpi-aarch64-linux-gnu) in auto mode
Setting up libfltk1.3-dev:arm64 (1.3.8-6.1build2) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.39-0ubuntu8) ...

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (arm64 included in any)

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 5.4.0-182-generic #202-Ubuntu SMP Fri Apr 26 16:08:13 UTC 2024 arm64 (aarch64)
Toolchain package versions: binutils_2.42-4ubuntu2 dpkg-dev_1.22.6ubuntu6 g++-13_13.2.0-23ubuntu4 gcc-13_13.2.0-23ubuntu4 libc6-dev_2.39-0ubuntu8 libstdc++-13-dev_13.2.0-23ubuntu4 libstdc++6_14-20240412-0ubuntu1 linux-libc-dev_6.8.0-31.31
Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1build1 apt_2.7.14build2 apt-utils_2.7.14build2 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu2 autotools-dev_20220109.1 base-files_13ubuntu10 base-passwd_3.6.3build1 bash_5.2.21-2ubuntu4 bash-completion_1:2.11-8 binutils_2.42-4ubuntu2 binutils-aarch64-linux-gnu_2.42-4ubuntu2 binutils-common_2.42-4ubuntu2 bsdextrautils_2.39.3-9ubuntu6 bsdutils_1:2.39.3-9ubuntu6 build-essential_12.10ubuntu1 bzip2_1.0.8-5.1 ca-certificates_20240203 cmake_3.28.3-1build7 cmake-data_3.28.3-1build7 coreutils_9.4-3ubuntu6 cpp_4:13.2.0-7ubuntu1 cpp-13_13.2.0-23ubuntu4 cpp-13-aarch64-linux-gnu_13.2.0-23ubuntu4 cpp-aarch64-linux-gnu_4:13.2.0-7ubuntu1 dash_0.5.12-6ubuntu5 debconf_1.5.86ubuntu1 debconf-i18n_1.5.86ubuntu1 debhelper_13.14.1ubuntu5 debianutils_5.17build1 debugedit_1:5.0-5build2 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1build1 dpkg_1.22.6ubuntu6 dpkg-dev_1.22.6ubuntu6 dwz_0.15-1build6 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libapparmor1_4.0.0-beta3-0ubuntu3 libapt-pkg6.0t64_2.7.14build2 libarchive-zip-perl_1.68-1 libarchive13t64_3.7.2-2 libargon2-1_0~20190702+dfsg-4build1 libasan8_14-20240412-0ubuntu1 libassuan0_2.5.6-1build1 libatomic1_14-20240412-0ubuntu1 libattr1_1:2.5.2-1build1 libaudit-common_1:3.1.2-2.1build1 libaudit1_1:3.1.2-2.1build1 libbinutils_2.42-4ubuntu2 libblkid1_2.39.3-9ubuntu6 libbrotli1_1.1.0-2build2 libbsd0_0.12.1-1build1 libbz2-1.0_1.0.8-5.1 libc-bin_2.39-0ubuntu8 libc-dev-bin_2.39-0ubuntu8 libc6_2.39-0ubuntu8 libc6-dev_2.39-0ubuntu8 libcairo2_1.18.0-3build1 libcap-ng0_0.8.4-2build2 libcap2_1:2.66-5ubuntu2 libcbor0.10_0.10.2-1.2ubuntu2 libcc1-0_14-20240412-0ubuntu1 libcom-err2_1.47.0-2.4~exp1ubuntu4 libcrypt-dev_1:4.4.36-4build1 libcrypt1_1:4.4.36-4build1 libcryptsetup12_2:2.7.0-1ubuntu4 libctf-nobfd0_2.42-4ubuntu2 libctf0_2.42-4ubuntu2 libcurl4t64_8.5.0-2ubuntu10 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.271ubuntu3 libdebhelper-perl_13.14.1ubuntu5 libdeflate-dev_1.19-1build1 libdeflate0_1.19-1build1 libdevmapper1.02.1_2:1.02.185-3ubuntu3 libdpkg-perl_1.22.6ubuntu6 libdrm-amdgpu1_2.4.120-2build1 libdrm-common_2.4.120-2build1 libdrm-nouveau2_2.4.120-2build1 libdrm-radeon1_2.4.120-2build1 libdrm2_2.4.120-2build1 libdw1t64_0.190-1.1build4 libedit2_3.1-20230828-1build1 libelf1t64_0.190-1.1build4 libevent-2.1-7t64_2.1.12-stable-9ubuntu2 libevent-core-2.1-7t64_2.1.12-stable-9ubuntu2 libevent-dev_2.1.12-stable-9ubuntu2 libevent-extra-2.1-7t64_2.1.12-stable-9ubuntu2 libevent-openssl-2.1-7t64_2.1.12-stable-9ubuntu2 libevent-pthreads-2.1-7t64_2.1.12-stable-9ubuntu2 libexpat1_2.6.1-2build1 libext2fs2t64_1.47.0-2.4~exp1ubuntu4 libfabric1_1.17.0-3build2 libfakeroot_1.33-1 libfdisk1_2.39.3-9ubuntu6 libffi8_3.4.6-1build1 libfftw3-bin_3.3.10-1ubuntu3 libfftw3-dev_3.3.10-1ubuntu3 libfftw3-double3_3.3.10-1ubuntu3 libfftw3-long3_3.3.10-1ubuntu3 libfftw3-single3_3.3.10-1ubuntu3 libfido2-1_1.14.0-1build3 libfile-stripnondeterminism-perl_1.13.1-1 libfltk-cairo1.3t64_1.3.8-6.1build2 libfltk-forms1.3t64_1.3.8-6.1build2 libfltk-gl1.3t64_1.3.8-6.1build2 libfltk-images1.3t64_1.3.8-6.1build2 libfltk1.3-dev_1.3.8-6.1build2 libfltk1.3t64_1.3.8-6.1build2 libfontconfig1_2.15.0-1.1ubuntu2 libfreetype6_2.13.2+dfsg-1build3 libgcc-13-dev_13.2.0-23ubuntu4 libgcc-s1_14-20240412-0ubuntu1 libgcrypt20_1.10.3-2build1 libgdbm-compat4t64_1.23-5.1build1 libgdbm6t64_1.23-5.1build1 libgfortran-13-dev_13.2.0-23ubuntu4 libgfortran5_14-20240412-0ubuntu1 libgl1_1.7.0-1build1 libgl1-mesa-dri_24.0.5-1ubuntu1 libglapi-mesa_24.0.5-1ubuntu1 libglvnd0_1.7.0-1build1 libglx-mesa0_24.0.5-1ubuntu1 libglx0_1.7.0-1build1 libgmp10_2:6.3.0+dfsg-2ubuntu6 libgnutls30t64_3.8.3-1.1ubuntu3 libgomp1_14-20240412-0ubuntu1 libgpg-error-l10n_1.47-3build2 libgpg-error0_1.47-3build2 libgpm2_1.20.7-11 libgprofng0_2.42-4ubuntu2 libgssapi-krb5-2_1.20.1-6ubuntu2 libhogweed6t64_3.9.1-2.2build1 libhwasan0_14-20240412-0ubuntu1 libhwloc-dev_2.10.0-1build1 libhwloc-plugins_2.10.0-1build1 libhwloc15_2.10.0-1build1 libibverbs-dev_50.0-2build2 libibverbs1_50.0-2build2 libicu74_74.2-1ubuntu3 libidn2-0_2.3.7-2build1 libip4tc2_1.8.10-3ubuntu2 libisl23_0.26-3build1 libitm1_14-20240412-0ubuntu1 libjansson4_2.14-2build2 libjbig-dev_2.1-6.1ubuntu2 libjbig0_2.1-6.1ubuntu2 libjpeg-dev_8c-2ubuntu11 libjpeg-turbo8_2.1.5-2ubuntu2 libjpeg-turbo8-dev_2.1.5-2ubuntu2 libjpeg8_8c-2ubuntu11 libjpeg8-dev_8c-2ubuntu11 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-jquery-ui_1.13.2+dfsg-1 libjson-c5_0.17-1build1 libjsoncpp25_1.9.5-6build1 libk5crypto3_1.20.1-6ubuntu2 libkeyutils1_1.6.3-3build1 libkmod2_31+20240202-2ubuntu7 libkrb5-3_1.20.1-6ubuntu2 libkrb5support0_1.20.1-6ubuntu2 libldap2_2.6.7+dfsg-1~exp1ubuntu8 liblerc-dev_4.0.0+ds-4ubuntu2 liblerc4_4.0.0+ds-4ubuntu2 libllvm17t64_1:17.0.6-9ubuntu1 liblocale-gettext-perl_1.07-6ubuntu5 liblockfile-bin_1.17-1build3 liblockfile1_1.17-1build3 liblsan0_14-20240412-0ubuntu1 libltdl-dev_2.4.7-7build1 libltdl7_2.4.7-7build1 liblz4-1_1.9.4-1build1 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libtext-charwidth-perl_0.04-11build3 libtext-iconv-perl_1.7-8build3 libtext-wrapi18n-perl_0.06-10 libtiff-dev_4.5.1+git230720-4ubuntu2 libtiff6_4.5.1+git230720-4ubuntu2 libtiffxx6_4.5.1+git230720-4ubuntu2 libtinfo6_6.4+20240113-1ubuntu2 libtirpc-common_1.3.4+ds-1.1build1 libtirpc-dev_1.3.4+ds-1.1build1 libtirpc3t64_1.3.4+ds-1.1build1 libtool_2.4.7-7build1 libtsan2_14-20240412-0ubuntu1 libubsan1_14-20240412-0ubuntu1 libuchardet0_0.0.8-1build1 libucx0_1.16.0+ds-5ubuntu1 libudev1_255.4-1ubuntu8 libunistring2_1.0-2 libunistring5_1.1-2build1 libuuid1_2.39.3-9ubuntu6 libuv1t64_1.48.0-1.1build1 libvulkan1_1.3.275.0-1build1 libwebp-dev_1.3.2-0.4build3 libwebp7_1.3.2-0.4build3 libwebpdecoder3_1.3.2-0.4build3 libwebpdemux2_1.3.2-0.4build3 libwebpmux3_1.3.2-0.4build3 libx11-6_2:1.8.7-1build1 libx11-data_2:1.8.7-1build1 libx11-dev_2:1.8.7-1build1 libx11-xcb1_2:1.8.7-1build1 libxau-dev_1:1.0.9-1build6 libxau6_1:1.0.9-1build6 libxcb-dri2-0_1.15-1ubuntu2 libxcb-dri3-0_1.15-1ubuntu2 libxcb-glx0_1.15-1ubuntu2 libxcb-present0_1.15-1ubuntu2 libxcb-randr0_1.15-1ubuntu2 libxcb-render0_1.15-1ubuntu2 libxcb-shm0_1.15-1ubuntu2 libxcb-sync1_1.15-1ubuntu2 libxcb-xfixes0_1.15-1ubuntu2 libxcb1_1.15-1ubuntu2 libxcb1-dev_1.15-1ubuntu2 libxcursor1_1:1.2.1-1build1 libxdmcp-dev_1:1.1.3-0ubuntu6 libxdmcp6_1:1.1.3-0ubuntu6 libxext6_2:1.3.4-1build2 libxfixes3_1:6.0.0-2build1 libxft2_2.3.6-1build1 libxinerama1_2:1.1.4-3build1 libxml2_2.9.14+dfsg-1.3ubuntu3 libxnvctrl0_510.47.03-0ubuntu4 libxrender1_1:0.9.10-1.1build1 libxshmfence1_1.3-1build5 libxxf86vm1_1:1.1.4-1build4 libxxhash0_0.8.2-2build1 libzstd-dev_1.5.5+dfsg2-2build1 libzstd1_1.5.5+dfsg2-2build1 linux-libc-dev_6.8.0-31.31 lockfile-progs_0.1.19build2 login_1:4.13+dfsg1-4ubuntu3 logsave_1.47.0-2.4~exp1ubuntu4 lto-disabled-list_47 m4_1.4.19-4build1 make_4.3-4.1build2 man-db_2.12.0-4build2 mawk_1.3.4.20240123-1build1 mount_2.39.3-9ubuntu6 ncurses-base_6.4+20240113-1ubuntu2 ncurses-bin_6.4+20240113-1ubuntu2 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zlib1g-dev_1:1.3.dfsg-3.1ubuntu2

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 3.0 (quilt)
Source: relion
Binary: relion, relion-gui
Architecture: any
Version: 3.1.3-3build3
Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Uploaders: Roland Fehrenbacher <rfehren@debian.org>, Andreas Tille <tille@debian.org>,
Homepage: https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/relion
Vcs-Git: https://salsa.debian.org/med-team/relion.git
Testsuite: autopkgtest
Build-Depends: cmake, debhelper-compat (= 13), libfftw3-dev, libfltk1.3-dev, libopenmpi-dev, libtiff-dev, fluid
Package-List:
 relion deb science optional arch=any
 relion-gui deb science optional arch=any
Checksums-Sha1:
 c6ca397db6c711f87305bd803f672345f7487bae 2345487 relion_3.1.3.orig.tar.gz
 c244a46404c635af863e95e35646d83be74fbef7 12188 relion_3.1.3-3build3.debian.tar.xz
Checksums-Sha256:
 f10934058e0670807b7004899d7b5103c21ad77841219352c66a33f98586d42e 2345487 relion_3.1.3.orig.tar.gz
 f44404396e692619c6ddbf260000343348d0331c773d47a8c6a4425efbc3243e 12188 relion_3.1.3-3build3.debian.tar.xz
Files:
 5ddaf9afe51d743c5f58f625d9fd1cb7 2345487 relion_3.1.3.orig.tar.gz
 3cb2b918f5f7b157fb65cfa0facc68f4 12188 relion_3.1.3-3build3.debian.tar.xz
Original-Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

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gpgv: Signature made Mon Apr  1 07:26:27 2024 UTC
gpgv:                using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./relion_3.1.3-3build3.dsc: no acceptable signature found
dpkg-source: info: extracting relion in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking relion_3.1.3.orig.tar.gz
dpkg-source: info: unpacking relion_3.1.3-3build3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 0001-Repair-wrong-comment-sign-pointed-out-by-Alexey-Roma.patch
dpkg-source: info: applying typos.patch

Check disk space
----------------

Sufficient free space for build

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=noautodbgsym parallel=4
HOME=/sbuild-nonexistent
LANG=C.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-28246702
SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-28246702
SCHROOT_COMMAND=env
SCHROOT_GID=2501
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=build-PACKAGEBUILD-28246702
SCHROOT_UID=2001
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=unknown
USER=buildd
V=1

dpkg-buildpackage
-----------------

Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon <buildd@bos02-arm64-065.buildd> -B -rfakeroot
dpkg-buildpackage: info: source package relion
dpkg-buildpackage: info: source version 3.1.3-3build3
dpkg-buildpackage: info: source distribution noble
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
 debian/rules clean
dh clean
   debian/rules override_dh_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_clean
rm -rf build
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
 debian/rules binary-arch
dh binary-arch
   dh_update_autotools_config -a
   dh_autoreconf -a
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
mkdir /<<PKGBUILDDIR>>/build
cd /<<PKGBUILDDIR>>/build; \
CC=gcc CXX=g++ cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_SKIP_RPATH=TRUE -DDoublePrec_GPU=ON -DGUI=ON -DCUDA=OFF /<<PKGBUILDDIR>>
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 3.5 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.


CMake Warning (dev) at /usr/share/cmake-3.28/Modules/CMakeDetermineCompilerId.cmake:96 (if):
  Policy CMP0054 is not set: Only interpret if() arguments as variables or
  keywords when unquoted.  Run "cmake --help-policy CMP0054" for policy
  details.  Use the cmake_policy command to set the policy and suppress this
  warning.

  Quoted variables like "CUDA" will no longer be dereferenced when the policy
  is set to NEW.  Since the policy is not set the OLD behavior will be used.
Call Stack (most recent call first):
  /usr/share/cmake-3.28/Modules/CMakeDetermineCCompiler.cmake:123 (CMAKE_DETERMINE_COMPILER_ID)
  CMakeLists.txt:6 (project)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- The C compiler identification is GNU 13.2.0
-- The CXX compiler identification is GNU 13.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- BUILD TYPE set to the default type:  'Release'
-- Setting fallback CUDA_ARCH=35
-- ALLOW_CTF_IN_SAGD enabled - This build of RELION allows modulation of particle images by a contrast transfer function inside stochastic average gradient descent, as specified in Claim 1 of patent US10,282,513B2
-- Setting cpu precision to double
-- Setting accelerated code precision to single
-- Using non-cuda compilation....
-- Found MPI_C: /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") 
-- Found MPI_CXX: /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") 
-- Found MPI: TRUE (found version "3.1")  
-- MPI_INCLUDE_PATH : /usr/lib/aarch64-linux-gnu/openmpi/include;/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi
-- MPI_LIBRARIES : /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so
-- MPI_CXX_INCLUDE_PATH : /usr/lib/aarch64-linux-gnu/openmpi/include;/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi
-- MPI_CXX_LIBRARIES : /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so
-- CMAKE_C_COMPILER : /usr/bin/gcc
-- CMAKE_CXX_COMPILER : /usr/bin/g++
-- MPI_C_COMPILER : /usr/bin/mpicc
-- MPI_CXX_COMPILER : /usr/bin/mpicxx
-- CMAKE_CXX_COMPILER_ID : GNU
-- Found X11: /usr/include   
-- Looking for XOpenDisplay in /usr/lib/aarch64-linux-gnu/libX11.so
-- Looking for XOpenDisplay in /usr/lib/aarch64-linux-gnu/libX11.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Found FLTK: fltk_images;fltk_forms;fltk  
-- X11 and FLTK were found
-- FLTK_LIBRARIES: fltk_images;fltk_forms;fltk;/usr/lib/aarch64-linux-gnu/libX11.so;/usr/lib/aarch64-linux-gnu/libm.so
-- Found FFTW
-- FFTW_PATH: /usr/include
-- FFTW_INCLUDES: /usr/include
-- FFTW_LIBRARIES: /usr/lib/aarch64-linux-gnu/libfftw3f.so;/usr/lib/aarch64-linux-gnu/libfftw3.so
-- Looking for sincos
-- Looking for sincos - found
-- Looking for __sincos
-- Looking for __sincos - not found
-- Found TIFF: /usr/lib/aarch64-linux-gnu/libtiff.so (found version "4.5.1")  
-- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3")  
-- Could NOT find PNG (missing: PNG_LIBRARY PNG_PNG_INCLUDE_DIR) 
BUILD_SHARED_LIBS = OFF
-- Building static libs (larger build size and binaries)
Running apps/CMakeLists.txt...
-- CMAKE_BINARY_DIR:/<<PKGBUILDDIR>>/build
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
-- Configuring done (26.6s)
-- Generating done (0.6s)
CMake Warning:
  Manually-specified variables were not used by the project:

    DoublePrec_GPU


-- Build files have been written to: /<<PKGBUILDDIR>>/build
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
/usr/bin/make -j4 -C build
make[2]: Entering directory '/<<PKGBUILDDIR>>/build'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/CMakeFiles /<<PKGBUILDDIR>>/build//CMakeFiles/progress.marks
/usr/bin/make  -f CMakeFiles/Makefile2 all
make[3]: Entering directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/depend
/usr/bin/make  -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/CMakeFiles/copy_scripts.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/relion_lib.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_printtable /<<PKGBUILDDIR>>/build/bin/relion_star_printtable
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_plottable /<<PKGBUILDDIR>>/build/bin/relion_star_plottable
[  1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o
[  1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -MF CMakeFiles/relion_lib.dir/__/__/macros.cpp.o.d -o CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -c /<<PKGBUILDDIR>>/build/macros.cpp
[  1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o -MF CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o.d -o CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o -c /<<PKGBUILDDIR>>/src/CPlot2D.cpp
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o -MF CMakeFiles/relion_lib.dir/__/args.cpp.o.d -o CMakeFiles/relion_lib.dir/__/args.cpp.o -c /<<PKGBUILDDIR>>/src/args.cpp
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_loopheader /<<PKGBUILDDIR>>/build/bin/relion_star_loopheader
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_datablock_stack /<<PKGBUILDDIR>>/build/bin/relion_star_datablock_stack
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_datablock_singlefiles /<<PKGBUILDDIR>>/build/bin/relion_star_datablock_singlefiles
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_datablock_ctfdat /<<PKGBUILDDIR>>/build/bin/relion_star_datablock_ctfdat
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/qsub.csh /<<PKGBUILDDIR>>/build/bin/relion_qsub.csh
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[  1%] Built target copy_scripts
[  1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o -MF CMakeFiles/relion_lib.dir/__/assembly.cpp.o.d -o CMakeFiles/relion_lib.dir/__/assembly.cpp.o -c /<<PKGBUILDDIR>>/src/assembly.cpp
[  2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -MF CMakeFiles/relion_lib.dir/__/autopicker.cpp.o.d -o CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -c /<<PKGBUILDDIR>>/src/autopicker.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/autopicker.h:10,
                 from /<<PKGBUILDDIR>>/src/autopicker.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[  2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/autopicker_mpi.cpp
[  3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -MF CMakeFiles/relion_lib.dir/__/backprojector.cpp.o.d -o CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -c /<<PKGBUILDDIR>>/src/backprojector.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/autopicker.h:10,
                 from /<<PKGBUILDDIR>>/src/autopicker_mpi.h:12,
                 from /<<PKGBUILDDIR>>/src/autopicker_mpi.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[  3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/complex.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/complex.cpp.o -MF CMakeFiles/relion_lib.dir/__/complex.cpp.o.d -o CMakeFiles/relion_lib.dir/__/complex.cpp.o -c /<<PKGBUILDDIR>>/src/complex.cpp
[  3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctf.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctf.cpp.o -c /<<PKGBUILDDIR>>/src/ctf.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/backprojector.h:33,
                 from /<<PKGBUILDDIR>>/src/backprojector.cpp:27:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/ctf.cpp:45:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[  4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o -c /<<PKGBUILDDIR>>/src/ctffind_runner.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/ctffind_runner.h:31,
                 from /<<PKGBUILDDIR>>/src/ctffind_runner.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[  4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/ctffind_runner_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/ctffind_runner.h:31,
                 from /<<PKGBUILDDIR>>/src/ctffind_runner_mpi.h:25,
                 from /<<PKGBUILDDIR>>/src/ctffind_runner_mpi.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[  4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/error.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/error.cpp.o -MF CMakeFiles/relion_lib.dir/__/error.cpp.o.d -o CMakeFiles/relion_lib.dir/__/error.cpp.o -c /<<PKGBUILDDIR>>/src/error.cpp
[  5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/euler.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/euler.cpp.o -MF CMakeFiles/relion_lib.dir/__/euler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/euler.cpp.o -c /<<PKGBUILDDIR>>/src/euler.cpp
[  5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/exp_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/exp_model.cpp.o -c /<<PKGBUILDDIR>>/src/exp_model.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/exp_model.h:24,
                 from /<<PKGBUILDDIR>>/src/exp_model.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[  6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/fftw.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/fftw.cpp.o -MF CMakeFiles/relion_lib.dir/__/fftw.cpp.o.d -o CMakeFiles/relion_lib.dir/__/fftw.cpp.o -c /<<PKGBUILDDIR>>/src/fftw.cpp
[  6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o -MF CMakeFiles/relion_lib.dir/__/filename.cpp.o.d -o CMakeFiles/relion_lib.dir/__/filename.cpp.o -c /<<PKGBUILDDIR>>/src/filename.cpp
[  6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o -MF CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o.d -o CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o -c /<<PKGBUILDDIR>>/src/flex_analyser.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/exp_model.h:24,
                 from /<<PKGBUILDDIR>>/src/flex_analyser.h:24,
                 from /<<PKGBUILDDIR>>/src/flex_analyser.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[  7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/funcs.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/funcs.cpp.o -MF CMakeFiles/relion_lib.dir/__/funcs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/funcs.cpp.o -c /<<PKGBUILDDIR>>/src/funcs.cpp
[  7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o -MF CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o.d -o CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o -c /<<PKGBUILDDIR>>/src/healpix_sampling.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/helix.h:30,
                 from /<<PKGBUILDDIR>>/src/healpix_sampling.h:31,
                 from /<<PKGBUILDDIR>>/src/healpix_sampling.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[  7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o -MF CMakeFiles/relion_lib.dir/__/helix.cpp.o.d -o CMakeFiles/relion_lib.dir/__/helix.cpp.o -c /<<PKGBUILDDIR>>/src/helix.cpp
[  8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o -MF CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o -c /<<PKGBUILDDIR>>/src/helix_inimodel2d.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/helix.h:30,
                 from /<<PKGBUILDDIR>>/src/helix.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/helix_inimodel2d.h:29,
                 from /<<PKGBUILDDIR>>/src/helix_inimodel2d.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[  8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/image.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/image.cpp.o -MF CMakeFiles/relion_lib.dir/__/image.cpp.o.d -o CMakeFiles/relion_lib.dir/__/image.cpp.o -c /<<PKGBUILDDIR>>/src/image.cpp
[  9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o -MF CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o.d -o CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o -c /<<PKGBUILDDIR>>/src/local_symmetry.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/image.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/local_symmetry.h:30,
                 from /<<PKGBUILDDIR>>/src/local_symmetry.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[  9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/local_symmetry_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/local_symmetry.h:30,
                 from /<<PKGBUILDDIR>>/src/local_symmetry_mpi.h:5,
                 from /<<PKGBUILDDIR>>/src/local_symmetry_mpi.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[  9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o -MF CMakeFiles/relion_lib.dir/__/mask.cpp.o.d -o CMakeFiles/relion_lib.dir/__/mask.cpp.o -c /<<PKGBUILDDIR>>/src/mask.cpp
[ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o -MF CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o -c /<<PKGBUILDDIR>>/src/matrix1d.cpp
[ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o -MF CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o -c /<<PKGBUILDDIR>>/src/matrix2d.cpp
[ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/memory.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/memory.cpp.o -MF CMakeFiles/relion_lib.dir/__/memory.cpp.o.d -o CMakeFiles/relion_lib.dir/__/memory.cpp.o -c /<<PKGBUILDDIR>>/src/memory.cpp
[ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o -MF CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o.d -o CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o -c /<<PKGBUILDDIR>>/src/metadata_container.cpp
[ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o -MF CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o.d -o CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o -c /<<PKGBUILDDIR>>/src/metadata_label.cpp
[ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o -MF CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o.d -o CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o -c /<<PKGBUILDDIR>>/src/metadata_table.cpp
[ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o -c /<<PKGBUILDDIR>>/src/micrograph_model.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/micrograph_model.cpp:23:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_model.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ml_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_model.cpp.o -c /<<PKGBUILDDIR>>/src/ml_model.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/ml_model.h:23,
                 from /<<PKGBUILDDIR>>/src/ml_model.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o -c /<<PKGBUILDDIR>>/src/ml_optimiser.cpp
[ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/ml_optimiser_mpi.cpp
[ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o -MF CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o -c /<<PKGBUILDDIR>>/src/motioncorr_runner.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/ml_model.h:23,
                 from /<<PKGBUILDDIR>>/src/ml_optimiser.h:35,
                 from /<<PKGBUILDDIR>>/src/ml_optimiser.cpp:44:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/ml_model.h:23,
                 from /<<PKGBUILDDIR>>/src/ml_optimiser.h:35,
                 from /<<PKGBUILDDIR>>/src/ml_optimiser_mpi.h:24,
                 from /<<PKGBUILDDIR>>/src/ml_optimiser_mpi.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/motioncorr_runner.h:32,
                 from /<<PKGBUILDDIR>>/src/motioncorr_runner.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/motioncorr_runner_mpi.cpp
[ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/mpi.cpp.o -c /<<PKGBUILDDIR>>/src/mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/motioncorr_runner.h:32,
                 from /<<PKGBUILDDIR>>/src/motioncorr_runner_mpi.h:25,
                 from /<<PKGBUILDDIR>>/src/motioncorr_runner_mpi.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o -MF CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o.d -o CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o -c /<<PKGBUILDDIR>>/src/multidim_array.cpp
[ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o -MF CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o.d -o CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o -c /<<PKGBUILDDIR>>/src/numerical_recipes.cpp
[ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/parallel.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/parallel.cpp.o -MF CMakeFiles/relion_lib.dir/__/parallel.cpp.o.d -o CMakeFiles/relion_lib.dir/__/parallel.cpp.o -c /<<PKGBUILDDIR>>/src/parallel.cpp
In file included from /<<PKGBUILDDIR>>/src/numerical_recipes.h:48,
                 from /<<PKGBUILDDIR>>/src/numerical_recipes.cpp:49:
In function ‘free_Tvector<double>(double*&, int, int)void’,
    inlined from ‘brent(double, double, double, double (*)(double*, void*), void*, double, double*, int, double*, double*)’ at /<<PKGBUILDDIR>>/src/numerical_recipes.cpp:594:25:
/<<PKGBUILDDIR>>/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
   74 |         free((char*)(v + nl));
      |         ~~~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/numerical_recipes.cpp: In function ‘brent(double, double, double, double (*)(double*, void*), void*, double, double*, int, double*, double*)’:
/<<PKGBUILDDIR>>/src/numerical_recipes.cpp:579:13: note: declared here
  579 |     RFLOAT *xt=NULL;
      |             ^~
In function ‘free_Tvector<double>(double*&, int, int)void’,
    inlined from ‘powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)’ at /<<PKGBUILDDIR>>/src/numerical_recipes.cpp:767:25:
/<<PKGBUILDDIR>>/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
   74 |         free((char*)(v + nl));
      |         ~~~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/numerical_recipes.cpp: In function ‘powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)’:
/<<PKGBUILDDIR>>/src/numerical_recipes.cpp:703:24: note: declared here
  703 |     RFLOAT *pt, *ptt, *xit;
      |                        ^~~
In function ‘free_Tvector<double>(double*&, int, int)void’,
    inlined from ‘powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)’ at /<<PKGBUILDDIR>>/src/numerical_recipes.cpp:768:25:
/<<PKGBUILDDIR>>/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
   74 |         free((char*)(v + nl));
      |         ~~~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/numerical_recipes.cpp: In function ‘powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)’:
/<<PKGBUILDDIR>>/src/numerical_recipes.cpp:703:18: note: declared here
  703 |     RFLOAT *pt, *ptt, *xit;
      |                  ^~~
In function ‘free_Tvector<double>(double*&, int, int)void’,
    inlined from ‘powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)’ at /<<PKGBUILDDIR>>/src/numerical_recipes.cpp:769:25:
/<<PKGBUILDDIR>>/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
   74 |         free((char*)(v + nl));
      |         ~~~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/numerical_recipes.cpp: In function ‘powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)’:
/<<PKGBUILDDIR>>/src/numerical_recipes.cpp:703:13: note: declared here
  703 |     RFLOAT *pt, *ptt, *xit;
      |             ^~
[ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o -MF CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o -c /<<PKGBUILDDIR>>/src/particle_subtractor.cpp
[ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o -c /<<PKGBUILDDIR>>/src/pipeline_control.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/ml_model.h:23,
                 from /<<PKGBUILDDIR>>/src/ml_optimiser.h:35,
                 from /<<PKGBUILDDIR>>/src/particle_subtractor.h:24,
                 from /<<PKGBUILDDIR>>/src/particle_subtractor.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o -c /<<PKGBUILDDIR>>/src/pipeline_jobs.cpp
[ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o -c /<<PKGBUILDDIR>>/src/pipeliner.cpp
[ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o -MF CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o.d -o CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o -c /<<PKGBUILDDIR>>/src/postprocessing.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/postprocessing.h:24,
                 from /<<PKGBUILDDIR>>/src/postprocessing.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o -MF CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o.d -o CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o -c /<<PKGBUILDDIR>>/src/preprocessing.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/preprocessing.h:29,
                 from /<<PKGBUILDDIR>>/src/preprocessing.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/preprocessing_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/preprocessing.h:29,
                 from /<<PKGBUILDDIR>>/src/preprocessing_mpi.h:24,
                 from /<<PKGBUILDDIR>>/src/preprocessing_mpi.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/projector.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/projector.cpp.o -MF CMakeFiles/relion_lib.dir/__/projector.cpp.o.d -o CMakeFiles/relion_lib.dir/__/projector.cpp.o -c /<<PKGBUILDDIR>>/src/projector.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/projector.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o -MF CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o -c /<<PKGBUILDDIR>>/src/reconstructor.cpp
[ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/reconstructor_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/backprojector.h:33,
                 from /<<PKGBUILDDIR>>/src/reconstructor.h:23,
                 from /<<PKGBUILDDIR>>/src/reconstructor.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/renderEER.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/renderEER.cpp.o -MF CMakeFiles/relion_lib.dir/__/renderEER.cpp.o.d -o CMakeFiles/relion_lib.dir/__/renderEER.cpp.o -c /<<PKGBUILDDIR>>/src/renderEER.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/backprojector.h:33,
                 from /<<PKGBUILDDIR>>/src/reconstructor.h:23,
                 from /<<PKGBUILDDIR>>/src/reconstructor_mpi.h:25,
                 from /<<PKGBUILDDIR>>/src/reconstructor_mpi.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/renderEER.cpp:10:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/renderEER.cpp: In member function ‘void EERRenderer::readLegacy(FILE*)’:
/<<PKGBUILDDIR>>/src/renderEER.cpp:191:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  191 |         fread(buf, sizeof(char), file_size, fh);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/scheduler.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/scheduler.cpp.o -MF CMakeFiles/relion_lib.dir/__/scheduler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/scheduler.cpp.o -c /<<PKGBUILDDIR>>/src/scheduler.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/scheduler.h:26,
                 from /<<PKGBUILDDIR>>/src/scheduler.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/strings.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/strings.cpp.o -MF CMakeFiles/relion_lib.dir/__/strings.cpp.o.d -o CMakeFiles/relion_lib.dir/__/strings.cpp.o -c /<<PKGBUILDDIR>>/src/strings.cpp
[ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/symmetries.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/symmetries.cpp.o -MF CMakeFiles/relion_lib.dir/__/symmetries.cpp.o.d -o CMakeFiles/relion_lib.dir/__/symmetries.cpp.o -c /<<PKGBUILDDIR>>/src/symmetries.cpp
[ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o -MF CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o -c /<<PKGBUILDDIR>>/src/tabfuncs.cpp
[ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o -c /<<PKGBUILDDIR>>/src/tiff_converter.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/tiff_converter.cpp:24:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/tiff_converter.cpp: In member function ‘void TIFFConverter::estimate(FileName)’:
/<<PKGBUILDDIR>>/src/tiff_converter.cpp:141:101: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘long int’ [-Wformat=]
  141 |                 printf(" %s Frame %03d #Changed %10d #Mismatch %10d, #Negative %10d, #Unreliable %10d / %10d\n",
      |                                                                                                  ~~~^
      |                                                                                                     |
      |                                                                                                     int
      |                                                                                                  %10ld
/<<PKGBUILDDIR>>/src/tiff_converter.cpp:141:108: warning: format ‘%d’ expects argument of type ‘int’, but argument 8 has type ‘long int’ [-Wformat=]
  141 |                 printf(" %s Frame %03d #Changed %10d #Mismatch %10d, #Negative %10d, #Unreliable %10d / %10d\n",
      |                                                                                                         ~~~^
      |                                                                                                            |
      |                                                                                                            int
      |                                                                                                         %10ld
/<<PKGBUILDDIR>>/src/tiff_converter.cpp: In member function ‘int TIFFConverter::checkMRCtype(FileName)’:
/<<PKGBUILDDIR>>/src/tiff_converter.cpp:309:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  309 |         fread(headers, sizeof(int), 24, mrcin);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/tiff_converter.cpp: In member function ‘void TIFFConverter::initialise(int, int)’:
/<<PKGBUILDDIR>>/src/tiff_converter.cpp:367:23: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  367 |                 system(("mkdir -p " + fn_out.beforeLastOf("/")).c_str());
      |                 ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/tiff_converter.cpp: In member function ‘void TIFFConverter::run()’:
/<<PKGBUILDDIR>>/src/tiff_converter.cpp:530:31: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  530 |                         system(("mkdir -p " + fn_tiff.beforeLastOf("/")).c_str());
      |                         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/time.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/time.cpp.o -MF CMakeFiles/relion_lib.dir/__/time.cpp.o.d -o CMakeFiles/relion_lib.dir/__/time.cpp.o -c /<<PKGBUILDDIR>>/src/time.cpp
[ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/transformations.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/transformations.cpp.o -MF CMakeFiles/relion_lib.dir/__/transformations.cpp.o.d -o CMakeFiles/relion_lib.dir/__/transformations.cpp.o -c /<<PKGBUILDDIR>>/src/transformations.cpp
[ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -MF CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o.d -o CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -c /<<PKGBUILDDIR>>/src/Healpix_2.15a/cxxutils.cc
[ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/healpix_base.cc.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -MF CMakeFiles/relion_lib.dir/__/Healpix_2.15a/healpix_base.cc.o.d -o CMakeFiles/relion_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -c /<<PKGBUILDDIR>>/src/Healpix_2.15a/healpix_base.cc
[ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/Fourier_helper.cpp
[ 24%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/Gaussian_pyramid.cpp
[ 24%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/aberration_fit.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/Fourier_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/Fourier_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/complex_io.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/aberration_fit.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/aberration_fit.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/convolution_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/complex_io.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/complex_io.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/convolution_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/convolution_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/damage_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/fsc_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/damage_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/distribution_helper.cpp
[ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/fftw_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/distribution_helper.h:25,
                 from /<<PKGBUILDDIR>>/src/jaz/distribution_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/fsc_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/fsc_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/fsc_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/image_log.cpp
[ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/interpolation.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/image_log.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/image_log.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/interpolation.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/interpolation.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/jaz_config.cpp
[ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/legacy_obs_model.cpp
[ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/local_motion_fit.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/legacy_obs_model.h:4,
                 from /<<PKGBUILDDIR>>/src/jaz/legacy_obs_model.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/local_motion_fit.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/local_motion_fit.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/micrograph_handler.cpp
[ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/new_ft.cpp
[ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/noise_helper.cpp
[ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/obs_model.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/micrograph_handler.h:31,
                 from /<<PKGBUILDDIR>>/src/jaz/micrograph_handler.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/jaz/noise_helper.h:25,
                 from /<<PKGBUILDDIR>>/src/jaz/noise_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/parallel_ft.cpp
[ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/reference_map.cpp
[ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/refinement_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/reference_map.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/reference_map.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/resampling_helper.cpp
[ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/slice_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/refinement_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/refinement_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/slice_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/slice_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/spectral_helper.cpp
[ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/stack_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/spectral_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/spectral_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/stack_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/stack_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/structure_tensor.cpp
[ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/svd_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/img_proc/filter_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/structure_tensor.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/t_complex.cpp
[ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/volume_converter.cpp
[ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/volume_integration.cpp
[ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/vtk_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/volume_converter.h:25,
                 from /<<PKGBUILDDIR>>/src/jaz/volume_converter.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/volume_integration.h:26,
                 from /<<PKGBUILDDIR>>/src/jaz/volume_integration.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/optimization/gradient_descent.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/vtk_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/vtk_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/optimization/lbfgs.cpp
[ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/optimization/nelder_mead.cpp
[ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/optimization/optimization.cpp
[ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/aberration_estimator.cpp
[ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/bfactor_refiner.cpp
[ 38%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/ctf_refiner.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/aberration_estimator.h:4,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/aberration_estimator.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/bfactor_refiner.h:4,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/bfactor_refiner.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/ctf_refiner.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/ctf_refiner.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 38%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/ctf_refiner_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/ctf_refiner.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/ctf_refiner_mpi.h:26,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/ctf_refiner_mpi.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/defocus_estimator.cpp
[ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/defocus_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/defocus_estimator.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/defocus_estimator.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/delocalisation_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/defocus_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/defocus_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/delocalisation_helper.h:4,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/delocalisation_helper.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/equation2x2.cpp
[ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/magnification_estimator.cpp
[ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/magnification_helper.cpp
[ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/modular_ctf_optimisation.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/magnification_estimator.h:28,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/magnification_estimator.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/magnification_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/magnification_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/modular_ctf_optimisation.h:5,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/modular_ctf_optimisation.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/tilt_estimator.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/tilt_estimator.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/tilt_estimator.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/ctf/tilt_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/tilt_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/tilt_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/motion/alignment_set.cpp
[ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/motion/frame_recombiner.cpp
[ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/motion/gp_motion_fit.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/frame_recombiner.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/frame_recombiner.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/gp_motion_fit.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/gp_motion_fit.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/motion/motion_estimator.cpp
[ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/motion/motion_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_estimator.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_estimator.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/motion/motion_param_estimator.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/alignment_set.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_param_estimator.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_param_estimator.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/motion/motion_refiner.cpp
[ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/motion/motion_refiner_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_refiner.h:25,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_refiner.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_refiner.h:25,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_refiner_mpi.h:27,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_refiner_mpi.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/motion/three_hyperparameter_fit.cpp
[ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/motion/two_hyperparameter_fit.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/alignment_set.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_param_estimator.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/three_hyperparameter_fit.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/alignment_set.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_param_estimator.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/two_hyperparameter_fit.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/math/Zernike.cpp
[ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/img_proc/color_helper.cpp
[ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/img_proc/filter_helper.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/img_proc/color_helper.h:5,
                 from /<<PKGBUILDDIR>>/src/jaz/img_proc/color_helper.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/img_proc/filter_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/img_proc/filter_helper.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/img_proc/image_op.cpp
[ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/tomo/backprojection_helper.cpp
[ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/tomo/imod_helper.cpp
[ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/tomo/projection_helper.cpp
[ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/tomo/tomo_stack.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/tomo/backprojection_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/tomo/backprojection_helper.cpp:23:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 49%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -c /<<PKGBUILDDIR>>/src/jaz/io/star_converter.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/tomo/tomo_stack.h:25,
                 from /<<PKGBUILDDIR>>/src/jaz/tomo/tomo_stack.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/io/star_converter.h:5,
                 from /<<PKGBUILDDIR>>/src/jaz/io/star_converter.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 49%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o -c /<<PKGBUILDDIR>>/src/jaz/d3x3/dsyev2.c
[ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o -c /<<PKGBUILDDIR>>/src/jaz/d3x3/dsyevc3.c
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cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/align_symmetry.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/autopick.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/autopick_mpi.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/build
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/build
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 53%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o
[ 53%] Building CXX object src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -c /<<PKGBUILDDIR>>/src/displayer.cpp
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -MF CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o.d -o CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -c /<<PKGBUILDDIR>>/src/apps/align_symmetry.cpp
[ 53%] Building CXX object src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -MF CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o.d -o CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/autopick_mpi.cpp
[ 54%] Building CXX object src/apps/CMakeFiles/autopick.dir/autopick.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/autopick.dir/autopick.cpp.o -MF CMakeFiles/autopick.dir/autopick.cpp.o.d -o CMakeFiles/autopick.dir/autopick.cpp.o -c /<<PKGBUILDDIR>>/src/apps/autopick.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/apps/align_symmetry.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/autopicker.h:10,
                 from /<<PKGBUILDDIR>>/src/apps/autopick.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/displayer.h:40,
                 from /<<PKGBUILDDIR>>/src/displayer.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/autopicker.h:10,
                 from /<<PKGBUILDDIR>>/src/autopicker_mpi.h:12,
                 from /<<PKGBUILDDIR>>/src/apps/autopick_mpi.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 54%] Linking CXX executable ../../bin/relion_autopick
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/autopick.dir/autopick.cpp.o -o ../../bin/relion_autopick  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
[ 55%] Linking CXX executable ../../bin/relion_autopick_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -o ../../bin/relion_autopick_mpi  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
[ 55%] Linking CXX executable ../../bin/relion_align_symmetry
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/align_symmetry.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -o ../../bin/relion_align_symmetry  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
[ 56%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -c /<<PKGBUILDDIR>>/src/gui_entries.cpp
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
[ 56%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -c /<<PKGBUILDDIR>>/src/gui_jobwindow.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 56%] Built target align_symmetry
[ 56%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -c /<<PKGBUILDDIR>>/src/gui_mainwindow.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/scheduler.h:26,
                 from /<<PKGBUILDDIR>>/src/gui_mainwindow.h:28,
                 from /<<PKGBUILDDIR>>/src/gui_mainwindow.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 56%] Built target autopick
/usr/bin/make  -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/convert_star.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 56%] Building CXX object src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o -MF CMakeFiles/convert_star.dir/convert_star.cpp.o.d -o CMakeFiles/convert_star.dir/convert_star.cpp.o -c /<<PKGBUILDDIR>>/src/apps/convert_star.cpp
[ 57%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -c /<<PKGBUILDDIR>>/src/manualpicker.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/io/star_converter.h:5,
                 from /<<PKGBUILDDIR>>/src/apps/convert_star.cpp:24:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 57%] Built target autopick_mpi
/usr/bin/make  -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/convert_to_tiff.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 57%] Building CXX object src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -MF CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o.d -o CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -c /<<PKGBUILDDIR>>/src/apps/convert_to_tiff.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/manualpicker.h:43,
                 from /<<PKGBUILDDIR>>/src/manualpicker.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 58%] Linking CXX executable ../../bin/relion_convert_star
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_star.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/convert_star.dir/convert_star.cpp.o -o ../../bin/relion_convert_star  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/tiff_converter.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/convert_to_tiff.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 58%] Linking CXX executable ../../bin/relion_convert_to_tiff
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_to_tiff.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -o ../../bin/relion_convert_to_tiff  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
[ 58%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -MF CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o.d -o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -c /<<PKGBUILDDIR>>/src/Healpix_2.15a/cxxutils.cc
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
[ 59%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -MF CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o.d -o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -c /<<PKGBUILDDIR>>/src/Healpix_2.15a/healpix_base.cc
/usr/bin/make  -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/convert_to_tiff_mpi.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 60%] Building CXX object src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -MF CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o.d -o CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/convert_to_tiff_mpi.cpp
[ 60%] Linking CXX static library ../../lib/librelion_gui_lib.a
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -P CMakeFiles/relion_gui_lib.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/relion_gui_lib.dir/link.txt --verbose=1
/usr/bin/ar qc ../../lib/librelion_gui_lib.a CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o
/usr/bin/ranlib ../../lib/librelion_gui_lib.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 60%] Built target relion_gui_lib
/usr/bin/make  -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/ctf_mask_test.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 60%] Building CXX object src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -MF CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o.d -o CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -c /<<PKGBUILDDIR>>/src/apps/ctf_mask_test.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/tiff_converter.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/convert_to_tiff_mpi.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/ctf_mask_test.cpp:7:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 60%] Linking CXX executable ../../bin/relion_convert_to_tiff_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_to_tiff_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -o ../../bin/relion_convert_to_tiff_mpi  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
[ 61%] Linking CXX executable ../../bin/relion_ctf_mask_test
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_mask_test.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -o ../../bin/relion_ctf_mask_test  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 61%] Built target convert_to_tiff
/usr/bin/make  -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/ctf_refine.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 61%] Building CXX object src/apps/CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -MF CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o.d -o CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -c /<<PKGBUILDDIR>>/src/apps/ctf_refine.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/ctf_refiner.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/ctf_refine.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 61%] Built target convert_star
/usr/bin/make  -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/ctf_refine_mpi.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 61%] Building CXX object src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -MF CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o.d -o CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/ctf_refine_mpi.cpp
[ 62%] Linking CXX executable ../../bin/relion_ctf_refine
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_refine.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -o ../../bin/relion_ctf_refine  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/ctf_refiner.h:24,
                 from /<<PKGBUILDDIR>>/src/jaz/ctf/ctf_refiner_mpi.h:26,
                 from /<<PKGBUILDDIR>>/src/apps/ctf_refine_mpi.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 62%] Linking CXX executable ../../bin/relion_ctf_refine_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_refine_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -o ../../bin/relion_ctf_refine_mpi  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 62%] Built target convert_to_tiff_mpi
/usr/bin/make  -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/ctf_toolbox.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 63%] Building CXX object src/apps/CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -MF CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o.d -o CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -c /<<PKGBUILDDIR>>/src/apps/ctf_toolbox.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/ctf_toolbox.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
[ 63%] Linking CXX executable ../../bin/relion_ctf_toolbox
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_toolbox.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -o ../../bin/relion_ctf_toolbox  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 63%] Built target ctf_mask_test
/usr/bin/make  -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/demodulate.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 63%] Building CXX object src/apps/CMakeFiles/demodulate.dir/demodulate.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/demodulate.dir/demodulate.cpp.o -MF CMakeFiles/demodulate.dir/demodulate.cpp.o.d -o CMakeFiles/demodulate.dir/demodulate.cpp.o -c /<<PKGBUILDDIR>>/src/apps/demodulate.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/vtk_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/demodulate.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
[ 64%] Linking CXX executable ../../bin/relion_demodulate
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/demodulate.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/demodulate.dir/demodulate.cpp.o -o ../../bin/relion_demodulate  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 64%] Built target ctf_refine
/usr/bin/make  -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/display.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 64%] Building CXX object src/apps/CMakeFiles/display.dir/display.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/display.dir/display.cpp.o -MF CMakeFiles/display.dir/display.cpp.o.d -o CMakeFiles/display.dir/display.cpp.o -c /<<PKGBUILDDIR>>/src/apps/display.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/display.cpp:25:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 65%] Linking CXX executable ../../bin/relion_display
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/display.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/display.dir/display.cpp.o -o ../../bin/relion_display  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/aarch64-linux-gnu/libfltk_images.so /usr/lib/aarch64-linux-gnu/libfltk_forms.so /usr/lib/aarch64-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 65%] Built target ctf_toolbox
/usr/bin/make  -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/estimate_gain.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 65%] Building CXX object src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -MF CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o.d -o CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -c /<<PKGBUILDDIR>>/src/apps/estimate_gain.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 65%] Built target ctf_refine_mpi
/usr/bin/make  -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/external_reconstruct.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 66%] Building CXX object src/apps/CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -MF CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o.d -o CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -c /<<PKGBUILDDIR>>/src/apps/external_reconstruct.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/estimate_gain.cpp:27:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/external_reconstruct.cpp:24:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
[ 66%] Linking CXX executable ../../bin/relion_estimate_gain
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/estimate_gain.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -o ../../bin/relion_estimate_gain  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
[ 66%] Linking CXX executable ../../bin/relion_external_reconstruct
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/external_reconstruct.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -o ../../bin/relion_external_reconstruct  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 66%] Built target demodulate
/usr/bin/make  -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/find_tiltpairs.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 66%] Building CXX object src/apps/CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -MF CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o.d -o CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -c /<<PKGBUILDDIR>>/src/apps/find_tiltpairs.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 66%] Built target display
/usr/bin/make  -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/flex_analyse.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 66%] Building CXX object src/apps/CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -MF CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o.d -o CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -c /<<PKGBUILDDIR>>/src/apps/flex_analyse.cpp
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/exp_model.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/../flex_analyser.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/flex_analyse.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 66%] Built target estimate_gain
/usr/bin/make  -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/flex_analyse_mpi.dir/DependInfo.cmake "--color="
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 66%] Building CXX object src/apps/CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -MF CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o.d -o CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/flex_analyse_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/exp_model.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/../flex_analyser.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/flex_analyse_mpi.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 67%] Linking CXX executable ../../bin/relion_find_tiltpairs
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/find_tiltpairs.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -o ../../bin/relion_find_tiltpairs  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
[ 68%] Linking CXX executable ../../bin/relion_flex_analyse
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -o ../../bin/relion_flex_analyse  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 68%] Built target external_reconstruct
/usr/bin/make  -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/helix_inimodel2d.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 69%] Building CXX object src/apps/CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -MF CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o.d -o CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -c /<<PKGBUILDDIR>>/src/apps/helix_inimodel2d.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/../helix_inimodel2d.h:29,
                 from /<<PKGBUILDDIR>>/src/apps/helix_inimodel2d.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In function ‘free_Tvector’,
    inlined from ‘gaussj’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.h:262:17,
    inlined from ‘solve’ at /usr/src/relion-3.1.3-3build3/src/matrix2d.h:1345:11,
    inlined from ‘optimiseTransformationMatrixContinuous’ at /usr/src/relion-3.1.3-3build3/src/apps/find_tiltpairs.cpp:377:8,
    inlined from ‘run’ at /usr/src/relion-3.1.3-3build3/src/apps/find_tiltpairs.cpp:425:42,
    inlined from ‘main’ at /usr/src/relion-3.1.3-3build3/src/apps/find_tiltpairs.cpp:480:10:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ipiv’ with nonzero offset 4 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.h: In function ‘main’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.h:198:26: note: declared here
In function ‘free_Tvector’,
    inlined from ‘gaussj’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.h:263:17,
    inlined from ‘solve’ at /usr/src/relion-3.1.3-3build3/src/matrix2d.h:1345:11,
    inlined from ‘optimiseTransformationMatrixContinuous’ at /usr/src/relion-3.1.3-3build3/src/apps/find_tiltpairs.cpp:377:8,
    inlined from ‘run’ at /usr/src/relion-3.1.3-3build3/src/apps/find_tiltpairs.cpp:425:42,
    inlined from ‘main’ at /usr/src/relion-3.1.3-3build3/src/apps/find_tiltpairs.cpp:480:10:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘indxr’ with nonzero offset 4 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.h: In function ‘main’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.h:198:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘gaussj’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.h:264:17,
    inlined from ‘solve’ at /usr/src/relion-3.1.3-3build3/src/matrix2d.h:1345:11,
    inlined from ‘optimiseTransformationMatrixContinuous’ at /usr/src/relion-3.1.3-3build3/src/apps/find_tiltpairs.cpp:377:8,
    inlined from ‘run’ at /usr/src/relion-3.1.3-3build3/src/apps/find_tiltpairs.cpp:425:42,
    inlined from ‘main’ at /usr/src/relion-3.1.3-3build3/src/apps/find_tiltpairs.cpp:480:10:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘indxc’ with nonzero offset 4 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.h: In function ‘main’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.h:198:10: note: declared here
[ 69%] Linking CXX executable ../../bin/relion_helix_inimodel2d
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_inimodel2d.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -o ../../bin/relion_helix_inimodel2d  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
[ 69%] Linking CXX executable ../../bin/relion_flex_analyse_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -o ../../bin/relion_flex_analyse_mpi  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 69%] Built target find_tiltpairs
/usr/bin/make  -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/helix_toolbox.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 70%] Building CXX object src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -MF CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o.d -o CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -c /<<PKGBUILDDIR>>/src/apps/helix_toolbox.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/helix.h:30,
                 from /<<PKGBUILDDIR>>/src/apps/helix_toolbox.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 70%] Built target helix_inimodel2d
/usr/bin/make  -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/image_handler.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 70%] Building CXX object src/apps/CMakeFiles/image_handler.dir/image_handler.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/image_handler.dir/image_handler.cpp.o -MF CMakeFiles/image_handler.dir/image_handler.cpp.o.d -o CMakeFiles/image_handler.dir/image_handler.cpp.o -c /<<PKGBUILDDIR>>/src/apps/image_handler.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/image_handler.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 70%] Linking CXX executable ../../bin/relion_helix_toolbox
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_toolbox.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -o ../../bin/relion_helix_toolbox  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 70%] Built target flex_analyse
/usr/bin/make  -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/import.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 70%] Building CXX object src/apps/CMakeFiles/import.dir/import.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/import.dir/import.cpp.o -MF CMakeFiles/import.dir/import.cpp.o.d -o CMakeFiles/import.dir/import.cpp.o -c /<<PKGBUILDDIR>>/src/apps/import.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/import.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 70%] Built target flex_analyse_mpi
/usr/bin/make  -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/localsym.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 71%] Building CXX object src/apps/CMakeFiles/localsym.dir/localsym.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/localsym.dir/localsym.cpp.o -MF CMakeFiles/localsym.dir/localsym.cpp.o.d -o CMakeFiles/localsym.dir/localsym.cpp.o -c /<<PKGBUILDDIR>>/src/apps/localsym.cpp
[ 72%] Linking CXX executable ../../bin/relion_image_handler
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/image_handler.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/image_handler.dir/image_handler.cpp.o -o ../../bin/relion_image_handler  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/local_symmetry.h:30,
                 from /<<PKGBUILDDIR>>/src/apps/localsym.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 72%] Linking CXX executable ../../bin/relion_localsym
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/localsym.dir/localsym.cpp.o -o ../../bin/relion_localsym  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
[ 72%] Linking CXX executable ../../bin/relion_import
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/import.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/import.dir/import.cpp.o -o ../../bin/relion_import  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 72%] Built target helix_toolbox
/usr/bin/make  -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/localsym_mpi.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 73%] Building CXX object src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -MF CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o.d -o CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/localsym_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/local_symmetry.h:30,
                 from /<<PKGBUILDDIR>>/src/local_symmetry_mpi.h:5,
                 from /<<PKGBUILDDIR>>/src/apps/localsym_mpi.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 73%] Linking CXX executable ../../bin/relion_localsym_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -o ../../bin/relion_localsym_mpi  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 73%] Built target import
/usr/bin/make  -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/relion.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 73%] Building CXX object src/apps/CMakeFiles/relion.dir/maingui.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/relion.dir/maingui.cpp.o -MF CMakeFiles/relion.dir/maingui.cpp.o.d -o CMakeFiles/relion.dir/maingui.cpp.o -c /<<PKGBUILDDIR>>/src/apps/maingui.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 73%] Built target image_handler
/usr/bin/make  -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/manualpick.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 73%] Building CXX object src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o -MF CMakeFiles/manualpick.dir/manualpick.cpp.o.d -o CMakeFiles/manualpick.dir/manualpick.cpp.o -c /<<PKGBUILDDIR>>/src/apps/manualpick.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/scheduler.h:26,
                 from /<<PKGBUILDDIR>>/src/gui_mainwindow.h:28,
                 from /<<PKGBUILDDIR>>/src/apps/maingui.cpp:23:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/manualpick.cpp:25:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 74%] Linking CXX executable ../../bin/relion
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/relion.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/relion.dir/maingui.cpp.o -o ../../bin/relion  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/aarch64-linux-gnu/libfltk_images.so /usr/lib/aarch64-linux-gnu/libfltk_forms.so /usr/lib/aarch64-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff 
[ 75%] Linking CXX executable ../../bin/relion_manualpick
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/manualpick.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/manualpick.dir/manualpick.cpp.o -o ../../bin/relion_manualpick  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/aarch64-linux-gnu/libfltk_images.so /usr/lib/aarch64-linux-gnu/libfltk_forms.so /usr/lib/aarch64-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 75%] Built target localsym
/usr/bin/make  -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/mask_create.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 75%] Building CXX object src/apps/CMakeFiles/mask_create.dir/mask_create.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/mask_create.dir/mask_create.cpp.o -MF CMakeFiles/mask_create.dir/mask_create.cpp.o.d -o CMakeFiles/mask_create.dir/mask_create.cpp.o -c /<<PKGBUILDDIR>>/src/apps/mask_create.cpp
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/mask_create.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
[ 75%] Linking CXX executable ../../bin/relion_mask_create
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mask_create.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/mask_create.dir/mask_create.cpp.o -o ../../bin/relion_mask_create  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 75%] Built target manualpick
/usr/bin/make  -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/merge_particles.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 76%] Building CXX object src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o -MF CMakeFiles/merge_particles.dir/merge_particles.cpp.o.d -o CMakeFiles/merge_particles.dir/merge_particles.cpp.o -c /<<PKGBUILDDIR>>/src/apps/merge_particles.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/io/star_converter.h:5,
                 from /<<PKGBUILDDIR>>/src/apps/merge_particles.cpp:2:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 76%] Linking CXX executable ../../bin/relion_merge_particles
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/merge_particles.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/merge_particles.dir/merge_particles.cpp.o -o ../../bin/relion_merge_particles  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 76%] Built target localsym_mpi
/usr/bin/make  -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/motion_refine.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 77%] Building CXX object src/apps/CMakeFiles/motion_refine.dir/motion_refine.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/motion_refine.dir/motion_refine.cpp.o -MF CMakeFiles/motion_refine.dir/motion_refine.cpp.o.d -o CMakeFiles/motion_refine.dir/motion_refine.cpp.o -c /<<PKGBUILDDIR>>/src/apps/motion_refine.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_refiner.h:25,
                 from /<<PKGBUILDDIR>>/src/apps/motion_refine.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 77%] Linking CXX executable ../../bin/relion_motion_refine
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/motion_refine.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/motion_refine.dir/motion_refine.cpp.o -o ../../bin/relion_motion_refine  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 77%] Built target merge_particles
/usr/bin/make  -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/motion_refine_mpi.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 77%] Building CXX object src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -MF CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o.d -o CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/motion_refine_mpi.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 77%] Built target relion
/usr/bin/make  -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/mrc2vtk.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 77%] Building CXX object src/apps/CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -MF CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o.d -o CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -c /<<PKGBUILDDIR>>/src/apps/mrc2vtk.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_refiner.h:25,
                 from /<<PKGBUILDDIR>>/src/jaz/motion/motion_refiner_mpi.h:27,
                 from /<<PKGBUILDDIR>>/src/apps/motion_refine_mpi.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/mrc2vtk.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 77%] Built target mask_create
/usr/bin/make  -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_FCC.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 78%] Building CXX object src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -MF CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o.d -o CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -c /<<PKGBUILDDIR>>/src/apps/particle_FCC.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/particle_FCC.cpp:7:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 78%] Linking CXX executable ../../bin/relion_mrc2vtk
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mrc2vtk.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -o ../../bin/relion_mrc2vtk  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
[ 79%] Linking CXX executable ../../bin/relion_motion_refine_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/motion_refine_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -o ../../bin/relion_motion_refine_mpi  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
[ 79%] Linking CXX executable ../../bin/relion_particle_FCC
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_FCC.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -o ../../bin/relion_particle_FCC  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 79%] Built target mrc2vtk
/usr/bin/make  -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_reposition.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 80%] Building CXX object src/apps/CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -MF CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o.d -o CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -c /<<PKGBUILDDIR>>/src/apps/particle_reposition.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/ml_model.h:23,
                 from /<<PKGBUILDDIR>>/src/ml_optimiser.h:35,
                 from /<<PKGBUILDDIR>>/src/apps/particle_reposition.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 80%] Built target motion_refine
/usr/bin/make  -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_select.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 80%] Building CXX object src/apps/CMakeFiles/particle_select.dir/particle_select.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/particle_select.dir/particle_select.cpp.o -MF CMakeFiles/particle_select.dir/particle_select.cpp.o.d -o CMakeFiles/particle_select.dir/particle_select.cpp.o -c /<<PKGBUILDDIR>>/src/apps/particle_select.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/ctf.h:50,
                 from /<<PKGBUILDDIR>>/src/jaz/stack_helper.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/particle_select.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 80%] Linking CXX executable ../../bin/relion_particle_reposition
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_reposition.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -o ../../bin/relion_particle_reposition  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
[ 81%] Linking CXX executable ../../bin/relion_particle_select
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_select.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/particle_select.dir/particle_select.cpp.o -o ../../bin/relion_particle_select  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 81%] Built target particle_FCC
/usr/bin/make  -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_subtract.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 81%] Building CXX object src/apps/CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -MF CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o.d -o CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -c /<<PKGBUILDDIR>>/src/apps/particle_subtract.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/ml_model.h:23,
                 from /<<PKGBUILDDIR>>/src/ml_optimiser.h:35,
                 from /<<PKGBUILDDIR>>/src/apps/../particle_subtractor.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/particle_subtract.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 82%] Linking CXX executable ../../bin/relion_particle_subtract
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -o ../../bin/relion_particle_subtract  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 82%] Built target motion_refine_mpi
/usr/bin/make  -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_subtract_mpi.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 82%] Building CXX object src/apps/CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -MF CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o.d -o CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/particle_subtract_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/ml_model.h:23,
                 from /<<PKGBUILDDIR>>/src/ml_optimiser.h:35,
                 from /<<PKGBUILDDIR>>/src/apps/../particle_subtractor.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/particle_subtract_mpi.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 82%] Linking CXX executable ../../bin/relion_particle_subtract_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -o ../../bin/relion_particle_subtract_mpi  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 82%] Built target particle_select
/usr/bin/make  -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_symmetry_expand.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 83%] Building CXX object src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -MF CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o.d -o CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -c /<<PKGBUILDDIR>>/src/apps/particle_symmetry_expand.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/particle_symmetry_expand.cpp:26:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
[ 83%] Linking CXX executable ../../bin/relion_particle_symmetry_expand
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_symmetry_expand.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -o ../../bin/relion_particle_symmetry_expand  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 83%] Built target particle_symmetry_expand
/usr/bin/make  -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/pipeliner.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 83%] Building CXX object src/apps/CMakeFiles/pipeliner.dir/pipeliner.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/pipeliner.dir/pipeliner.cpp.o -MF CMakeFiles/pipeliner.dir/pipeliner.cpp.o.d -o CMakeFiles/pipeliner.dir/pipeliner.cpp.o -c /<<PKGBUILDDIR>>/src/apps/pipeliner.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 83%] Built target particle_reposition
/usr/bin/make  -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/plot_delocalisation.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 83%] Building CXX object src/apps/CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -MF CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o.d -o CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -c /<<PKGBUILDDIR>>/src/apps/plot_delocalisation.cpp
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/plot_delocalisation.cpp:7:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 84%] Linking CXX executable ../../bin/relion_pipeliner
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/pipeliner.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/pipeliner.dir/pipeliner.cpp.o -o ../../bin/relion_pipeliner  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
[ 85%] Linking CXX executable ../../bin/relion_plot_delocalisation
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/plot_delocalisation.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -o ../../bin/relion_plot_delocalisation  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 85%] Built target particle_subtract
/usr/bin/make  -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/postprocess.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 85%] Building CXX object src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o -MF CMakeFiles/postprocess.dir/postprocess.cpp.o.d -o CMakeFiles/postprocess.dir/postprocess.cpp.o -c /<<PKGBUILDDIR>>/src/apps/postprocess.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/postprocessing.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/postprocess.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 85%] Linking CXX executable ../../bin/relion_postprocess
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/postprocess.dir/postprocess.cpp.o -o ../../bin/relion_postprocess  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 85%] Built target particle_subtract_mpi
/usr/bin/make  -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/postprocess_mpi.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 86%] Building CXX object src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -MF CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o.d -o CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/postprocess_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/postprocessing.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/postprocess_mpi.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
[ 86%] Linking CXX executable ../../bin/relion_postprocess_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -o ../../bin/relion_postprocess_mpi  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 86%] Built target plot_delocalisation
/usr/bin/make  -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/prepare_subtomo.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 86%] Building CXX object src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -MF CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o.d -o CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -c /<<PKGBUILDDIR>>/src/apps/prepare_subtomo.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 86%] Built target pipeliner
/usr/bin/make  -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/preprocess.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 86%] Building CXX object src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o -MF CMakeFiles/preprocess.dir/preprocess.cpp.o.d -o CMakeFiles/preprocess.dir/preprocess.cpp.o -c /<<PKGBUILDDIR>>/src/apps/preprocess.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 86%] Built target postprocess
/usr/bin/make  -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/preprocess_mpi.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/helix.h:30,
                 from /<<PKGBUILDDIR>>/src/apps/prepare_subtomo.cpp:22:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 86%] Building CXX object src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -MF CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o.d -o CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/preprocess_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/preprocessing.h:29,
                 from /<<PKGBUILDDIR>>/src/apps/preprocess.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/preprocessing.h:29,
                 from /<<PKGBUILDDIR>>/src/preprocessing_mpi.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/preprocess_mpi.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 87%] Linking CXX executable ../../bin/relion_preprocess
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/preprocess.dir/preprocess.cpp.o -o ../../bin/relion_preprocess  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
[ 87%] Linking CXX executable ../../bin/relion_preprocess_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -o ../../bin/relion_preprocess_mpi  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 87%] Built target postprocess_mpi
/usr/bin/make  -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/project.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 88%] Building CXX object src/apps/CMakeFiles/project.dir/project.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/project.dir/project.cpp.o -MF CMakeFiles/project.dir/project.cpp.o.d -o CMakeFiles/project.dir/project.cpp.o -c /<<PKGBUILDDIR>>/src/apps/project.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/apps/project.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 89%] Linking CXX executable ../../bin/relion_prepare_subtomo
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/prepare_subtomo.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -o ../../bin/relion_prepare_subtomo  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 89%] Built target preprocess
/usr/bin/make  -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/reconstruct.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 89%] Building CXX object src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o -MF CMakeFiles/reconstruct.dir/reconstruct.cpp.o.d -o CMakeFiles/reconstruct.dir/reconstruct.cpp.o -c /<<PKGBUILDDIR>>/src/apps/reconstruct.cpp
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/backprojector.h:33,
                 from /<<PKGBUILDDIR>>/src/reconstructor.h:23,
                 from /<<PKGBUILDDIR>>/src/apps/reconstruct.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 89%] Linking CXX executable ../../bin/relion_project
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/project.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/project.dir/project.cpp.o -o ../../bin/relion_project  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 89%] Built target preprocess_mpi
/usr/bin/make  -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/reconstruct_mpi.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 89%] Building CXX object src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -MF CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o.d -o CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/reconstruct_mpi.cpp
[ 90%] Linking CXX executable ../../bin/relion_reconstruct
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/reconstruct.dir/reconstruct.cpp.o -o ../../bin/relion_reconstruct  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/backprojector.h:33,
                 from /<<PKGBUILDDIR>>/src/reconstructor.h:23,
                 from /<<PKGBUILDDIR>>/src/reconstructor_mpi.h:25,
                 from /<<PKGBUILDDIR>>/src/apps/reconstruct_mpi.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 90%] Built target prepare_subtomo
/usr/bin/make  -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/refine.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 90%] Building CXX object src/apps/CMakeFiles/refine.dir/refine.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/refine.dir/refine.cpp.o -MF CMakeFiles/refine.dir/refine.cpp.o.d -o CMakeFiles/refine.dir/refine.cpp.o -c /<<PKGBUILDDIR>>/src/apps/refine.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/ml_model.h:23,
                 from /<<PKGBUILDDIR>>/src/ml_optimiser.h:35,
                 from /<<PKGBUILDDIR>>/src/apps/refine.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 91%] Linking CXX executable ../../bin/relion_reconstruct_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -o ../../bin/relion_reconstruct_mpi  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
[ 91%] Linking CXX executable ../../bin/relion_refine
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/refine.dir/refine.cpp.o -o ../../bin/relion_refine  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 91%] Built target project
/usr/bin/make  -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/refine_mpi.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 92%] Building CXX object src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -MF CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o.d -o CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/refine_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/projector.h:25,
                 from /<<PKGBUILDDIR>>/src/ml_model.h:23,
                 from /<<PKGBUILDDIR>>/src/ml_optimiser.h:35,
                 from /<<PKGBUILDDIR>>/src/ml_optimiser_mpi.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/refine_mpi.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 92%] Built target reconstruct
/usr/bin/make  -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/reposition.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 92%] Building CXX object src/apps/CMakeFiles/reposition.dir/reposition.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/reposition.dir/reposition.cpp.o -MF CMakeFiles/reposition.dir/reposition.cpp.o.d -o CMakeFiles/reposition.dir/reposition.cpp.o -c /<<PKGBUILDDIR>>/src/apps/reposition.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/apps/reposition.cpp:1:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 92%] Built target reconstruct_mpi
/usr/bin/make  -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/run_ctffind.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 92%] Building CXX object src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -MF CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o.d -o CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -c /<<PKGBUILDDIR>>/src/apps/run_ctffind.cpp
[ 93%] Linking CXX executable ../../bin/relion_reposition
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reposition.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/reposition.dir/reposition.cpp.o -o ../../bin/relion_reposition  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/ctffind_runner.h:31,
                 from /<<PKGBUILDDIR>>/src/apps/run_ctffind.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 93%] Linking CXX executable ../../bin/relion_refine_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -o ../../bin/relion_refine_mpi  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
[ 93%] Linking CXX executable ../../bin/relion_run_ctffind
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -o ../../bin/relion_run_ctffind  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 93%] Built target refine
/usr/bin/make  -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/run_ctffind_mpi.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 94%] Building CXX object src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -MF CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o.d -o CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/run_ctffind_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/ctffind_runner.h:31,
                 from /<<PKGBUILDDIR>>/src/ctffind_runner_mpi.h:25,
                 from /<<PKGBUILDDIR>>/src/apps/run_ctffind_mpi.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 94%] Built target run_ctffind
/usr/bin/make  -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/run_motioncorr.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 95%] Building CXX object src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -MF CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o.d -o CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -c /<<PKGBUILDDIR>>/src/apps/run_motioncorr.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/motioncorr_runner.h:32,
                 from /<<PKGBUILDDIR>>/src/apps/run_motioncorr.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 95%] Linking CXX executable ../../bin/relion_run_ctffind_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind_mpi.dir/link.txt --verbose=1
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -o ../../bin/relion_run_ctffind_mpi  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
[ 95%] Linking CXX executable ../../bin/relion_run_motioncorr
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -o ../../bin/relion_run_motioncorr  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
[ 95%] Built target reposition
/usr/bin/make  -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/run_motioncorr_mpi.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 95%] Building CXX object src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -MF CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o.d -o CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/apps/run_motioncorr_mpi.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/motioncorr_runner.h:32,
                 from /<<PKGBUILDDIR>>/src/motioncorr_runner_mpi.h:25,
                 from /<<PKGBUILDDIR>>/src/apps/run_motioncorr_mpi.cpp:20:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 96%] Linking CXX executable ../../bin/relion_run_motioncorr_mpi
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr_mpi.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -o ../../bin/relion_run_motioncorr_mpi  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 96%] Built target run_ctffind_mpi
/usr/bin/make  -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/scheduler.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 96%] Building CXX object src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o -MF CMakeFiles/scheduler.dir/scheduler.cpp.o.d -o CMakeFiles/scheduler.dir/scheduler.cpp.o -c /<<PKGBUILDDIR>>/src/apps/scheduler.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/obs_model.h:24,
                 from /<<PKGBUILDDIR>>/src/scheduler.h:26,
                 from /<<PKGBUILDDIR>>/src/apps/scheduler.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 96%] Built target run_motioncorr
/usr/bin/make  -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/stack_create.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 97%] Building CXX object src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o -MF CMakeFiles/stack_create.dir/stack_create.cpp.o.d -o CMakeFiles/stack_create.dir/stack_create.cpp.o -c /<<PKGBUILDDIR>>/src/apps/stack_create.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/stack_create.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 97%] Linking CXX executable ../../bin/relion_scheduler
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/scheduler.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/scheduler.dir/scheduler.cpp.o -o ../../bin/relion_scheduler  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 97%] Built target refine_mpi
/usr/bin/make  -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/star_handler.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 98%] Building CXX object src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o -MF CMakeFiles/star_handler.dir/star_handler.cpp.o.d -o CMakeFiles/star_handler.dir/star_handler.cpp.o -c /<<PKGBUILDDIR>>/src/apps/star_handler.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/star_handler.cpp:21:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 98%] Built target run_motioncorr_mpi
/usr/bin/make  -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/tiltpair_plot.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 98%] Building CXX object src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -MF CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o.d -o CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -c /<<PKGBUILDDIR>>/src/apps/tiltpair_plot.cpp
[ 98%] Linking CXX executable ../../bin/relion_stack_create
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/stack_create.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/stack_create.dir/stack_create.cpp.o -o ../../bin/relion_stack_create  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/apps/tiltpair_plot.cpp:25:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
[ 99%] Linking CXX executable ../../bin/relion_tiltpair_plot
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiltpair_plot.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -o ../../bin/relion_tiltpair_plot  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
[ 99%] Linking CXX executable ../../bin/relion_star_handler
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/star_handler.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/star_handler.dir/star_handler.cpp.o -o ../../bin/relion_star_handler  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 99%] Built target tiltpair_plot
/usr/bin/make  -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/tomo_test.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
[ 99%] Building CXX object src/apps/CMakeFiles/tomo_test.dir/tomo_test.cpp.o
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<<PKGBUILDDIR>>/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>> -I/usr/lib/fltk -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -MD -MT src/apps/CMakeFiles/tomo_test.dir/tomo_test.cpp.o -MF CMakeFiles/tomo_test.dir/tomo_test.cpp.o.d -o CMakeFiles/tomo_test.dir/tomo_test.cpp.o -c /<<PKGBUILDDIR>>/src/apps/tomo_test.cpp
In file included from /<<PKGBUILDDIR>>/src/image.h:455,
                 from /<<PKGBUILDDIR>>/src/jaz/tomo/tomo_stack.h:25,
                 from /<<PKGBUILDDIR>>/src/apps/tomo_test.cpp:2:
/<<PKGBUILDDIR>>/src/rwTIFF.h: In member function ‘int Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                ^~~~~
In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31,
                 from /<<PKGBUILDDIR>>/src/image.h:57:
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
   43 |         uint32 width, length; // apparent dimensions in the file
      |                       ^~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                ^~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                              ^~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
   44 |         uint16 sampleFormat, bitsPerSample, resolutionUnit;
      |                                             ^~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                ^~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations]
  185 |                         uint32 cur_width, cur_length;
      |                                           ^~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here
   86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                ^~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
/<<PKGBUILDDIR>>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations]
  186 |                         uint16 cur_sampleFormat, cur_bitsPerSample;
      |                                                  ^~~~~~~~~~~~~~~~~
/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here
   83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
      |                                      ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 99%] Built target stack_create
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
[100%] Linking CXX executable ../../bin/relion_tomo_test
cd /<<PKGBUILDDIR>>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tomo_test.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/relion-3.1.3-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -fopenmp -std=c++0x -O3 -DNDEBUG  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now  -rdynamic CMakeFiles/tomo_test.dir/tomo_test.cpp.o -o ../../bin/relion_tomo_test  ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[100%] Built target scheduler
In function ‘free_Tvector’,
    inlined from ‘brent’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:594:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘brent’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:579:13: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:767:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:24: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:768:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:18: note: declared here
In function ‘free_Tvector’,
    inlined from ‘powell’ at /usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:769:25:
/usr/src/relion-3.1.3-3build3/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object]
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp: In function ‘powell’:
/usr/src/relion-3.1.3-3build3/src/numerical_recipes.cpp:703:13: note: declared here
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[100%] Built target star_handler
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[100%] Built target tomo_test
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   create-stamp debian/debhelper-build-stamp
   dh_prep -a
   debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
/usr/bin/make -C build install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp/cli
make[2]: Entering directory '/<<PKGBUILDDIR>>/build'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/CMakeFiles /<<PKGBUILDDIR>>/build//CMakeFiles/progress.marks
/usr/bin/make  -f CMakeFiles/Makefile2 all
make[3]: Entering directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/CMakeFiles/copy_scripts.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_printtable /<<PKGBUILDDIR>>/build/bin/relion_star_printtable
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_plottable /<<PKGBUILDDIR>>/build/bin/relion_star_plottable
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_loopheader /<<PKGBUILDDIR>>/build/bin/relion_star_loopheader
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_datablock_stack /<<PKGBUILDDIR>>/build/bin/relion_star_datablock_stack
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_datablock_singlefiles /<<PKGBUILDDIR>>/build/bin/relion_star_datablock_singlefiles
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/star_datablock_ctfdat /<<PKGBUILDDIR>>/build/bin/relion_star_datablock_ctfdat
/usr/bin/cmake -E copy /<<PKGBUILDDIR>>/scripts/qsub.csh /<<PKGBUILDDIR>>/build/bin/relion_qsub.csh
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[  0%] Built target copy_scripts
/usr/bin/make  -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/relion_lib.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/relion_lib.dir/build'.
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[ 53%] Built target relion_lib
/usr/bin/make  -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/relion_gui_lib.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/relion_gui_lib.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 56%] Built target relion_gui_lib
/usr/bin/make  -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/align_symmetry.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/align_symmetry.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 56%] Built target align_symmetry
/usr/bin/make  -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/autopick.dir/DependInfo.cmake "--color="
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/usr/bin/make  -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/autopick.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 57%] Built target autopick
/usr/bin/make  -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/autopick_mpi.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/autopick_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 58%] Built target autopick_mpi
/usr/bin/make  -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/convert_star.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/convert_star.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 59%] Built target convert_star
/usr/bin/make  -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/convert_to_tiff.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/convert_to_tiff.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 59%] Built target convert_to_tiff
/usr/bin/make  -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/convert_to_tiff_mpi.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 60%] Built target convert_to_tiff_mpi
/usr/bin/make  -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/ctf_mask_test.dir/DependInfo.cmake "--color="
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/usr/bin/make  -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_mask_test.dir/build'.
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[ 61%] Built target ctf_mask_test
/usr/bin/make  -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/ctf_refine.dir/DependInfo.cmake "--color="
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make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_refine.dir/build'.
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[ 62%] Built target ctf_refine
/usr/bin/make  -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/ctf_refine_mpi.dir/DependInfo.cmake "--color="
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[ 62%] Built target ctf_refine_mpi
/usr/bin/make  -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/ctf_toolbox.dir/DependInfo.cmake "--color="
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[ 63%] Built target ctf_toolbox
/usr/bin/make  -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/demodulate.dir/DependInfo.cmake "--color="
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make[4]: Nothing to be done for 'src/apps/CMakeFiles/demodulate.dir/build'.
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[ 64%] Built target demodulate
/usr/bin/make  -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/display.dir/DependInfo.cmake "--color="
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
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[ 65%] Built target display
/usr/bin/make  -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/estimate_gain.dir/DependInfo.cmake "--color="
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[ 65%] Built target estimate_gain
/usr/bin/make  -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/external_reconstruct.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/external_reconstruct.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 66%] Built target external_reconstruct
/usr/bin/make  -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/find_tiltpairs.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/find_tiltpairs.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 67%] Built target find_tiltpairs
/usr/bin/make  -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/flex_analyse.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/flex_analyse.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 68%] Built target flex_analyse
/usr/bin/make  -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/flex_analyse_mpi.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/flex_analyse_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 68%] Built target flex_analyse_mpi
/usr/bin/make  -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/helix_inimodel2d.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/helix_inimodel2d.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 69%] Built target helix_inimodel2d
/usr/bin/make  -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/helix_toolbox.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/helix_toolbox.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 70%] Built target helix_toolbox
/usr/bin/make  -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/image_handler.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/image_handler.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 71%] Built target image_handler
/usr/bin/make  -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/import.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/import.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 71%] Built target import
/usr/bin/make  -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/localsym.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/localsym.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 72%] Built target localsym
/usr/bin/make  -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/localsym_mpi.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/localsym_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 73%] Built target localsym_mpi
/usr/bin/make  -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/relion.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/relion.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 74%] Built target relion
/usr/bin/make  -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/manualpick.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/manualpick.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 75%] Built target manualpick
/usr/bin/make  -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/mask_create.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/mask_create.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 75%] Built target mask_create
/usr/bin/make  -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/merge_particles.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/merge_particles.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 76%] Built target merge_particles
/usr/bin/make  -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/motion_refine.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/motion_refine.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 77%] Built target motion_refine
/usr/bin/make  -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/motion_refine_mpi.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/motion_refine_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 78%] Built target motion_refine_mpi
/usr/bin/make  -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/mrc2vtk.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/mrc2vtk.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 78%] Built target mrc2vtk
/usr/bin/make  -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_FCC.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_FCC.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 79%] Built target particle_FCC
/usr/bin/make  -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_reposition.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_reposition.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 80%] Built target particle_reposition
/usr/bin/make  -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_select.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_select.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 81%] Built target particle_select
/usr/bin/make  -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_subtract.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_subtract.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 82%] Built target particle_subtract
/usr/bin/make  -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_subtract_mpi.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_subtract_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 82%] Built target particle_subtract_mpi
/usr/bin/make  -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/particle_symmetry_expand.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_symmetry_expand.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 83%] Built target particle_symmetry_expand
/usr/bin/make  -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/pipeliner.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/pipeliner.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 84%] Built target pipeliner
/usr/bin/make  -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/plot_delocalisation.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/plot_delocalisation.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 85%] Built target plot_delocalisation
/usr/bin/make  -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/postprocess.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/postprocess.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 85%] Built target postprocess
/usr/bin/make  -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/postprocess_mpi.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/postprocess_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 86%] Built target postprocess_mpi
/usr/bin/make  -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/prepare_subtomo.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/prepare_subtomo.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 87%] Built target prepare_subtomo
/usr/bin/make  -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/preprocess.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/preprocess.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 88%] Built target preprocess
/usr/bin/make  -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/preprocess_mpi.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/preprocess_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 88%] Built target preprocess_mpi
/usr/bin/make  -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/project.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/project.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 89%] Built target project
/usr/bin/make  -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/reconstruct.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/reconstruct.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 90%] Built target reconstruct
/usr/bin/make  -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/reconstruct_mpi.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/reconstruct_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 91%] Built target reconstruct_mpi
/usr/bin/make  -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/refine.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/refine.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 91%] Built target refine
/usr/bin/make  -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/refine_mpi.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/refine_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 92%] Built target refine_mpi
/usr/bin/make  -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/reposition.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/reposition.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 93%] Built target reposition
/usr/bin/make  -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/run_ctffind.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_ctffind.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 93%] Built target run_ctffind
/usr/bin/make  -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/run_ctffind_mpi.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_ctffind_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 94%] Built target run_ctffind_mpi
/usr/bin/make  -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/run_motioncorr.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_motioncorr.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 95%] Built target run_motioncorr
/usr/bin/make  -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/run_motioncorr_mpi.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_motioncorr_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 96%] Built target run_motioncorr_mpi
/usr/bin/make  -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/scheduler.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/scheduler.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 96%] Built target scheduler
/usr/bin/make  -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/stack_create.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/stack_create.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 97%] Built target stack_create
/usr/bin/make  -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/star_handler.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/star_handler.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 98%] Built target star_handler
/usr/bin/make  -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/tiltpair_plot.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/tiltpair_plot.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[ 99%] Built target tiltpair_plot
/usr/bin/make  -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
cd /<<PKGBUILDDIR>>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/apps /<<PKGBUILDDIR>>/build /<<PKGBUILDDIR>>/build/src/apps /<<PKGBUILDDIR>>/build/src/apps/CMakeFiles/tomo_test.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/make  -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build'
make[4]: Nothing to be done for 'src/apps/CMakeFiles/tomo_test.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build'
[100%] Built target tomo_test
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/CMakeFiles 0
/usr/bin/make  -f CMakeFiles/Makefile2 preinstall
make[3]: Entering directory '/<<PKGBUILDDIR>>/build'
make[3]: Nothing to be done for 'preinstall'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_select
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_helix_toolbox
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_demodulate
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_star_handler
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_stack_create
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_plot_delocalisation
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_autopick_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_star_plottable
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_import
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_manualpick
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_star_printtable
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_prepare_subtomo
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_pipeliner
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_subtract
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_star_datablock_singlefiles
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_convert_star
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_preprocess
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_FCC
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_autopick
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_merge_particles
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_ctf_refine_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_helix_inimodel2d
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_localsym_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_tomo_test
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_align_symmetry
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_mask_create
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_ctf_toolbox
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_refine_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_qsub.csh
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_motion_refine_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_run_ctffind
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_reposition
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_mrc2vtk
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_star_datablock_ctfdat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_tiltpair_plot
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_localsym
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_find_tiltpairs
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_star_loopheader
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_flex_analyse
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_refine
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_postprocess_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_estimate_gain
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_run_motioncorr_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_preprocess_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_scheduler
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_convert_to_tiff
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_ctf_mask_test
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_run_motioncorr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_star_datablock_stack
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_display
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_reconstruct
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_reposition
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_motion_refine
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_image_handler
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_external_reconstruct
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_ctf_refine
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_postprocess
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_reconstruct_mpi
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_project
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_align_symmetry
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_autopick
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_autopick_mpi
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_convert_star
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_convert_to_tiff
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_ctf_mask_test
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_ctf_refine
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_ctf_refine_mpi
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_ctf_toolbox
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_demodulate
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_display
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_estimate_gain
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_external_reconstruct
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_find_tiltpairs
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_flex_analyse
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_helix_inimodel2d
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_helix_toolbox
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_image_handler
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_import
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_localsym
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_localsym_mpi
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_manualpick
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_mask_create
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_merge_particles
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_motion_refine
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_motion_refine_mpi
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_mrc2vtk
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_FCC
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_reposition
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_select
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_subtract
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_pipeliner
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_plot_delocalisation
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_postprocess
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_postprocess_mpi
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_prepare_subtomo
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_preprocess
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_preprocess_mpi
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_project
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_reconstruct
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_reconstruct_mpi
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_refine
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_refine_mpi
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_reposition
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_run_ctffind
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_run_motioncorr
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_run_motioncorr_mpi
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_scheduler
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_stack_create
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_star_handler
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_tiltpair_plot
-- Up-to-date: /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/relion_tomo_test
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build'
mkdir -p /<<PKGBUILDDIR>>/debian/tmp/gui/usr/bin
rm /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/*.csh # Useless ...
set -e; for prog in relion relion_display relion_manualpick; do \
  mv /<<PKGBUILDDIR>>/debian/tmp/cli/usr/bin/$prog \
    /<<PKGBUILDDIR>>/debian/tmp/gui/usr/bin; done
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_install -a
   dh_installdocs -a
   dh_installchangelogs -a
   dh_lintian -a
   dh_perl -a
   dh_link -a
   dh_strip_nondeterminism -a
   dh_compress -a
   dh_fixperms -a
   dh_missing -a
   dh_dwz -a
   dh_strip -a
debugedit: debian/relion-gui/usr/bin/relion_manualpick: Unknown DWARF DW_FORM_0x1f20
debugedit: debian/relion/usr/bin/relion_particle_select: Unknown DWARF DW_FORM_0x1f20
26b425feef8ddc9f745a306cf7dcd02e95b745a8
de75cd0ad7d9b939957f57b733c28598028b09ad
debugedit: debian/relion-gui/usr/bin/relion_display: Unknown DWARF DW_FORM_0x1f20
6bda7feac9825d62e2412c7417d3decddd06c618
debugedit: debian/relion/usr/bin/relion_helix_toolbox: Unknown DWARF DW_FORM_0x1f20
50b608962b015d4dd3a678837ff3e8266a973555
debugedit: debian/relion-gui/usr/bin/relion: Unknown DWARF DW_FORM_0x1f20
92bdee69b547802410cd7c0ca84a377a6686805c
debugedit: debian/relion/usr/bin/relion_demodulate: Unknown DWARF DW_FORM_0x1f20
972f15e996befca7b37c7adb77cc3ed732a9e47c
debugedit: debian/relion/usr/bin/relion_star_handler: Unknown DWARF DW_FORM_0x1f20
9b0f7723231010bc8c1d1be257b46616e58bb7f1
debugedit: debian/relion/usr/bin/relion_stack_create: Unknown DWARF DW_FORM_0x1f20
862f551a936b1dd5c0366090488ee3dbac3795d0
debugedit: debian/relion/usr/bin/relion_plot_delocalisation: Unknown DWARF DW_FORM_0x1f20
f21e9decd737f9ba5209a5c853134204e880da87
debugedit: debian/relion/usr/bin/relion_autopick_mpi: Unknown DWARF DW_FORM_0x1f20
e7651bdc2b2bdddb517e6386ad4b07463dab9603
debugedit: debian/relion/usr/bin/relion_particle_symmetry_expand: Unknown DWARF DW_FORM_0x1f20
733840b0525be56df96d18df03c935b3242a3f17
debugedit: debian/relion/usr/bin/relion_import: Unknown DWARF DW_FORM_0x1f20
b7db8795dac13f20b702b22e34e4b112ddeb5d8f
debugedit: debian/relion/usr/bin/relion_prepare_subtomo: Unknown DWARF DW_FORM_0x1f20
4831325c7bd80bd3cbf961b77a2b684bbcf17dec
debugedit: debian/relion/usr/bin/relion_pipeliner: Unknown DWARF DW_FORM_0x1f20
c6f533aace371e06a7e0d9210a8643153a23ebd9
debugedit: debian/relion/usr/bin/relion_particle_subtract: Unknown DWARF DW_FORM_0x1f20
8c8a83de178af6c74fd846e1cf197a1ccd4fb1c4
debugedit: debian/relion/usr/bin/relion_convert_star: Unknown DWARF DW_FORM_0x1f20
e4b40c04f5fb53bc6c2170a9308dc9a32cf024a4
debugedit: debian/relion/usr/bin/relion_preprocess: Unknown DWARF DW_FORM_0x1f20
b32abad6bdc021efd2ff65b1f05ca8339361332c
debugedit: debian/relion/usr/bin/relion_particle_FCC: Unknown DWARF DW_FORM_0x1f20
cd9bed0c25fcfc9a5f5f29a4617485404dfeeae4
debugedit: debian/relion/usr/bin/relion_autopick: Unknown DWARF DW_FORM_0x1f20
4dd275d6a1c6cee4041935e4d4cacdaa8f93238f
debugedit: debian/relion/usr/bin/relion_merge_particles: Unknown DWARF DW_FORM_0x1f20
ce3a27235698bf8196935654cfa16878520259be
debugedit: debian/relion/usr/bin/relion_ctf_refine_mpi: Unknown DWARF DW_FORM_0x1f20
e2c6c37ed693813299b249a1c95be8f29f85fc50
debugedit: debian/relion/usr/bin/relion_helix_inimodel2d: Unknown DWARF DW_FORM_0x1f20
6edcc7e057d04090e49da8371f3a51115ae6ce5b
debugedit: debian/relion/usr/bin/relion_localsym_mpi: Unknown DWARF DW_FORM_0x1f20
dc3b2ddc0c44010ea2ec849c7eeb9d30cee9413d
debugedit: debian/relion/usr/bin/relion_tomo_test: Unknown DWARF DW_FORM_0x1f21
ff5602aa5ab58016fd7043150c0fd8afb4bd5f30
debugedit: debian/relion/usr/bin/relion_align_symmetry: Unknown DWARF DW_FORM_0x1f20
2a7620f22503ead4091eecd0d92b7fb483ca4c5a
debugedit: debian/relion/usr/bin/relion_mask_create: Unknown DWARF DW_FORM_0x1f20
edd11eb6bf31a3c5f42ef6ecdad374b49177c42b
debugedit: debian/relion/usr/bin/relion_ctf_toolbox: Unknown DWARF DW_FORM_0x1f20
88fa67f99292875535651bb7c243a30068af8cad
debugedit: debian/relion/usr/bin/relion_refine_mpi: Unknown DWARF DW_FORM_0x1f20
04dc16173d130e0784aba8ef3d7b916fffa6c9f3
debugedit: debian/relion/usr/bin/relion_motion_refine_mpi: Unknown DWARF DW_FORM_0x1f20
711fa4cd7a69c3604bb872b996b5b2f288e39d18
debugedit: debian/relion/usr/bin/relion_run_ctffind: Unknown DWARF DW_FORM_0x1f20
3c590b151960c8f0564a544435c2d95a723ab788
debugedit: debian/relion/usr/bin/relion_reposition: Unknown DWARF DW_FORM_0x1f20
2da35820369142aacd3ed8f78020810d59ebfcba
debugedit: debian/relion/usr/bin/relion_particle_subtract_mpi: Unknown DWARF DW_FORM_0x1f20
05a8498bc753c8b604f0406fb31529bf659417fc
debugedit: debian/relion/usr/bin/relion_mrc2vtk: Unknown DWARF DW_FORM_0x1f20
a5b3e29f773259497456a6ccc79bfb6ea003ef27
debugedit: debian/relion/usr/bin/relion_tiltpair_plot: Unknown DWARF DW_FORM_0x1f20
802bcff1d125e7abfe8cd44dc134b17a37c94f80
debugedit: debian/relion/usr/bin/relion_run_ctffind_mpi: Unknown DWARF DW_FORM_0x1f20
ebec44505be7a5a9eb9cf6785aafff63419055d5
debugedit: debian/relion/usr/bin/relion_localsym: Unknown DWARF DW_FORM_0x1f20
195b68eef389b0ac241a18afbca79b5051d9f713
debugedit: debian/relion/usr/bin/relion_find_tiltpairs: Unknown DWARF DW_FORM_0x1f20
ed7e2d01ca62997a0027bf3b8dc82804d52d4a4c
debugedit: debian/relion/usr/bin/relion_flex_analyse_mpi: Unknown DWARF DW_FORM_0x1f20
72f22a984a4ae2884b262d77c524fe3e508ab0da
debugedit: debian/relion/usr/bin/relion_flex_analyse: Unknown DWARF DW_FORM_0x1f20
0212ddb2c8009e8c1a0d0f83243d32a0487575a6
debugedit: debian/relion/usr/bin/relion_refine: Unknown DWARF DW_FORM_0x1f21
9fea2f538357905116290f66befab10b0ec96d78
debugedit: debian/relion/usr/bin/relion_postprocess_mpi: Unknown DWARF DW_FORM_0x1f20
ff9dac72952c1b1ab5e373d4ab9985abc1691408
debugedit: debian/relion/usr/bin/relion_estimate_gain: Unknown DWARF DW_FORM_0x1f20
f6ef9ce6853704c4dfc4cbb3c20042f006ee4434
debugedit: debian/relion/usr/bin/relion_run_motioncorr_mpi: Unknown DWARF DW_FORM_0x1f20
0e2773c82dc357ebb42d5157fe1ec6eec05ff38d
debugedit: debian/relion/usr/bin/relion_preprocess_mpi: Unknown DWARF DW_FORM_0x1f20
08cf61808d2c3f3334cff33dfee0eb3c67059b1a
debugedit: debian/relion/usr/bin/relion_scheduler: Unknown DWARF DW_FORM_0x1f20
743ca1c641f21969c1580420d38fd78aef8749cd
debugedit: debian/relion/usr/bin/relion_convert_to_tiff_mpi: Unknown DWARF DW_FORM_0x1f20
d3b61ce6353bc88270d96c9988c4e10fd3868f14
debugedit: debian/relion/usr/bin/relion_convert_to_tiff: Unknown DWARF DW_FORM_0x1f20
f698e15b0c57328a7c114d9d53ce3dfbfdfc52be
debugedit: debian/relion/usr/bin/relion_ctf_mask_test: Unknown DWARF DW_FORM_0x1f20
905d158393f4531dbc8ba49a27921211ebc87f1b
debugedit: debian/relion/usr/bin/relion_run_motioncorr: Unknown DWARF DW_FORM_0x1f20
d1c34dfed6a6785c6c23d3d553a5da55714d98b5
debugedit: debian/relion/usr/bin/relion_reconstruct: Unknown DWARF DW_FORM_0x1f20
b2c3ad3e863be3315578d77ba9ca18d07a681b11
debugedit: debian/relion/usr/bin/relion_particle_reposition: Unknown DWARF DW_FORM_0x1f20
030e50317db5d27d3161ae4576035ba1f9e04993
debugedit: debian/relion/usr/bin/relion_motion_refine: Unknown DWARF DW_FORM_0x1f20
d7639f2b0c5a1646e1dfebaa5bfd643f537cb234
debugedit: debian/relion/usr/bin/relion_image_handler: Unknown DWARF DW_FORM_0x1f20
886fd9e33230e744c6630171b964f84816e858fc
debugedit: debian/relion/usr/bin/relion_external_reconstruct: Unknown DWARF DW_FORM_0x1f20
22e41f34b5f91b0f8f46338c479f3722f752c507
debugedit: debian/relion/usr/bin/relion_ctf_refine: Unknown DWARF DW_FORM_0x1f20
d354979b9b0a4b3c3966afeef599ee9d8b6e23a3
debugedit: debian/relion/usr/bin/relion_postprocess: Unknown DWARF DW_FORM_0x1f20
789cd95fb52d3b85ba7d09f08ee3be4709b9bf49
debugedit: debian/relion/usr/bin/relion_reconstruct_mpi: Unknown DWARF DW_FORM_0x1f20
8d7bc2d5bf9453aff7e3f4ba75e10dfcafb0257c
debugedit: debian/relion/usr/bin/relion_project: Unknown DWARF DW_FORM_0x1f20
3659eb754448797f4dd852ce5820c69a6203e5f3
   dh_makeshlibs -a
   dh_shlibdeps -a
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 from: /lib/ld-linux-aarch64.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 from: /lib/ld-linux-aarch64.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged
   dh_installdeb -a
   dh_gencontrol -a
   dh_md5sums -a
   dh_builddeb -a
INFO: pkgstriptranslations version 154
INFO: pkgstriptranslations version 154
pkgstriptranslations: processing relion-gui (in debian/relion-gui); do_strip: , oemstrip: 
pkgstriptranslations: processing relion (in debian/relion); do_strip: , oemstrip: 
pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com
pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com
pkgstripfiles: processing control file: debian/relion-gui/DEBIAN/control, package relion-gui, directory debian/relion-gui
INFO: pkgstripfiles: waiting for lock (relion-gui) ...
pkgstripfiles: processing control file: debian/relion/DEBIAN/control, package relion, directory debian/relion
pkgstripfiles: Running PNG optimization (using 4 cpus) for package relion ...
pkgstripfiles: No PNG files.
dpkg-deb: building package 'relion' in '../relion_3.1.3-3build3_arm64.deb'.
Searching for duplicated docs in dependency relion...
  symlinking changelog.Debian.gz in relion-gui to file in relion
pkgstripfiles: Running PNG optimization (using 4 cpus) for package relion-gui ...
pkgstripfiles: No PNG files.
dpkg-deb: building package 'relion-gui' in '../relion-gui_3.1.3-3build3_arm64.deb'.
 dpkg-genbuildinfo --build=any -O../relion_3.1.3-3build3_arm64.buildinfo
 dpkg-genchanges --build=any -mLaunchpad Build Daemon <buildd@bos02-arm64-065.buildd> -O../relion_3.1.3-3build3_arm64.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2024-05-19T15:01:00Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


relion_3.1.3-3build3_arm64.changes:
-----------------------------------

Format: 1.8
Date: Mon, 01 Apr 2024 18:26:26 +1100
Source: relion
Binary: relion relion-gui
Built-For-Profiles: noudeb
Architecture: arm64
Version: 3.1.3-3build3
Distribution: noble
Urgency: medium
Maintainer: Launchpad Build Daemon <buildd@bos02-arm64-065.buildd>
Changed-By: William Grant <wgrant@ubuntu.com>
Description:
 relion     - toolkit for 3D reconstructions in cryo-electron microscopy
 relion-gui - toolkit for 3D reconstructions in cryo-electron microscopy (gui a
Changes:
 relion (3.1.3-3build3) noble; urgency=medium
 .
   * No-change rebuild for CVE-2024-3094
Checksums-Sha1:
 42d8d66cd9ba2854de3a18d77c459a6201265dad 1194516 relion-gui_3.1.3-3build3_arm64.deb
 17b135955c59f5e05c244226b4cd47f1b412cd49 12009 relion_3.1.3-3build3_arm64.buildinfo
 8589eb1f9e831525046cea542499019a050d7f26 13077300 relion_3.1.3-3build3_arm64.deb
Checksums-Sha256:
 64c95ead8605702cfa78f1be4f0a2abdc6ff536d44f2df5948725b2d55bda9ee 1194516 relion-gui_3.1.3-3build3_arm64.deb
 160f0066521381fb11c93f0cfd4d98e335ac621ed43b8fd4258a832169e64850 12009 relion_3.1.3-3build3_arm64.buildinfo
 c16527cb6f861a4ffc417b39994e9ad99cc2a5627febb5724687934dbfbca46d 13077300 relion_3.1.3-3build3_arm64.deb
Files:
 9e5124d252e45ac8da0b37e9e258036d 1194516 science optional relion-gui_3.1.3-3build3_arm64.deb
 5db115a733014bc2134b46cfc15b9964 12009 science optional relion_3.1.3-3build3_arm64.buildinfo
 1a0bb480562ff5494aff8b3c315b8095 13077300 science optional relion_3.1.3-3build3_arm64.deb
Original-Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
/<<BUILDDIR>>/relion_3.1.3-3build3_arm64.changes.new could not be renamed to /<<BUILDDIR>>/relion_3.1.3-3build3_arm64.changes: Illegal seek
Distribution field may be wrong!!!
+------------------------------------------------------------------------------+
| Buildinfo                                                                    |
+------------------------------------------------------------------------------+

Format: 1.0
Source: relion
Binary: relion relion-gui
Architecture: arm64
Version: 3.1.3-3build3
Checksums-Md5:
 9e5124d252e45ac8da0b37e9e258036d 1194516 relion-gui_3.1.3-3build3_arm64.deb
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Build-Origin: Ubuntu
Build-Architecture: arm64
Build-Date: Sun, 19 May 2024 15:00:59 +0000
Build-Path: /<<PKGBUILDDIR>>
Build-Tainted-By:
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Environment:
 DEB_BUILD_OPTIONS="noautodbgsym parallel=4"
 DEB_BUILD_PROFILES="noudeb"
 LANG="C.UTF-8"
 LC_ALL="C.UTF-8"
 SOURCE_DATE_EPOCH="1711956386"


+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


relion-gui_3.1.3-3build3_arm64.deb
----------------------------------

 new Debian package, version 2.0.
 size 1194516 bytes: control archive=989 bytes.
    1224 bytes,    23 lines      control
     308 bytes,     5 lines      md5sums
 Package: relion-gui
 Source: relion
 Version: 3.1.3-3build3
 Architecture: arm64
 Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
 Installed-Size: 4388
 Depends: relion (= 3.1.3-3build3), libc6 (>= 2.38), libfftw3-double3 (>= 3.3.10), libfltk1.3t64 (>= 1.3.4), libgcc-s1 (>= 3.3.1), libgomp1 (>= 4.9), libstdc++6 (>= 13.1), libtiff6 (>= 4.0.3)
 Conflicts: relion-cuda-gui
 Breaks: relion-bin, relion-bin+gui, relion-bin+mpi, relion-bin+mpi+gui
 Replaces: relion-bin, relion-bin+gui, relion-bin+mpi, relion-bin+mpi+gui
 Section: science
 Priority: optional
 Homepage: https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page
 Description: toolkit for 3D reconstructions in cryo-electron microscopy (gui apps)
  RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone
  computer program for Maximum A Posteriori refinement of (multiple) 3D
  reconstructions or 2D class averages in cryo-electron microscopy.
  .
  RELION provides a GUI, several command-line tools in parallel (MPI) and serial
  versions, optionally with CUDA/GPU support.
  .
  relion-gui provides the graphical user interface without CUDA/GPU support.
 Original-Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

drwxr-xr-x root/root         0 2024-04-01 07:26 ./
drwxr-xr-x root/root         0 2024-04-01 07:26 ./usr/
drwxr-xr-x root/root         0 2024-04-01 07:26 ./usr/bin/
-rwxr-xr-x root/root   2434768 2024-04-01 07:26 ./usr/bin/relion
-rwxr-xr-x root/root   1116584 2024-04-01 07:26 ./usr/bin/relion_display
-rwxr-xr-x root/root    919976 2024-04-01 07:26 ./usr/bin/relion_manualpick
drwxr-xr-x root/root         0 2024-04-01 07:26 ./usr/share/
drwxr-xr-x root/root         0 2024-04-01 07:26 ./usr/share/doc/
drwxr-xr-x root/root         0 2024-04-01 07:26 ./usr/share/doc/relion-gui/
lrwxrwxrwx root/root         0 2024-04-01 07:26 ./usr/share/doc/relion-gui/changelog.Debian.gz -> ../relion/changelog.Debian.gz
-rw-r--r-- root/root      7408 2022-12-06 10:56 ./usr/share/doc/relion-gui/copyright
drwxr-xr-x root/root         0 2024-04-01 07:26 ./usr/share/lintian/
drwxr-xr-x root/root         0 2024-04-01 07:26 ./usr/share/lintian/overrides/
-rw-r--r-- root/root        15 2022-12-06 10:56 ./usr/share/lintian/overrides/relion-gui


relion_3.1.3-3build3_arm64.deb
------------------------------

 new Debian package, version 2.0.
 size 13077300 bytes: control archive=2661 bytes.
    1240 bytes,    23 lines      control
    4218 bytes,    66 lines      md5sums
 Package: relion
 Version: 3.1.3-3build3
 Architecture: arm64
 Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
 Installed-Size: 73416
 Depends: openmpi-gcc | openmpi-bin, libc6 (>= 2.38), libfftw3-double3 (>= 3.3.10), libfftw3-single3 (>= 3.3.10), libgcc-s1 (>= 3.3.1), libgomp1 (>= 4.9), libopenmpi3t64 (>= 4.1.6), libstdc++6 (>= 13.1), libtiff6 (>= 4.0.3)
 Conflicts: relion-cuda
 Breaks: relion-bin, relion-bin+gui, relion-bin+mpi, relion-bin+mpi+gui
 Replaces: relion-bin, relion-bin+gui, relion-bin+mpi, relion-bin+mpi+gui
 Section: science
 Priority: optional
 Homepage: https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page
 Description: toolkit for 3D reconstructions in cryo-electron microscopy
  RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone
  computer program for Maximum A Posteriori refinement of (multiple) 3D
  reconstructions or 2D class averages in cryo-electron microscopy.
  .
  RELION provides a GUI, several command-line tools in parallel (MPI) and serial
  versions, optionally with CUDA/GPU support.
  .
  relion provides the serial and parallel (MPI) command-line tools without
  CUDA/GPU support.
 Original-Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

drwxr-xr-x root/root         0 2024-04-01 07:26 ./
drwxr-xr-x root/root         0 2024-04-01 07:26 ./usr/
drwxr-xr-x root/root         0 2024-04-01 07:26 ./usr/bin/
-rwxr-xr-x root/root    788896 2024-04-01 07:26 ./usr/bin/relion_align_symmetry
-rwxr-xr-x root/root   1640864 2024-04-01 07:26 ./usr/bin/relion_autopick
-rwxr-xr-x root/root   1771936 2024-04-01 07:26 ./usr/bin/relion_autopick_mpi
-rwxr-xr-x root/root   1247648 2024-04-01 07:26 ./usr/bin/relion_convert_star
-rwxr-xr-x root/root    985504 2024-04-01 07:26 ./usr/bin/relion_convert_to_tiff
-rwxr-xr-x root/root   1051040 2024-04-01 07:26 ./usr/bin/relion_convert_to_tiff_mpi
-rwxr-xr-x root/root   1313184 2024-04-01 07:26 ./usr/bin/relion_ctf_mask_test
-rwxr-xr-x root/root   1706400 2024-04-01 07:26 ./usr/bin/relion_ctf_refine
-rwxr-xr-x root/root   1771936 2024-04-01 07:26 ./usr/bin/relion_ctf_refine_mpi
-rwxr-xr-x root/root    919968 2024-04-01 07:26 ./usr/bin/relion_ctf_toolbox
-rwxr-xr-x root/root   1247648 2024-04-01 07:26 ./usr/bin/relion_demodulate
-rwxr-xr-x root/root    788896 2024-04-01 07:26 ./usr/bin/relion_estimate_gain
-rwxr-xr-x root/root    919968 2024-04-01 07:26 ./usr/bin/relion_external_reconstruct
-rwxr-xr-x root/root    526752 2024-04-01 07:26 ./usr/bin/relion_find_tiltpairs
-rwxr-xr-x root/root   1903008 2024-04-01 07:26 ./usr/bin/relion_flex_analyse
-rwxr-xr-x root/root   1903008 2024-04-01 07:26 ./usr/bin/relion_flex_analyse_mpi
-rwxr-xr-x root/root    985504 2024-04-01 07:26 ./usr/bin/relion_helix_inimodel2d
-rwxr-xr-x root/root   1313184 2024-04-01 07:26 ./usr/bin/relion_helix_toolbox
-rwxr-xr-x root/root   1051040 2024-04-01 07:26 ./usr/bin/relion_image_handler
-rwxr-xr-x root/root    919960 2024-04-01 07:26 ./usr/bin/relion_import
-rwxr-xr-x root/root   1575328 2024-04-01 07:26 ./usr/bin/relion_localsym
-rwxr-xr-x root/root   1706400 2024-04-01 07:26 ./usr/bin/relion_localsym_mpi
-rwxr-xr-x root/root   1247648 2024-04-01 07:26 ./usr/bin/relion_mask_create
-rwxr-xr-x root/root    854432 2024-04-01 07:26 ./usr/bin/relion_merge_particles
-rwxr-xr-x root/root   2034096 2024-04-01 07:26 ./usr/bin/relion_motion_refine
-rwxr-xr-x root/root   2099632 2024-04-01 07:26 ./usr/bin/relion_motion_refine_mpi
-rwxr-xr-x root/root    657816 2024-04-01 07:26 ./usr/bin/relion_mrc2vtk
-rwxr-xr-x root/root   1444256 2024-04-01 07:26 ./usr/bin/relion_particle_FCC
-rwxr-xr-x root/root   2361760 2024-04-01 07:26 ./usr/bin/relion_particle_reposition
-rwxr-xr-x root/root   1247640 2024-04-01 07:26 ./usr/bin/relion_particle_select
-rwxr-xr-x root/root   2361760 2024-04-01 07:26 ./usr/bin/relion_particle_subtract
-rwxr-xr-x root/root   2427296 2024-04-01 07:26 ./usr/bin/relion_particle_subtract_mpi
-rwxr-xr-x root/root    985504 2024-04-01 07:26 ./usr/bin/relion_particle_symmetry_expand
-rwxr-xr-x root/root   1182096 2024-04-01 07:26 ./usr/bin/relion_pipeliner
-rwxr-xr-x root/root   1247648 2024-04-01 07:26 ./usr/bin/relion_plot_delocalisation
-rwxr-xr-x root/root    854432 2024-04-01 07:26 ./usr/bin/relion_postprocess
-rwxr-xr-x root/root    854432 2024-04-01 07:26 ./usr/bin/relion_postprocess_mpi
-rwxr-xr-x root/root    788896 2024-04-01 07:26 ./usr/bin/relion_prepare_subtomo
-rwxr-xr-x root/root   1313184 2024-04-01 07:26 ./usr/bin/relion_preprocess
-rwxr-xr-x root/root   1444256 2024-04-01 07:26 ./usr/bin/relion_preprocess_mpi
-rwxr-xr-x root/root   1771936 2024-04-01 07:26 ./usr/bin/relion_project
-rwxr-xr-x root/root   1771936 2024-04-01 07:26 ./usr/bin/relion_reconstruct
-rwxr-xr-x root/root   1837472 2024-04-01 07:26 ./usr/bin/relion_reconstruct_mpi
-rwxr-xr-x root/root   2296224 2024-04-01 07:26 ./usr/bin/relion_refine
-rwxr-xr-x root/root   2427296 2024-04-01 07:26 ./usr/bin/relion_refine_mpi
-rwxr-xr-x root/root   1444248 2024-04-01 07:26 ./usr/bin/relion_reposition
-rwxr-xr-x root/root    985504 2024-04-01 07:26 ./usr/bin/relion_run_ctffind
-rwxr-xr-x root/root   1051040 2024-04-01 07:26 ./usr/bin/relion_run_ctffind_mpi
-rwxr-xr-x root/root   1247648 2024-04-01 07:26 ./usr/bin/relion_run_motioncorr
-rwxr-xr-x root/root   1313184 2024-04-01 07:26 ./usr/bin/relion_run_motioncorr_mpi
-rwxr-xr-x root/root   1771928 2024-04-01 07:26 ./usr/bin/relion_scheduler
-rwxr-xr-x root/root    985504 2024-04-01 07:26 ./usr/bin/relion_stack_create
-rwxr-xr-x root/root      1055 2024-04-01 07:26 ./usr/bin/relion_star_datablock_ctfdat
-rwxr-xr-x root/root       714 2024-04-01 07:26 ./usr/bin/relion_star_datablock_singlefiles
-rwxr-xr-x root/root       767 2024-04-01 07:26 ./usr/bin/relion_star_datablock_stack
-rwxr-xr-x root/root    985504 2024-04-01 07:26 ./usr/bin/relion_star_handler
-rwxr-xr-x root/root       675 2024-04-01 07:26 ./usr/bin/relion_star_loopheader
-rwxr-xr-x root/root      1217 2024-04-01 07:26 ./usr/bin/relion_star_plottable
-rwxr-xr-x root/root      2263 2024-04-01 07:26 ./usr/bin/relion_star_printtable
-rwxr-xr-x root/root    592288 2024-04-01 07:26 ./usr/bin/relion_tiltpair_plot
-rwxr-xr-x root/root   1182112 2024-04-01 07:26 ./usr/bin/relion_tomo_test
drwxr-xr-x root/root         0 2024-04-01 07:26 ./usr/share/
drwxr-xr-x root/root         0 2024-04-01 07:26 ./usr/share/doc/
drwxr-xr-x root/root         0 2024-04-01 07:26 ./usr/share/doc/relion/
-rw-r--r-- root/root      1433 2021-08-31 10:17 ./usr/share/doc/relion/AUTHORS
-rw-r--r-- root/root      2810 2021-08-31 10:17 ./usr/share/doc/relion/README.md.gz
-rw-r--r-- root/root      1275 2024-04-01 07:26 ./usr/share/doc/relion/changelog.Debian.gz
-rw-r--r-- root/root      7408 2022-12-06 10:56 ./usr/share/doc/relion/copyright
drwxr-xr-x root/root         0 2024-04-01 07:26 ./usr/share/lintian/
drwxr-xr-x root/root         0 2024-04-01 07:26 ./usr/share/lintian/overrides/
-rw-r--r-- root/root        15 2022-12-06 10:56 ./usr/share/lintian/overrides/relion


+------------------------------------------------------------------------------+
| Post Build                                                                   |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not removing build depends: as requested

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: arm64
Build Type: any
Build-Space: 2900028
Build-Time: 4674
Distribution: noble
Host Architecture: arm64
Install-Time: 43
Job: relion_3.1.3-3build3.dsc
Machine Architecture: arm64
Package: relion
Package-Time: 4720
Source-Version: 3.1.3-3build3
Space: 2900028
Status: successful
Version: 3.1.3-3build3
--------------------------------------------------------------------------------
Finished at 2024-05-19T15:01:00Z
Build needed 01:18:40, 2900028k disk space
RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-28246702
Scanning for processes to kill in build PACKAGEBUILD-28246702