RUN: /bin/echo ['echo', 'Forking build subprocess...'] Forking build subprocess... RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', '790567-1851245', '/home/buildd/filecache-default/d1f3d964cb4177bc7330894159c6f3c2b5321741'] Synching the system clock with the buildd NTP service... 18 Nov 13:54:08 ntpdate[9415]: adjust time server 10.211.37.1 offset 0.036836 sec Unpacking chroot for build 790567-1851245 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', '790567-1851245'] Mounting chroot for build 790567-1851245 RUN: /usr/share/launchpad-buildd/slavebin/apply-ogre-model ['apply-ogre-model', '790567-1851245', 'universe'] Attempting OGRE for universe in build-790567-1851245 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', '790567-1851245', 'deb http://ftpmaster.internal/ubuntu jaunty main universe'] Overriding sources.list in build-790567-1851245 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', '790567-1851245'] Updating debian chroot for build 790567-1851245 Get:1 http://ftpmaster.internal jaunty Release.gpg [189B] Get:2 http://ftpmaster.internal jaunty Release [74.6kB] Get:3 http://ftpmaster.internal jaunty/main Packages [1260kB] Get:4 http://ftpmaster.internal jaunty/universe Packages [4700kB] Fetched 6035kB in 8s (744kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: base-files bzip2 cpio cpp cpp-4.3 fakeroot g++ g++-4.3 gcc gcc-4.3 gcc-4.3-base libbz2-1.0 libc6 libc6-dev libdb4.7 libgcc1 libgomp1 libncurses5 libpam-foreground libpam-modules libpam-runtime libpam0g libslang2 libstdc++6 libstdc++6-4.3-dev linux-libc-dev login ncurses-base ncurses-bin passwd python2.5-minimal tzdata 32 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 657kB/26.0MB of archives. After this operation, 508kB of additional disk space will be used. WARNING: The following packages cannot be authenticated! linux-libc-dev libc6-dev libgomp1 cpp-4.3 gcc-4.3-base libgcc1 gcc-4.3 g++-4.3 libstdc++6-4.3-dev libstdc++6 libc6 libdb4.7 libpam-runtime libpam0g libpam-modules base-files login ncurses-bin libncurses5 ncurses-base libslang2 passwd python2.5-minimal tzdata bzip2 libbz2-1.0 cpio cpp fakeroot gcc g++ libpam-foreground Authentication warning overridden. Get:1 http://ftpmaster.internal jaunty/main linux-libc-dev 2.6.27-9.18 [657kB] Extracting templates from packages: 93% Extracting templates from packages: 100% Preconfiguring packages ... Fetched 657kB in 0s (9356kB/s) (Reading database ... 10689 files and directories currently installed.) Preparing to replace linux-libc-dev 2.6.27-7.14 (using .../linux-libc-dev_2.6.27-9.18_i386.deb) ... Unpacking replacement linux-libc-dev ... Preparing to replace libc6-dev 2.8+20081027-0ubuntu6 (using .../libc6-dev_2.8+20081027-0ubuntu10_i386.deb) ... Unpacking replacement libc6-dev ... Preparing to replace libgomp1 4.3.2-2ubuntu1 (using .../libgomp1_4.3.2-2ubuntu2_i386.deb) ... Unpacking replacement libgomp1 ... Preparing to replace cpp-4.3 4.3.2-2ubuntu1 (using .../cpp-4.3_4.3.2-2ubuntu2_i386.deb) ... Unpacking replacement cpp-4.3 ... Preparing to replace gcc-4.3-base 4.3.2-2ubuntu1 (using .../gcc-4.3-base_4.3.2-2ubuntu2_i386.deb) ... Unpacking replacement gcc-4.3-base ... Setting up gcc-4.3-base (4.3.2-2ubuntu2) ... (Reading database ... 10689 files and directories currently installed.) Preparing to replace libgcc1 1:4.3.2-2ubuntu1 (using .../libgcc1_1%3a4.3.2-2ubuntu2_i386.deb) ... Unpacking replacement libgcc1 ... Setting up libgcc1 (1:4.3.2-2ubuntu2) ... Processing triggers for libc6 ... ldconfig deferred processing now taking place (Reading database ... 10689 files and directories currently installed.) Preparing to replace gcc-4.3 4.3.2-2ubuntu1 (using .../gcc-4.3_4.3.2-2ubuntu2_i386.deb) ... Unpacking replacement gcc-4.3 ... Preparing to replace g++-4.3 4.3.2-2ubuntu1 (using .../g++-4.3_4.3.2-2ubuntu2_i386.deb) ... Unpacking replacement g++-4.3 ... Preparing to replace libstdc++6-4.3-dev 4.3.2-2ubuntu1 (using .../libstdc++6-4.3-dev_4.3.2-2ubuntu2_i386.deb) ... Unpacking replacement libstdc++6-4.3-dev ... Preparing to replace libstdc++6 4.3.2-2ubuntu1 (using .../libstdc++6_4.3.2-2ubuntu2_i386.deb) ... Unpacking replacement libstdc++6 ... Setting up libstdc++6 (4.3.2-2ubuntu2) ... Processing triggers for libc6 ... ldconfig deferred processing now taking place (Reading database ... 10689 files and directories currently installed.) Preparing to replace libc6 2.8+20081027-0ubuntu6 (using .../libc6_2.8+20081027-0ubuntu10_i386.deb) ... Unpacking replacement libc6 ... Setting up libc6 (2.8+20081027-0ubuntu10) ... Installing new version of config file /etc/init.d/glibc.sh ... Processing triggers for libc6 ... ldconfig deferred processing now taking place (Reading database ... 10689 files and directories currently installed.) Preparing to replace libdb4.7 4.7.25-5 (using .../libdb4.7_4.7.25-5ubuntu1_i386.deb) ... Unpacking replacement libdb4.7 ... Setting up libdb4.7 (4.7.25-5ubuntu1) ... (Reading database ... 10689 files and directories currently installed.) Preparing to replace libpam-runtime 1.0.1-4ubuntu5 (using .../libpam-runtime_1.0.1-4ubuntu5.3_all.deb) ... Unpacking replacement libpam-runtime ... Setting up libpam-runtime (1.0.1-4ubuntu5.3) ... (Reading database ... 10689 files and directories currently installed.) Preparing to replace libpam0g 1.0.1-4ubuntu5 (using .../libpam0g_1.0.1-4ubuntu5.3_i386.deb) ... Unpacking replacement libpam0g ... Setting up libpam0g (1.0.1-4ubuntu5.3) ... Processing triggers for libc6 ... ldconfig deferred processing now taking place (Reading database ... 10689 files and directories currently installed.) Preparing to replace libpam-modules 1.0.1-4ubuntu5 (using .../libpam-modules_1.0.1-4ubuntu5.3_i386.deb) ... Unpacking replacement libpam-modules ... Setting up libpam-modules (1.0.1-4ubuntu5.3) ... (Reading database ... 10689 files and directories currently installed.) Preparing to replace base-files 4.0.5ubuntu2 (using .../base-files_4.0.6ubuntu1_i386.deb) ... Unpacking replacement base-files ... Setting up base-files (4.0.6ubuntu1) ... (Reading database ... 10689 files and directories currently installed.) Preparing to replace login 1:4.1.1-1ubuntu1 (using .../login_1%3a4.1.1-5ubuntu3_i386.deb) ... Unpacking replacement login ... Setting up login (1:4.1.1-5ubuntu3) ... Installing new version of config file /etc/pam.d/login ... Installing new version of config file /etc/login.defs ... Installing new version of config file /etc/securetty ... (Reading database ... 10687 files and directories currently installed.) Preparing to replace ncurses-bin 5.6+20071124-1ubuntu2 (using .../ncurses-bin_5.7-2ubuntu1_i386.deb) ... Unpacking replacement ncurses-bin ... Setting up ncurses-bin (5.7-2ubuntu1) ... (Reading database ... 10690 files and directories currently installed.) Preparing to replace libncurses5 5.6+20071124-1ubuntu2 (using .../libncurses5_5.7-2ubuntu1_i386.deb) ... Unpacking replacement libncurses5 ... Setting up libncurses5 (5.7-2ubuntu1) ... Processing triggers for libc6 ... ldconfig deferred processing now taking place (Reading database ... 10690 files and directories currently installed.) Preparing to replace ncurses-base 5.6+20071124-1ubuntu2 (using .../ncurses-base_5.7-2ubuntu1_all.deb) ... Unpacking replacement ncurses-base ... Setting up ncurses-base (5.7-2ubuntu1) ... (Reading database ... 10699 files and directories currently installed.) Preparing to replace libslang2 2.1.3-3ubuntu1 (using .../libslang2_2.1.3-3ubuntu3_i386.deb) ... Unpacking replacement libslang2 ... Setting up libslang2 (2.1.3-3ubuntu3) ... Processing triggers for libc6 ... ldconfig deferred processing now taking place (Reading database ... 10699 files and directories currently installed.) Preparing to replace passwd 1:4.1.1-1ubuntu1 (using .../passwd_1%3a4.1.1-5ubuntu3_i386.deb) ... Unpacking replacement passwd ... Setting up passwd (1:4.1.1-5ubuntu3) ... (Reading database ... 10699 files and directories currently installed.) Preparing to replace python2.5-minimal 2.5.2-11.1ubuntu1 (using .../python2.5-minimal_2.5.2-13ubuntu1_i386.deb) ... Unpacking replacement python2.5-minimal ... Setting up python2.5-minimal (2.5.2-13ubuntu1) ... (Reading database ... 10699 files and directories currently installed.) Preparing to replace tzdata 2008i-2 (using .../tzdata_2008i-3_all.deb) ... Unpacking replacement tzdata ... Setting up tzdata (2008i-3) ... Current default timezone: 'Etc/UTC' Local time is now: Tue Nov 18 13:55:25 UTC 2008. Universal Time is now: Tue Nov 18 13:55:25 UTC 2008. Run 'dpkg-reconfigure tzdata' if you wish to change it. (Reading database ... 10699 files and directories currently installed.) Preparing to replace bzip2 1.0.5-0.1ubuntu1 (using .../bzip2_1.0.5-1ubuntu1_i386.deb) ... Unpacking replacement bzip2 ... Preparing to replace libbz2-1.0 1.0.5-0.1ubuntu1 (using .../libbz2-1.0_1.0.5-1ubuntu1_i386.deb) ... Unpacking replacement libbz2-1.0 ... Preparing to replace cpio 2.9-13ubuntu2 (using .../cpio_2.9-14ubuntu1_i386.deb) ... Unpacking replacement cpio ... Preparing to replace cpp 4:4.3.1-1ubuntu2 (using .../cpp_4%3a4.3.2-2ubuntu1_i386.deb) ... Unpacking replacement cpp ... Preparing to replace fakeroot 1.9.5ubuntu1 (using .../fakeroot_1.10.1ubuntu1_i386.deb) ... Unpacking replacement fakeroot ... Preparing to replace gcc 4:4.3.1-1ubuntu2 (using .../gcc_4%3a4.3.2-2ubuntu1_i386.deb) ... Removing old gcc doc directory. Unpacking replacement gcc ... Preparing to replace g++ 4:4.3.1-1ubuntu2 (using .../g++_4%3a4.3.2-2ubuntu1_i386.deb) ... Unpacking replacement g++ ... Preparing to replace libpam-foreground 0.4-1 (using .../libpam-foreground_0.5_i386.deb) ... Unpacking replacement libpam-foreground ... Setting up linux-libc-dev (2.6.27-9.18) ... Setting up libc6-dev (2.8+20081027-0ubuntu10) ... Setting up libgomp1 (4.3.2-2ubuntu2) ... Setting up cpp-4.3 (4.3.2-2ubuntu2) ... Setting up gcc-4.3 (4.3.2-2ubuntu2) ... Setting up libbz2-1.0 (1.0.5-1ubuntu1) ... Setting up bzip2 (1.0.5-1ubuntu1) ... Setting up cpio (2.9-14ubuntu1) ... Setting up cpp (4:4.3.2-2ubuntu1) ... Setting up fakeroot (1.10.1ubuntu1) ... Setting up gcc (4:4.3.2-2ubuntu1) ... Setting up libpam-foreground (0.5) ... Setting up libstdc++6-4.3-dev (4.3.2-2ubuntu2) ... Setting up g++-4.3 (4.3.2-2ubuntu2) ... Setting up g++ (4:4.3.2-2ubuntu1) ... Processing triggers for libc6 ... ldconfig deferred processing now taking place RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', '790567-1851245', '--nolog', '--batch', '--archive=ubuntu', '-A', '--purpose=PRIMARY', '--dist=jaunty', '--comp=universe', 'mustang_3.0-1ubuntu1.dsc'] Initiating build Automatic build of mustang_3.0-1ubuntu1 on rothera by sbuild/i386 1.170.5 Build started at 20081118-1355 ****************************************************************************** mustang_3.0-1ubuntu1.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 5), dpatch Checking for already installed source dependencies... debhelper: missing dpatch: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper dpatch Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: dmsetup libdevmapper1.02.1 sysvutils perl-doc Use 'apt-get autoremove' to remove them. The following extra packages will be installed: bsdmainutils file gettext gettext-base groff-base html2text intltool-debian libmagic1 man-db po-debconf Suggested packages: wamerican wordlist whois vacation dh-make curl cvs gettext-doc groff less www-browser libmail-box-perl Recommended packages: patchutils libmail-sendmail-perl libcompress-zlib-perl The following NEW packages will be installed: bsdmainutils debhelper dpatch file gettext gettext-base groff-base html2text intltool-debian libmagic1 man-db po-debconf 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. Need to get 0B/5397kB of archives. After this operation, 20.0MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libmagic1 file bsdmainutils gettext-base groff-base man-db html2text gettext intltool-debian po-debconf debhelper dpatch dpkg-preconfigure: unable to re-open stdin: Authentication warning overridden. Selecting previously deselected package libmagic1. (Reading database ... 10701 files and directories currently installed.) Unpacking libmagic1 (from .../libmagic1_4.26-1_i386.deb) ... Selecting previously deselected package file. Unpacking file (from .../archives/file_4.26-1_i386.deb) ... Selecting previously deselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_6.1.10ubuntu3_i386.deb) ... Selecting previously deselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.17-4ubuntu1_i386.deb) ... Selecting previously deselected package groff-base. Unpacking groff-base (from .../groff-base_1.18.1.1-21_i386.deb) ... Selecting previously deselected package man-db. Unpacking man-db (from .../man-db_2.5.2-3_i386.deb) ... Selecting previously deselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-5_i386.deb) ... Selecting previously deselected package gettext. Unpacking gettext (from .../gettext_0.17-4ubuntu1_i386.deb) ... Selecting previously deselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously deselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.15ubuntu1_all.deb) ... Selecting previously deselected package debhelper. Unpacking debhelper (from .../debhelper_7.0.17ubuntu1_all.deb) ... Selecting previously deselected package dpatch. Unpacking dpatch (from .../archives/dpatch_2.0.30_all.deb) ... Setting up libmagic1 (4.26-1) ... Setting up file (4.26-1) ... Setting up bsdmainutils (6.1.10ubuntu3) ... Setting up gettext-base (0.17-4ubuntu1) ... Setting up groff-base (1.18.1.1-21) ... Setting up man-db (2.5.2-3) ... Building database of manual pages ... ... skipping, since this is a buildd Setting up html2text (1.3.2a-5) ... Setting up gettext (0.17-4ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.15ubuntu1) ... Setting up debhelper (7.0.17ubuntu1) ... Setting up dpatch (2.0.30) ... Processing triggers for libc6 ... ldconfig deferred processing now taking place Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.8+20081027-0ubuntu10 make_3.81-5 dpkg-dev_1.14.22ubuntu1 g++-4.3_4.3.2-2ubuntu2 gcc-4.3_4.3.2-2ubuntu2 binutils_2.19-0ubuntu1 libstdc++6_4.3.2-2ubuntu2 libstdc++6-4.3-dev_4.3.2-2ubuntu2 ------------------------------------------------------------------------------ sh: gcc: not found dpkg-source: warning: Couldn't determine gcc system type, falling back to default (native compilation) gpg: Signature made Tue Nov 18 13:42:39 2008 GMT using DSA key ID 404825E7 gpg: Can't check signature: public key not found dpkg-source: extracting mustang in mustang-3.0 dpkg-source: unpacking mustang_3.0.orig.tar.gz dpkg-source: applying /home/buildd/build-790567-1851245/mustang_3.0-1ubuntu1.diff.gz dpkg-buildpackage: set CFLAGS to default value: -g -O2 dpkg-buildpackage: set CPPFLAGS to default value: dpkg-buildpackage: set LDFLAGS to default value: -Wl,-Bsymbolic-functions dpkg-buildpackage: set FFLAGS to default value: -g -O2 dpkg-buildpackage: set CXXFLAGS to default value: -g -O2 dpkg-buildpackage: source package mustang dpkg-buildpackage: source version 3.0-1ubuntu1 dpkg-buildpackage: host architecture i386 /usr/bin/fakeroot debian/rules clean dpatch deapply-all 04-gcc-4.3-exit not applied to ./ . 03-test_zf-cchh not applied to ./ . 02-main.cpp not applied to ./ . fakesync not applied to ./ . rm -rf patch-stamp patch-stampT debian/patched dh_testdir dh_testroot rm -f build-arch-stamp build-indep-stamp # Clean up after the build process. rm -f obj/*.o rm -f bin/MUSTANG_v.3 rm -f mustang.1 dh_clean debian/rules build test -d debian/patched || install -d debian/patched dpatch apply-all applying patch fakesync to ./ ... ok. applying patch 02-main.cpp to ./ ... ok. applying patch 03-test_zf-cchh to ./ ... ok. applying patch 04-gcc-4.3-exit to ./ ... ok. dpatch cat-all >>patch-stampT mv -f patch-stampT patch-stamp dh_testdir # Compile Mustang: /usr/bin/make CPPFLAGS="-Wall -g -O2" make[1]: Entering directory `/build/buildd/mustang-3.0' g++ -Wall -g -O2 -c ./src/globals.cpp -o ./obj/globals.o g++ -Wall -g -O2 -c ./src/CmdLineParser_2.cpp -o ./obj/CmdLineParser.o g++ -Wall -g -O2 -c ./src/distmat.cpp -o ./obj/distmat.o g++ -Wall -g -O2 -c ./src/sse_RK.cpp -o ./obj/sse_RK.o g++ -Wall -g -O2 -c ./src/read_structures.cpp -o ./obj/read_structures.o g++ -Wall -g -O2 -c ./src/primary_lib_gen.cpp -o ./obj/primary_lib_gen.o g++ -Wall -g -O2 -c ./src/pairwise_global_structalgn.cpp -o ./obj/pairwise_global_structalgn.o g++ -Wall -g -O2 -c ./src/pdb_ripper_2.cpp -o ./obj/pdb_ripper.o ./src/pdb_ripper_2.cpp: In function 'int CHECK_NCHAINS_IN_PDB(char*)': ./src/pdb_ripper_2.cpp:62: warning: suggest parentheses around && within || ./src/pdb_ripper_2.cpp: In function 'int CHECK_NRESIDUES_IN_PDB(char*)': ./src/pdb_ripper_2.cpp:100: warning: suggest parentheses around && within || g++ -Wall -g -O2 -c ./src/merge_global_local_libs.cpp -o ./obj/merge_global_local_libs.o g++ -Wall -g -O2 -c ./src/ew_2.cpp -o ./obj/ew.o ./src/ew_2.cpp: In function 'void CALCULATE_EDGE_WEIGHTS(int, int, float***)': ./src/ew_2.cpp:282: warning: unused variable 'seq_iden' ./src/ew_2.cpp:526: warning: unused variable 'PRUNING_WINDOW_MIN' g++ -Wall -g -O2 -c ./src/refine_pairalgn_2.cpp -o ./obj/refine_pairalgn.o ./src/refine_pairalgn_2.cpp: In function 'void REFINE_PAIRWISE_ALIGNMENT(int, int, float**)': ./src/refine_pairalgn_2.cpp:86: warning: unused variable 'X' ./src/refine_pairalgn_2.cpp:78: warning: unused variable 'prev_indx' g++ -Wall -g -O2 -c ./src/superpose_weightedRMS.cpp -o ./obj/superpose_weightedRMS.o g++ -Wall -g -O2 -c ./src/superpose_2.cpp -o ./obj/superpose_2.o g++ -Wall -g -O2 -c ./src/jacobi.cpp -o ./obj/jacobi.o g++ -Wall -g -O2 -c ./src/3D_manip_functions.cpp -o ./obj/3D_manip_functions.o ./src/3D_manip_functions.cpp: In function 'void superpose(int, float (*)[500], float (*)[500], float (*)[4], float*, float&)': ./src/3D_manip_functions.cpp:311: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result g++ -Wall -g -O2 -c ./src/extended_lib_gen_3.cpp -o ./obj/extended_lib_gen.o ./src/extended_lib_gen_3.cpp: In function 'void EXTENDED_LIBRARY_GENERATION()': ./src/extended_lib_gen_3.cpp:195: warning: unused variable 'BBB' ./src/extended_lib_gen_3.cpp:204: warning: unused variable 'AAA' ./src/extended_lib_gen_3.cpp:214: warning: unused variable 'BBB' g++ -Wall -g -O2 -c ./src/progress_align_3.cpp -o ./obj/progress_align.o ./src/progress_align_3.cpp: In function 'float STR_ALGN_INIT(float*, float*)': ./src/progress_align_3.cpp:275: warning: control reaches end of non-void function g++ -Wall -g -O2 -c ./src/neighbour_joining.cpp -o ./obj/neighbour_joining.o g++ -Wall -g -O2 -c ./src/upgma.cpp -o ./obj/upgma.o g++ -Wall -g -O2 -c ./src/superpose_on_core_2.cpp -o ./obj/superpose_on_core.o ./src/superpose_on_core_2.cpp: In function 'void SUPERPOSE_ON_CORE(char**)': ./src/superpose_on_core_2.cpp:457: warning: unused variable 'temp_coords' g++ -Wall -g -O2 -c ./src/multiple_superposition.cpp -o ./obj/multiple_superposition.o ./src/multiple_superposition.cpp: In function 'void MTRXYZ(float (*)[3], float, float, float)': ./src/multiple_superposition.cpp:216: warning: array subscript is above array bounds g++ -Wall -g -O2 -c ./src/output_algn.cpp -o ./obj/output_algn.o ./src/output_algn.cpp: In function 'void OUTPUT_ALGN_MSF(time_t)': ./src/output_algn.cpp:162: warning: unused variable 'LineWidth' ./src/output_algn.cpp: In function 'void OUTPUT_ALGN_HTML(time_t)': ./src/output_algn.cpp:467: warning: comparison between signed and unsigned integer expressions ./src/output_algn.cpp: In function 'void OUTPUT_ALGN_POSTSCRIPT(time_t)': ./src/output_algn.cpp:730: warning: spurious trailing '%' in format ./src/output_algn.cpp:773: warning: spurious trailing '%' in format ./src/output_algn.cpp:825: warning: spurious trailing '%' in format g++ -Wall -g -O2 -c ./src/main.cpp -o ./obj/main.o ./src/main.cpp: In function 'void DE_ALLOC_MAXIMAL_FRAGMENT_LIB()': ./src/main.cpp:203: warning: unused variable 'ptr1' ./src/main.cpp:203: warning: unused variable 'ptr2' ./src/main.cpp:204: warning: unused variable 'Size' g++ -Wall -g -O2 -o bin/MUSTANG_v.3 ./obj/globals.o ./obj/CmdLineParser.o ./obj/distmat.o ./obj/sse_RK.o ./obj/read_structures.o ./obj/primary_lib_gen.o ./obj/pairwise_global_structalgn.o ./obj/pdb_ripper.o ./obj/merge_global_local_libs.o ./obj/ew.o ./obj/refine_pairalgn.o ./obj/superpose_weightedRMS.o ./obj/superpose_2.o ./obj/jacobi.o ./obj/3D_manip_functions.o ./obj/extended_lib_gen.o ./obj/progress_align.o ./obj/neighbour_joining.o ./obj/upgma.o ./obj/superpose_on_core.o ./obj/multiple_superposition.o ./obj/output_algn.o ./obj/main.o make[1]: Leaving directory `/build/buildd/mustang-3.0' cp mustang mustang.1 touch build-arch-stamp # get rid of the test?.pdf files, they are not used # in the example rm -f test/data/pdbs/test*.pdb /usr/bin/fakeroot debian/rules binary dh_testdir dh_testroot dh_installexamples -s debian/runtest debian/test_zf-CCHH-small install -D -m755 bin/MUSTANG_v.3 debian/mustang/usr/bin/mustang /usr/bin/make -f debian/rules DH_OPTIONS=-s binary-common make[1]: Entering directory `/build/buildd/mustang-3.0' dh_testdir dh_testroot dh_installchangelogs dh_installdocs dh_installman dh_strip dh_strip debug symbol extraction: all non-arch-all packages for this build platform i386: mustang dh_strip debug symbol extraction: packages to act on: mustang dh_strip debug symbol extraction: ignored packages: pkgstriptranslations: processing control file: ./debian/mustang-dbgsym/DEBIAN/control, package mustang-dbgsym, directory ./debian/mustang-dbgsym pkgstriptranslations: mustang-dbgsym does not contain translations, skipping pkgstriptranslations: no translation files, not creating tarball pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com warning, `/build/buildd/mustang-3.0/debian/mustang-dbgsym/DEBIAN/control' contains user-defined field `Original-Maintainer' dpkg-deb: ignoring 1 warnings about the control file(s) dpkg-deb: building package `mustang-dbgsym' in `../mustang-dbgsym_3.0-1ubuntu1_i386.ddeb'. dh_compress -X.pdb dh_fixperms dh_installdeb dh_shlibdeps dh_gencontrol dpkg-gencontrol: warning: unknown substitution variable ${misc:Depends} dh_md5sums dh_builddeb pkgstriptranslations: processing control file: ./debian/mustang/DEBIAN/control, package mustang, directory ./debian/mustang pkgstriptranslations: mustang does not contain translations, skipping pkgstriptranslations: no translation files, not creating tarball pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com warning, `debian/mustang/DEBIAN/control' contains user-defined field `Original-Maintainer' dpkg-deb: ignoring 1 warnings about the control file(s) dpkg-deb: building package `mustang' in `../mustang_3.0-1ubuntu1_i386.deb'. make[1]: Leaving directory `/build/buildd/mustang-3.0' # get rid of the test?.pdf files, they are not used # in the example rm -f test/data/pdbs/test*.pdb dh_testdir dh_testroot dh_installexamples -i data/test/pdbs data/test/test_zf-CCHH /usr/bin/make -f debian/rules DH_OPTIONS=-i binary-common make[1]: Entering directory `/build/buildd/mustang-3.0' dh_testdir dh_testroot dh_installchangelogs dh_installdocs dh_installman dh_strip dh_strip debug symbol extraction: all non-arch-all packages for this build platform i386: mustang dh_strip debug symbol extraction: packages to act on: dh_strip debug symbol extraction: ignored packages: dh_compress -X.pdb dh_fixperms dh_installdeb dh_shlibdeps dh_gencontrol dh_md5sums dh_builddeb pkgstriptranslations: processing control file: ./debian/mustang/DEBIAN/control, package mustang, directory ./debian/mustang pkgstriptranslations: mustang does not contain translations, skipping pkgstriptranslations: processing control file: ./debian/mustang-testdata/DEBIAN/control, package mustang-testdata, directory ./debian/mustang-testdata pkgstriptranslations: mustang-testdata does not contain translations, skipping pkgstriptranslations: no translation files, not creating tarball pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com warning, `debian/mustang-testdata/DEBIAN/control' contains user-defined field `Original-Maintainer' dpkg-deb: ignoring 1 warnings about the control file(s) dpkg-deb: building package `mustang-testdata' in `../mustang-testdata_3.0-1ubuntu1_all.deb'. make[1]: Leaving directory `/build/buildd/mustang-3.0' dpkg-genchanges -b -mUbuntu/i386 Build Daemon >../mustang_3.0-1ubuntu1_i386.changes dpkg-genchanges: binary-only upload - not including any source code dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20081118-1356 Publishing debug debs. chroot-autobuild/build/buildd/mustang_3.0-1ubuntu1_i386.deb: new debian package, version 2.0. size 76412 bytes: control archive= 1034 bytes. 1100 bytes, 22 lines control 415 bytes, 6 lines md5sums Package: mustang Version: 3.0-1ubuntu1 Architecture: i386 Maintainer: Ubuntu MOTU Developers Installed-Size: 220 Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.2.1) Suggests: mustang-testdata Section: science Priority: optional Homepage: http://www.cs.mu.oz.au/~arun/mustang/ Description: multiple structural alignment of proteins Mustang is an algorithm to align multiple protein structures. Given a set of PDB files, the program uses the spatial information in the Calpha atoms of the set to produce a sequence alignment. Based on a progressive pairwise heuristic the algorithm then proceeds through a number of refinement passes. Mustang reports the multiple sequence alignment and the corresponding superposition of structures. . When using this program please cite A.S. Konagurthu, J.C. Whisstock, P.J. Stuckey, A.M. Lesk, "MUSTANG: A multiple structural alignment algorithm." Proteins: Structure, Function, and Bioinformatics. 64(3):559-574. Original-Maintainer: Debian-Med Packaging Team chroot-autobuild/build/buildd/mustang-testdata_3.0-1ubuntu1_all.deb: new debian package, version 2.0. size 85052 bytes: control archive= 1077 bytes. 521 bytes, 14 lines control 1751 bytes, 20 lines md5sums Package: mustang-testdata Source: mustang Version: 3.0-1ubuntu1 Architecture: all Maintainer: Ubuntu MOTU Developers Installed-Size: 388 Enhances: mustang Section: science Priority: optional Homepage: http://www.cs.mu.oz.au/~arun/mustang/ Description: multiple structural alignment of proteins, test data This package contains a larger set of test data than what comes with the binary package. Original-Maintainer: Debian-Med Packaging Team chroot-autobuild/build/buildd/mustang_3.0-1ubuntu1_i386.deb: drwxr-xr-x root/root 0 2008-11-18 13:56 ./ drwxr-xr-x root/root 0 2008-11-18 13:56 ./usr/ drwxr-xr-x root/root 0 2008-11-18 13:56 ./usr/share/ drwxr-xr-x root/root 0 2008-11-18 13:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2008-11-18 13:56 ./usr/share/doc/mustang/ drwxr-xr-x root/root 0 2008-11-18 13:56 ./usr/share/doc/mustang/examples/ -rw-r--r-- root/root 551 2008-11-18 13:55 ./usr/share/doc/mustang/examples/runtest -rw-r--r-- root/root 1663 2008-11-18 13:55 ./usr/share/doc/mustang/examples/test_zf-CCHH-small -rw-r--r-- root/root 4059 2008-11-18 13:55 ./usr/share/doc/mustang/copyright -rw-r--r-- root/root 1268 2008-11-18 13:55 ./usr/share/doc/mustang/changelog.Debian.gz drwxr-xr-x root/root 0 2008-11-18 13:56 ./usr/share/man/ drwxr-xr-x root/root 0 2008-11-18 13:56 ./usr/share/man/man1/ -rw-r--r-- root/root 1853 2008-11-18 13:56 ./usr/share/man/man1/mustang.1.gz drwxr-xr-x root/root 0 2008-11-18 13:56 ./usr/bin/ -rwxr-xr-x root/root 157212 2008-11-18 13:56 ./usr/bin/mustang chroot-autobuild/build/buildd/mustang-testdata_3.0-1ubuntu1_all.deb: drwxr-xr-x root/root 0 2008-11-18 13:56 ./ drwxr-xr-x root/root 0 2008-11-18 13:56 ./usr/ drwxr-xr-x root/root 0 2008-11-18 13:56 ./usr/share/ drwxr-xr-x root/root 0 2008-11-18 13:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2008-11-18 13:56 ./usr/share/doc/mustang-testdata/ drwxr-xr-x root/root 0 2008-11-18 13:56 ./usr/share/doc/mustang-testdata/examples/ drwxr-xr-x root/root 0 2008-11-18 13:55 ./usr/share/doc/mustang-testdata/examples/pdbs/ -rw-r--r-- root/root 16877 2008-11-18 13:55 ./usr/share/doc/mustang-testdata/examples/pdbs/1ard.pdb -rw-r--r-- root/root 14867 2008-11-18 13:55 ./usr/share/doc/mustang-testdata/examples/pdbs/1bboN.pdb -rw-r--r-- root/root 16073 2008-11-18 13:55 ./usr/share/doc/mustang-testdata/examples/pdbs/1paa.pdb -rw-r--r-- root/root 16475 2008-11-18 13:55 ./usr/share/doc/mustang-testdata/examples/pdbs/1sp1.pdb -rw-r--r-- root/root 18016 2008-11-18 13:55 ./usr/share/doc/mustang-testdata/examples/pdbs/1sp2.pdb -rw-r--r-- root/root 17413 2008-11-18 13:55 ./usr/share/doc/mustang-testdata/examples/pdbs/1zaa1.pdb -rw-r--r-- root/root 15738 2008-11-18 13:55 ./usr/share/doc/mustang-testdata/examples/pdbs/1zaa2.pdb -rw-r--r-- root/root 14733 2008-11-18 13:55 ./usr/share/doc/mustang-testdata/examples/pdbs/1zaa3.pdb -rw-r--r-- root/root 17815 2008-11-18 13:55 ./usr/share/doc/mustang-testdata/examples/pdbs/1zfd.pdb -rw-r--r-- root/root 13929 2008-11-18 13:55 ./usr/share/doc/mustang-testdata/examples/pdbs/1znf.pdb -rw-r--r-- root/root 13795 2008-11-18 13:55 ./usr/share/doc/mustang-testdata/examples/pdbs/1znm.pdb -rw-r--r-- root/root 19490 2008-11-18 13:55 ./usr/share/doc/mustang-testdata/examples/pdbs/2drp1.pdb -rw-r--r-- root/root 15805 2008-11-18 13:55 ./usr/share/doc/mustang-testdata/examples/pdbs/2drp2.pdb -rw-r--r-- root/root 16676 2008-11-18 13:55 ./usr/share/doc/mustang-testdata/examples/pdbs/3znf.pdb -rw-r--r-- root/root 16877 2008-11-18 13:55 ./usr/share/doc/mustang-testdata/examples/pdbs/5znf.pdb -rw-r--r-- root/root 35559 2008-11-18 13:55 ./usr/share/doc/mustang-testdata/examples/pdbs/test1.pdb -rw-r--r-- root/root 34344 2008-11-18 13:55 ./usr/share/doc/mustang-testdata/examples/pdbs/test2.pdb -rw-r--r-- root/root 1875 2008-11-18 13:55 ./usr/share/doc/mustang-testdata/examples/test_zf-CCHH -rw-r--r-- root/root 4059 2008-11-18 13:55 ./usr/share/doc/mustang-testdata/copyright -rw-r--r-- root/root 1268 2008-11-18 13:55 ./usr/share/doc/mustang-testdata/changelog.Debian.gz mustang_3.0-1ubuntu1_i386.changes: Format: 1.8 Date: Tue, 18 Nov 2008 13:48:49 +0100 Source: mustang Binary: mustang mustang-testdata Architecture: i386 all Version: 3.0-1ubuntu1 Distribution: jaunty Urgency: low Maintainer: Ubuntu/i386 Build Daemon Changed-By: Morten Kjeldgaard Description: mustang - multiple structural alignment of proteins mustang-testdata - multiple structural alignment of proteins, test data Launchpad-Bugs-Fixed: 296534 Changes: mustang (3.0-1ubuntu1) jaunty; urgency=low . * Fakesync of package from Debian (LP: #296534). Upstream changed tarball without bumping the version number, so we cannot do a normal sync from Debian. The tarball in this package is unchanged from -0ubuntu1. The deltas to the Debian tarball is introduced as a patch (debian/patches/fakesync.dpatch). debian/*: same as 3.0-1. debian/control: normal Ubuntu maintainer transmogrification. Checksums-Sha1: 028f599f5cb365dada6f519e172cf3740c24cd55 76412 mustang_3.0-1ubuntu1_i386.deb 4b1a8e72dc0ff456fde944bf5b190e80d73f665a 85052 mustang-testdata_3.0-1ubuntu1_all.deb Checksums-Sha256: 14b0e1a660522777c58b3fd91994e0a1f683ce26ce4cab4d8b752b071f63daeb 76412 mustang_3.0-1ubuntu1_i386.deb f1f25b8667a1afc1b1a9ac540d8965cf881f0df09272fe4736c21b8ef4f754d1 85052 mustang-testdata_3.0-1ubuntu1_all.deb Files: ecf774783912db84b242b6927aba3a7f 76412 science optional mustang_3.0-1ubuntu1_i386.deb 28762927b6204ade0ce9187ee592ff18 85052 science optional mustang-testdata_3.0-1ubuntu1_all.deb Original-Maintainer: Debian-Med Packaging Team ****************************************************************************** Built successfully Purging chroot-autobuild/build/buildd/mustang-3.0 ------------------------------------------------------------------------------ /usr/bin/sudo dpkg --root=/home/buildd/build-790567-1851245/chroot-autobuild --purge po-debconf intltool-debian groff-base libmagic1 gettext file dpatch bsdmainutils html2text gettext-base man-db debhelper (Reading database ... 11747 files and directories currently installed.) Removing dpatch ... Purging configuration files for dpatch ... Removing debhelper ... Removing po-debconf ... Removing intltool-debian ... Removing gettext ... Removing file ... Purging configuration files for file ... Removing html2text ... Purging configuration files for html2text ... Removing gettext-base ... Removing man-db ... Purging configuration files for man-db ... Removing catpages as well as /var/cache/man hierarchy. dpkg - warning: while removing man-db, directory `/usr/share/doc/man-db/examples' not empty so not removed. dpkg - warning: while removing man-db, directory `/usr/share/doc/man-db' not empty so not removed. dpkg - warning: while removing man-db, directory `/usr/share/man-db' not empty so not removed. dpkg - warning: while removing man-db, directory `/usr/share/bug/man-db' not empty so not removed. dpkg - warning: while removing man-db, directory `/usr/lib/man-db' not empty so not removed. Removing groff-base ... Purging configuration files for groff-base ... Removing libmagic1 ... Purging configuration files for libmagic1 ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Processing triggers for libc6 ... ldconfig deferred processing now taking place ****************************************************************************** Finished at 20081118-1356 Build needed 00:00:31, 4728k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['/usr/share/launchpad-buildd/slavebin/scan-for-processes', '790567-1851245'] Scanning for processes to kill in build 790567-1851245... Scanning for processes to kill in build /home/buildd/build-790567-1851245/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', '790567-1851245'] Unmounting chroot for build 790567-1851245... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', '790567-1851245'] Removing build 790567-1851245