RUN: /bin/echo ['echo', 'Forking build subprocess...'] Forking build subprocess... RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', '790565-1851243', '/home/buildd/filecache-default/05ed72be0d6b3618e2e22266fc9a300b75f69100'] Synching the system clock with the buildd NTP service... 8 Dec 14:15:54 ntpdate[22198]: adjust time server 10.211.37.1 offset 0.010976 sec Unpacking chroot for build 790565-1851243 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', '790565-1851243'] Mounting chroot for build 790565-1851243 RUN: /usr/share/launchpad-buildd/slavebin/apply-ogre-model ['apply-ogre-model', '790565-1851243', 'universe'] Attempting OGRE for universe in build-790565-1851243 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', '790565-1851243', 'deb http://ftpmaster.internal/ubuntu jaunty main universe'] Overriding sources.list in build-790565-1851243 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', '790565-1851243'] Updating debian chroot for build 790565-1851243 Get:1 http://ftpmaster.internal jaunty Release.gpg [189B] Get:2 http://ftpmaster.internal jaunty Release [74.6kB] Ign http://ftpmaster.internal jaunty/main Packages/DiffIndex Get:3 http://ftpmaster.internal jaunty/universe Packages [3807kB] Get:4 http://ftpmaster.internal jaunty/main Packages [1215kB] Fetched 5096kB in 12s (400kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: binutils cpp-4.3 debianutils g++-4.3 gcc-4.3 gcc-4.3-base libc6 libc6-dev libgcc1 libgnutls26 libgomp1 libstdc++6 libstdc++6-4.3-dev linux-libc-dev login passwd procps 17 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 0B/20.3MB of archives. After this operation, 283kB of additional disk space will be used. WARNING: The following packages cannot be authenticated! debianutils login linux-libc-dev libc6-dev libgomp1 gcc-4.3-base libstdc++6 cpp-4.3 binutils gcc-4.3 g++-4.3 libstdc++6-4.3-dev libgcc1 libc6 passwd libgnutls26 procps Preconfiguring packages ... Authentication warning overridden. (Reading database ... 9539 files and directories currently installed.) Preparing to replace debianutils 2.30ubuntu1 (using .../debianutils_2.30ubuntu2_armel.deb) ... Unpacking replacement debianutils ... Setting up debianutils (2.30ubuntu2) ... (Reading database ... 9539 files and directories currently installed.) Preparing to replace login 1:4.1.1-5ubuntu3 (using .../login_1%3a4.1.1-6ubuntu1_armel.deb) ... Unpacking replacement login ... Setting up login (1:4.1.1-6ubuntu1) ... (Reading database ... 9539 files and directories currently installed.) Preparing to replace linux-libc-dev 2.6.27-9.18 (using .../linux-libc-dev_2.6.28-2.3_armel.deb) ... Unpacking replacement linux-libc-dev ... Preparing to replace libc6-dev 2.8+20081027-0ubuntu10 (using .../libc6-dev_2.9-0ubuntu5_armel.deb) ... Unpacking replacement libc6-dev ... Preparing to replace libgomp1 4.3.2-2ubuntu4 (using .../libgomp1_4.3.2-2ubuntu6_armel.deb) ... Unpacking replacement libgomp1 ... Preparing to replace gcc-4.3-base 4.3.2-2ubuntu4 (using .../gcc-4.3-base_4.3.2-2ubuntu6_armel.deb) ... Unpacking replacement gcc-4.3-base ... Setting up gcc-4.3-base (4.3.2-2ubuntu6) ... (Reading database ... 9550 files and directories currently installed.) Preparing to replace libstdc++6 4.3.2-2ubuntu4 (using .../libstdc++6_4.3.2-2ubuntu6_armel.deb) ... Unpacking replacement libstdc++6 ... Setting up libstdc++6 (4.3.2-2ubuntu6) ... Processing triggers for libc6 ... ldconfig deferred processing now taking place (Reading database ... 9550 files and directories currently installed.) Preparing to replace cpp-4.3 4.3.2-2ubuntu4 (using .../cpp-4.3_4.3.2-2ubuntu6_armel.deb) ... Unpacking replacement cpp-4.3 ... Preparing to replace binutils 2.19-0ubuntu2 (using .../binutils_2.19-0ubuntu3_armel.deb) ... Unpacking replacement binutils ... Preparing to replace gcc-4.3 4.3.2-2ubuntu4 (using .../gcc-4.3_4.3.2-2ubuntu6_armel.deb) ... Unpacking replacement gcc-4.3 ... Preparing to replace g++-4.3 4.3.2-2ubuntu4 (using .../g++-4.3_4.3.2-2ubuntu6_armel.deb) ... Unpacking replacement g++-4.3 ... Preparing to replace libstdc++6-4.3-dev 4.3.2-2ubuntu4 (using .../libstdc++6-4.3-dev_4.3.2-2ubuntu6_armel.deb) ... Unpacking replacement libstdc++6-4.3-dev ... Preparing to replace libgcc1 1:4.3.2-2ubuntu4 (using .../libgcc1_1%3a4.3.2-2ubuntu6_armel.deb) ... Unpacking replacement libgcc1 ... Setting up libgcc1 (1:4.3.2-2ubuntu6) ... Processing triggers for libc6 ... ldconfig deferred processing now taking place (Reading database ... 9550 files and directories currently installed.) Preparing to replace libc6 2.8+20081027-0ubuntu10 (using .../libc6_2.9-0ubuntu5_armel.deb) ... Unpacking replacement libc6 ... Setting up libc6 (2.9-0ubuntu5) ... Processing triggers for libc6 ... ldconfig deferred processing now taking place (Reading database ... 9550 files and directories currently installed.) Preparing to replace passwd 1:4.1.1-5ubuntu3 (using .../passwd_1%3a4.1.1-6ubuntu1_armel.deb) ... Unpacking replacement passwd ... Setting up passwd (1:4.1.1-6ubuntu1) ... (Reading database ... 9550 files and directories currently installed.) Preparing to replace libgnutls26 2.4.2-3 (using .../libgnutls26_2.4.2-4_armel.deb) ... Unpacking replacement libgnutls26 ... Preparing to replace procps 1:3.2.7-9ubuntu2 (using .../procps_1%3a3.2.7-9ubuntu3_armel.deb) ... Unpacking replacement procps ... Setting up linux-libc-dev (2.6.28-2.3) ... Setting up libc6-dev (2.9-0ubuntu5) ... Setting up libgomp1 (4.3.2-2ubuntu6) ... Setting up cpp-4.3 (4.3.2-2ubuntu6) ... Setting up binutils (2.19-0ubuntu3) ... Setting up gcc-4.3 (4.3.2-2ubuntu6) ... Setting up libgnutls26 (2.4.2-4) ... Setting up procps (1:3.2.7-9ubuntu3) ... Installing new version of config file /etc/sysctl.d/10-process-security.conf ... * Setting kernel variables (/etc/sysctl.conf)...  [ OK ] * Setting kernel variables (/etc/sysctl.d/10-console-messages.conf)...  [ OK ] * Setting kernel variables (/etc/sysctl.d/10-network-security.conf)...  [ OK ] * Setting kernel variables (/etc/sysctl.d/10-process-security.conf)...  error: "vm.mmap_min_addr" is an unknown key [fail] * Setting kernel variables (/etc/sysctl.d/10-tcp-timestamps-workaround.conf)...  [ OK ] Setting up libstdc++6-4.3-dev (4.3.2-2ubuntu6) ... Setting up g++-4.3 (4.3.2-2ubuntu6) ... Processing triggers for libc6 ... ldconfig deferred processing now taking place modified: mtab RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', '790565-1851243', '--nolog', '--batch', '--archive=ubuntu', '--purpose=PRIMARY', '--dist=jaunty', '--comp=universe', 'mustang_3.0-1ubuntu1.dsc'] Initiating build Automatic build of mustang_3.0-1ubuntu1 on nageia by sbuild/armel 1.170.5 Build started at 20081208-1416 ****************************************************************************** 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 extra packages will be installed: bsdmainutils curl file gettext gettext-base groff-base html2text intltool-debian libcompress-raw-zlib-perl libcompress-zlib-perl libcroco3 libcurl3 libglib2.0-0 libglib2.0-data libio-compress-base-perl libio-compress-zlib-perl libmagic1 libmail-sendmail-perl libsys-hostname-long-perl libxml2 man-db patchutils po-debconf sgml-base xml-core Suggested packages: wamerican wordlist whois vacation dh-make cvs gettext-doc groff less www-browser libmail-box-perl sgml-base-doc The following NEW packages will be installed: bsdmainutils curl debhelper dpatch file gettext gettext-base groff-base html2text intltool-debian libcompress-raw-zlib-perl libcompress-zlib-perl libcroco3 libcurl3 libglib2.0-0 libglib2.0-data libio-compress-base-perl libio-compress-zlib-perl libmagic1 libmail-sendmail-perl libsys-hostname-long-perl libxml2 man-db patchutils po-debconf sgml-base xml-core 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. Need to get 0B/7849kB of archives. After this operation, 29.8MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libmagic1 file bsdmainutils gettext-base groff-base libcompress-raw-zlib-perl libio-compress-base-perl libio-compress-zlib-perl libcompress-zlib-perl libxml2 man-db sgml-base xml-core libcurl3 curl html2text libglib2.0-0 libcroco3 gettext intltool-debian po-debconf debhelper dpatch libglib2.0-data libsys-hostname-long-perl libmail-sendmail-perl patchutils dpkg-preconfigure: unable to re-open stdin: Authentication warning overridden. Selecting previously deselected package libmagic1. (Reading database ... 9550 files and directories currently installed.) Unpacking libmagic1 (from .../libmagic1_4.26-1_armel.deb) ... Selecting previously deselected package file. Unpacking file (from .../archives/file_4.26-1_armel.deb) ... Selecting previously deselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_6.1.10ubuntu3_armel.deb) ... Selecting previously deselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.17-6ubuntu1_armel.deb) ... Selecting previously deselected package groff-base. Unpacking groff-base (from .../groff-base_1.18.1.1-21_armel.deb) ... Selecting previously deselected package libcompress-raw-zlib-perl. Unpacking libcompress-raw-zlib-perl (from .../libcompress-raw-zlib-perl_2.015-1_armel.deb) ... Selecting previously deselected package libio-compress-base-perl. Unpacking libio-compress-base-perl (from .../libio-compress-base-perl_2.015-1_all.deb) ... Selecting previously deselected package libio-compress-zlib-perl. Unpacking libio-compress-zlib-perl (from .../libio-compress-zlib-perl_2.015-1_all.deb) ... Selecting previously deselected package libcompress-zlib-perl. Unpacking libcompress-zlib-perl (from .../libcompress-zlib-perl_2.015-1_all.deb) ... Selecting previously deselected package libxml2. Unpacking libxml2 (from .../libxml2_2.6.32.dfsg-5ubuntu1_armel.deb) ... Selecting previously deselected package man-db. Unpacking man-db (from .../man-db_2.5.3-1_armel.deb) ... Selecting previously deselected package sgml-base. Unpacking sgml-base (from .../sgml-base_1.26_all.deb) ... Selecting previously deselected package xml-core. Unpacking xml-core (from .../archives/xml-core_0.12_all.deb) ... Selecting previously deselected package libcurl3. Unpacking libcurl3 (from .../libcurl3_7.18.2-7ubuntu2_armel.deb) ... Selecting previously deselected package curl. Unpacking curl (from .../curl_7.18.2-7ubuntu2_armel.deb) ... Selecting previously deselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-5_armel.deb) ... Selecting previously deselected package libglib2.0-0. Unpacking libglib2.0-0 (from .../libglib2.0-0_2.19.2-0ubuntu2_armel.deb) ... Selecting previously deselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.1-2_armel.deb) ... Selecting previously deselected package gettext. Unpacking gettext (from .../gettext_0.17-6ubuntu1_armel.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) ... Selecting previously deselected package libglib2.0-data. Unpacking libglib2.0-data (from .../libglib2.0-data_2.19.2-0ubuntu2_all.deb) ... Selecting previously deselected package libsys-hostname-long-perl. Unpacking libsys-hostname-long-perl (from .../libsys-hostname-long-perl_1.4-2_all.deb) ... Selecting previously deselected package libmail-sendmail-perl. Unpacking libmail-sendmail-perl (from .../libmail-sendmail-perl_0.79.16-1_all.deb) ... Selecting previously deselected package patchutils. Unpacking patchutils (from .../patchutils_0.2.31-4_armel.deb) ... Setting up libmagic1 (4.26-1) ... Setting up file (4.26-1) ... Setting up bsdmainutils (6.1.10ubuntu3) ... Setting up gettext-base (0.17-6ubuntu1) ... Setting up groff-base (1.18.1.1-21) ... Setting up libcompress-raw-zlib-perl (2.015-1) ... Setting up libio-compress-base-perl (2.015-1) ... Setting up libio-compress-zlib-perl (2.015-1) ... Setting up libcompress-zlib-perl (2.015-1) ... Setting up libxml2 (2.6.32.dfsg-5ubuntu1) ... Setting up man-db (2.5.3-1) ... Building database of manual pages ... ... skipping, since this is a buildd Setting up sgml-base (1.26) ... Setting up xml-core (0.12) ... Setting up libcurl3 (7.18.2-7ubuntu2) ... Setting up curl (7.18.2-7ubuntu2) ... Setting up html2text (1.3.2a-5) ... Setting up libglib2.0-0 (2.19.2-0ubuntu2) ... Setting up libcroco3 (0.6.1-2) ... Setting up gettext (0.17-6ubuntu1) ... 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) ... Setting up libglib2.0-data (2.19.2-0ubuntu2) ... Setting up libsys-hostname-long-perl (1.4-2) ... Setting up libmail-sendmail-perl (0.79.16-1) ... Setting up patchutils (0.2.31-4) ... Processing triggers for libc6 ... ldconfig deferred processing now taking place modified: mtab Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.9-0ubuntu5 make_3.81-5 dpkg-dev_1.14.22ubuntu1 g++-4.3_4.3.2-2ubuntu6 gcc-4.3_4.3.2-2ubuntu6 binutils_2.19-0ubuntu3 libstdc++6_4.3.2-2ubuntu6 libstdc++6-4.3-dev_4.3.2-2ubuntu6 ------------------------------------------------------------------------------ sh: gcc: command 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: info: unpacking mustang_3.0.orig.tar.gz dpkg-source: info: applying 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 armel /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-arch 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 armel: 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_armel.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_armel.deb'. make[1]: Leaving directory `/build/buildd/mustang-3.0' dpkg-genchanges -B -mUbuntu/armel Build Daemon >../mustang_3.0-1ubuntu1_armel.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20081208-1419 Publishing debug debs. chroot-autobuild/build/buildd/mustang_3.0-1ubuntu1_armel.deb: new debian package, version 2.0. size 82324 bytes: control archive= 1033 bytes. 1097 bytes, 22 lines control 415 bytes, 6 lines md5sums Package: mustang Version: 3.0-1ubuntu1 Architecture: armel Maintainer: Ubuntu MOTU Developers Installed-Size: 220 Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.3), libstdc++6 (>= 4.3) 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_3.0-1ubuntu1_armel.deb: drwxr-xr-x root/root 0 2008-12-08 14:19 ./ drwxr-xr-x root/root 0 2008-12-08 14:19 ./usr/ drwxr-xr-x root/root 0 2008-12-08 14:19 ./usr/share/ drwxr-xr-x root/root 0 2008-12-08 14:19 ./usr/share/doc/ drwxr-xr-x root/root 0 2008-12-08 14:19 ./usr/share/doc/mustang/ -rw-r--r-- root/root 4059 2008-12-08 14:17 ./usr/share/doc/mustang/copyright drwxr-xr-x root/root 0 2008-12-08 14:19 ./usr/share/doc/mustang/examples/ -rw-r--r-- root/root 551 2008-12-08 14:17 ./usr/share/doc/mustang/examples/runtest -rw-r--r-- root/root 1663 2008-12-08 14:17 ./usr/share/doc/mustang/examples/test_zf-CCHH-small -rw-r--r-- root/root 1268 2008-12-08 14:17 ./usr/share/doc/mustang/changelog.Debian.gz drwxr-xr-x root/root 0 2008-12-08 14:19 ./usr/share/man/ drwxr-xr-x root/root 0 2008-12-08 14:19 ./usr/share/man/man1/ -rw-r--r-- root/root 1853 2008-12-08 14:19 ./usr/share/man/man1/mustang.1.gz drwxr-xr-x root/root 0 2008-12-08 14:19 ./usr/bin/ -rwxr-xr-x root/root 157132 2008-12-08 14:19 ./usr/bin/mustang mustang_3.0-1ubuntu1_armel.changes: Format: 1.8 Date: Tue, 18 Nov 2008 13:48:49 +0100 Source: mustang Binary: mustang mustang-testdata Architecture: armel Version: 3.0-1ubuntu1 Distribution: jaunty Urgency: low Maintainer: Ubuntu/armel 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: dcc0ceae242f00f65d02b04b8c4ce332a699e620 82324 mustang_3.0-1ubuntu1_armel.deb Checksums-Sha256: f0853ca140aafa011ea3ec8b0d92a3bb15e674dc0426d02ae28bb855a82972f8 82324 mustang_3.0-1ubuntu1_armel.deb Files: 81fd80f53538129c2241034afecaae4c 82324 science optional mustang_3.0-1ubuntu1_armel.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-790565-1851243/chroot-autobuild --purge intltool-debian groff-base libglib2.0-0 libio-compress-base-perl libcurl3 libcompress-zlib-perl gettext file libglib2.0-data xml-core dpatch html2text curl gettext-base debhelper sgml-base po-debconf patchutils libcroco3 libmagic1 libcompress-raw-zlib-perl libxml2 libio-compress-zlib-perl libsys-hostname-long-perl libmail-sendmail-perl bsdmainutils man-db (Reading database ... 10880 files and directories currently installed.) Removing libcompress-zlib-perl ... Removing libglib2.0-data ... Removing xml-core ... Purging configuration files for xml-core ... dpkg - warning: while removing xml-core, directory `/etc/sgml' not empty so not removed. Removing dpatch ... Purging configuration files for dpatch ... Removing curl ... Removing debhelper ... Removing sgml-base ... Purging configuration files for sgml-base ... Removing po-debconf ... Removing patchutils ... Removing libio-compress-zlib-perl ... Removing libmail-sendmail-perl ... Removing man-db ... Purging configuration files for man-db ... Removing intltool-debian ... Removing groff-base ... Purging configuration files for groff-base ... Removing libio-compress-base-perl ... Removing libcurl3 ... Purging configuration files for libcurl3 ... Removing gettext ... Removing file ... Purging configuration files for file ... Removing html2text ... Purging configuration files for html2text ... Removing gettext-base ... Removing libcroco3 ... Purging configuration files for libcroco3 ... Removing libmagic1 ... Purging configuration files for libmagic1 ... Removing libcompress-raw-zlib-perl ... Removing libxml2 ... Purging configuration files for libxml2 ... Removing libsys-hostname-long-perl ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Removing libglib2.0-0 ... Purging configuration files for libglib2.0-0 ... Processing triggers for libc6 ... ldconfig deferred processing now taking place ****************************************************************************** Finished at 20081208-1419 Build needed 00:02:24, 4320k disk space Can't open average time db /var/debbuild/avg-build-times Can't open average space db /var/debbuild/avg-build-space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['/usr/share/launchpad-buildd/slavebin/scan-for-processes', '790565-1851243'] Scanning for processes to kill in build 790565-1851243... Scanning for processes to kill in build /home/buildd/build-790565-1851243/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', '790565-1851243'] Unmounting chroot for build 790565-1851243... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', '790565-1851243'] Removing build 790565-1851243