https://launchpad.net/ubuntu/+archive/test-rebuild-20220617-kinetic/+build/24051775 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lgw01-amd64-004 5.4.0-120-generic #136-Ubuntu SMP Fri Jun 10 13:40:48 UTC 2022 x86_64 Buildd toolchain package versions: launchpad-buildd_215~563~ubuntu20.04.1 python3-lpbuildd_215~563~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.4 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 23 Jun 09:45:08 ntpdate[1827]: adjust time server 10.211.37.1 offset 0.004804 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24051775 --image-type chroot /home/buildd/filecache-default/4d18961cd05542d5def75b14497015b674c37821 Creating target for build PACKAGEBUILD-24051775 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24051775 Starting target for build PACKAGEBUILD-24051775 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24051775 'deb http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic main' 'deb http://ftpmaster.internal/ubuntu kinetic main universe' Overriding sources.list in build-PACKAGEBUILD-24051775 RUN: /usr/share/launchpad-buildd/bin/in-target add-trusted-keys --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24051775 Adding trusted keys to build-PACKAGEBUILD-24051775 pub rsa1024/1E9377A2BA9EF27F 2009-10-22 [SC] Key fingerprint = 60C3 1780 3A41 BA51 845E 371A 1E93 77A2 BA9E F27F uid Launchpad Toolchain builds RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24051775 Updating target for build PACKAGEBUILD-24051775 Get:1 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic InRelease [23.8 kB] Get:2 http://ftpmaster.internal/ubuntu kinetic InRelease [267 kB] Get:3 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 Packages [9632 B] Get:4 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main Translation-en [4132 B] Get:5 http://ftpmaster.internal/ubuntu kinetic/main amd64 Packages [1398 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main Translation-en [510 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/universe amd64 Packages [14.3 MB] Get:8 http://ftpmaster.internal/ubuntu kinetic/universe Translation-en [5729 kB] Fetched 22.2 MB in 3s (6583 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: libgprofng0 util-linux-extra The following packages will be upgraded: adduser apt base-files binutils binutils-common binutils-x86-64-linux-gnu bsdutils cpp-11 dpkg dpkg-dev e2fsprogs fakeroot g++-11 gcc-11 gcc-11-base gcc-12-base init init-system-helpers libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libbinutils libblkid1 libcap-ng0 libcc1-0 libcom-err2 libctf-nobfd0 libctf0 libdb5.3 libdpkg-perl libext2fs2 libfakeroot libgcc-11-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libgpg-error0 libip4tc2 libitm1 libkeyutils1 liblsan0 liblzma5 libmount1 libncurses6 libncursesw6 libpng16-16 libquadmath0 libreadline8 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libss2 libssl3 libstdc++-11-dev libstdc++6 libsystemd0 libtinfo6 libtsan0 libubsan1 libudev1 libuuid1 libzstd1 login logsave lto-disabled-list mawk mount ncurses-base ncurses-bin openssl passwd pinentry-curses policyrcd-script-zg2 readline-common systemd systemd-sysv util-linux xz-utils 83 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 79.7 MB of archives. After this operation, 5304 kB of additional disk space will be used. Get:1 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 libctf0 amd64 2.38.50.20220615-4ubuntu1 [103 kB] Get:2 http://ftpmaster.internal/ubuntu kinetic/main amd64 base-files amd64 12.2ubuntu1 [62.6 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic/main amd64 bsdutils amd64 1:2.38-4ubuntu1 [80.7 kB] Get:4 http://ftpmaster.internal/ubuntu kinetic/main amd64 libzstd1 amd64 1.5.2+dfsg-1 [270 kB] Get:5 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 libctf-nobfd0 amd64 2.38.50.20220615-4ubuntu1 [107 kB] Get:6 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 binutils-x86-64-linux-gnu amd64 2.38.50.20220615-4ubuntu1 [2476 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/main amd64 libatomic1 amd64 12.1.0-2ubuntu1 [10.4 kB] Get:8 http://ftpmaster.internal/ubuntu kinetic/main amd64 libubsan1 amd64 12.1.0-2ubuntu1 [969 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic/main amd64 libquadmath0 amd64 12.1.0-2ubuntu1 [152 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic/main amd64 liblsan0 amd64 12.1.0-2ubuntu1 [1060 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic/main amd64 libitm1 amd64 12.1.0-2ubuntu1 [29.5 kB] Get:12 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgomp1 amd64 12.1.0-2ubuntu1 [125 kB] Get:13 http://ftpmaster.internal/ubuntu kinetic/main amd64 gcc-12-base amd64 12.1.0-2ubuntu1 [18.8 kB] Get:14 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgcc-s1 amd64 12.1.0-2ubuntu1 [54.2 kB] Get:15 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcc1-0 amd64 12.1.0-2ubuntu1 [46.6 kB] Get:16 http://ftpmaster.internal/ubuntu kinetic/main amd64 libstdc++6 amd64 12.1.0-2ubuntu1 [679 kB] Get:17 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 libbinutils amd64 2.38.50.20220615-4ubuntu1 [655 kB] Get:18 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgpg-error0 amd64 1.45-2 [69.0 kB] Get:19 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgcrypt20 amd64 1.10.1-2ubuntu1 [524 kB] Get:20 http://ftpmaster.internal/ubuntu kinetic/main amd64 liblzma5 amd64 5.2.5-2.1 [99.2 kB] Get:21 http://ftpmaster.internal/ubuntu kinetic/main amd64 systemd-sysv amd64 249.11-0ubuntu4 [10.2 kB] Get:22 http://ftpmaster.internal/ubuntu kinetic/main amd64 libapparmor1 amd64 3.0.4-2ubuntu3 [38.0 kB] Get:23 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgnutls30 amd64 3.7.6-2ubuntu1 [968 kB] Get:24 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 binutils amd64 2.38.50.20220615-4ubuntu1 [3292 B] Get:25 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 binutils-common amd64 2.38.50.20220615-4ubuntu1 [224 kB] Get:26 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 libgprofng0 amd64 2.38.50.20220615-4ubuntu1 [963 kB] Get:27 http://ftpmaster.internal/ubuntu kinetic/main amd64 libip4tc2 amd64 1.8.7-1ubuntu6 [19.7 kB] Get:28 http://ftpmaster.internal/ubuntu kinetic/main amd64 libblkid1 amd64 2.38-4ubuntu1 [103 kB] Get:29 http://ftpmaster.internal/ubuntu kinetic/main amd64 libselinux1 amd64 3.4-1 [77.6 kB] Get:30 http://ftpmaster.internal/ubuntu kinetic/main amd64 libmount1 amd64 2.38-4ubuntu1 [121 kB] Get:31 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsmartcols1 amd64 2.38-4ubuntu1 [50.8 kB] Get:32 http://ftpmaster.internal/ubuntu kinetic/main amd64 login amd64 1:4.11.1+dfsg1-2ubuntu1 [183 kB] Get:33 http://ftpmaster.internal/ubuntu kinetic/main amd64 util-linux-extra amd64 2.38-4ubuntu1 [83.8 kB] Get:34 http://ftpmaster.internal/ubuntu kinetic/main amd64 util-linux amd64 2.38-4ubuntu1 [1069 kB] Get:35 http://ftpmaster.internal/ubuntu kinetic/main amd64 mount amd64 2.38-4ubuntu1 [114 kB] Get:36 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsemanage-common all 3.4-1 [9828 B] Get:37 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsepol2 amd64 3.4-2 [294 kB] Get:38 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsemanage2 amd64 3.4-1 [91.8 kB] Get:39 http://ftpmaster.internal/ubuntu kinetic/main amd64 passwd amd64 1:4.11.1+dfsg1-2ubuntu1 [765 kB] Get:40 http://ftpmaster.internal/ubuntu kinetic/main amd64 adduser all 3.121ubuntu1 [150 kB] Get:41 http://ftpmaster.internal/ubuntu kinetic/main amd64 systemd amd64 249.11-0ubuntu4 [4517 kB] Get:42 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsystemd0 amd64 249.11-0ubuntu4 [314 kB] Get:43 http://ftpmaster.internal/ubuntu kinetic/main amd64 libudev1 amd64 249.11-0ubuntu4 [76.1 kB] Get:44 http://ftpmaster.internal/ubuntu kinetic/main amd64 libapt-pkg6.0 amd64 2.5.0 [896 kB] Get:45 http://ftpmaster.internal/ubuntu kinetic/main amd64 dpkg amd64 1.21.8ubuntu1 [1333 kB] Get:46 http://ftpmaster.internal/ubuntu kinetic/main amd64 ncurses-bin amd64 6.3+20220423-2 [183 kB] Get:47 http://ftpmaster.internal/ubuntu kinetic/main amd64 init-system-helpers all 1.63 [38.7 kB] Get:48 http://ftpmaster.internal/ubuntu kinetic/main amd64 ncurses-base all 6.3+20220423-2 [21.2 kB] Get:49 http://ftpmaster.internal/ubuntu kinetic/main amd64 apt amd64 2.5.0 [1370 kB] Get:50 http://ftpmaster.internal/ubuntu kinetic/main amd64 logsave amd64 1.46.5-2ubuntu2 [9914 B] Get:51 http://ftpmaster.internal/ubuntu kinetic/main amd64 libext2fs2 amd64 1.46.5-2ubuntu2 [205 kB] Get:52 http://ftpmaster.internal/ubuntu kinetic/main amd64 e2fsprogs amd64 1.46.5-2ubuntu2 [585 kB] Get:53 http://ftpmaster.internal/ubuntu kinetic/main amd64 init amd64 1.63 [5674 B] Get:54 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcap-ng0 amd64 0.7.9-4 [12.1 kB] Get:55 http://ftpmaster.internal/ubuntu kinetic/main amd64 libdb5.3 amd64 5.3.28+dfsg1-0.9 [717 kB] Get:56 http://ftpmaster.internal/ubuntu kinetic/main amd64 libncurses6 amd64 6.3+20220423-2 [110 kB] Get:57 http://ftpmaster.internal/ubuntu kinetic/main amd64 libncursesw6 amd64 6.3+20220423-2 [146 kB] Get:58 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RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-24051775 amd64 kinetic -c chroot:build-PACKAGEBUILD-24051775 --arch=amd64 --dist=kinetic --nolog -A primer3_2.5.0-1.dsc Initiating build PACKAGEBUILD-24051775 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-120-generic #136-Ubuntu SMP Fri Jun 10 13:40:48 UTC 2022 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lgw01-amd64-004.buildd +==============================================================================+ | primer3 2.5.0-1 (amd64) Thu, 23 Jun 2022 09:45:33 +0000 | +==============================================================================+ Package: primer3 Version: 2.5.0-1 Source Version: 2.5.0-1 Distribution: kinetic Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-24051775/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/primer3-r4xpKT/resolver-OmgFdG' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- primer3_2.5.0-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/primer3-r4xpKT/primer3-2.5.0' with '<>' I: NOTICE: Log filtering will replace 'build/primer3-r4xpKT' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [370 B] Get:5 copy:/<>/apt_archive ./ Packages [452 B] Fetched 1779 B in 0s (111 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 additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libdw1 libelf1 libfile-stripnondeterminism-perl libicu71 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libdw1 libelf1 libfile-stripnondeterminism-perl libicu71 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy 0 upgraded, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 18.5 MB of archives. After this operation, 66.4 MB of additional disk space will be used. 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Processing triggers for libc-bin (2.35-0ubuntu3) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-120-generic #136-Ubuntu SMP Fri Jun 10 13:40:48 UTC 2022 amd64 (x86_64) Toolchain package versions: binutils_2.38.50.20220615-4ubuntu1 dpkg-dev_1.21.8ubuntu1 g++-11_11.3.0-3ubuntu1 gcc-11_11.3.0-3ubuntu1 libc6-dev_2.35-0ubuntu3 libstdc++-11-dev_11.3.0-3ubuntu1 libstdc++6_12.1.0-2ubuntu1 linux-libc-dev_5.15.0-27.28 Package versions: adduser_3.121ubuntu1 advancecomp_2.1-2.1ubuntu2 apt_2.5.0 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-6 autotools-dev_20220109.1 base-files_12.2ubuntu1 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tar_1.34+dfsg-1build3 tzdata_2022a-0ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_25ubuntu2 util-linux_2.38-4ubuntu1 util-linux-extra_2.38-4ubuntu1 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-2ubuntu9 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: primer3 Binary: primer3, primer3-examples Architecture: any all Version: 2.5.0-1 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Charles Plessy , Andreas Tille Homepage: http://primer3.sourceforge.net Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/primer3 Vcs-Git: https://salsa.debian.org/med-team/primer3.git Testsuite: autopkgtest Testsuite-Triggers: valgrind Build-Depends: debhelper-compat (= 13) Package-List: primer3 deb science optional arch=any primer3-examples deb science optional arch=all Checksums-Sha1: 3f44264ed77faf250ac2cb51e61c7966b809d79a 31824182 primer3_2.5.0.orig.tar.gz bfd72fa0e84541c2535a256ea43b89072efd61fe 12656 primer3_2.5.0-1.debian.tar.xz Checksums-Sha256: 7581e2fa3228ef0ee1ffa427b2aa0a18fc635d561208327471daf59d1b804da0 31824182 primer3_2.5.0.orig.tar.gz 3e989fc51bb2cc37fd941f8cb74cbb2db08212770cbf026f49cd4693b87d0be0 12656 primer3_2.5.0-1.debian.tar.xz Files: cd6d2c578a06df022b37c6dbf74fc29e 31824182 primer3_2.5.0.orig.tar.gz 637ff928e81cf9850c7688409c21d610 12656 primer3_2.5.0-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmFphXMRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEjLw//baooJAvAHGTvXXu2t1QvYMTCRrPpsLNd 6k764QhLT1X4UTWLVjepPxN4wh902277RAJkiVylkFkT3wwDWd4AM6CV8vC4UfMz 9zz93saiYNQGmFY2VaDK3evAY2k5JYjki7ZwAeVVEL1kLtbgwODs4foPqP1sikTG pMkPg7C6g5jRtGk8acL6Oi9OCXBmIAokRg4moDpLKmDrhXApqN4gNTlaupAPmwQn C5NfHsxR6fQ6SDh60WF4bAcewopyge2Tuu+CQaYcdTB6mjDhy6g9aBboVtWGzQq9 9Km55gdwvXNWLk2Nq+F0VuuAIa+Rm3VElBT5tLuNM0xjHzYAtaPHtCMfT9ZQjj9n 388mZq2MGbxbXo/JDAiMNYl2xFbuFwZ6MfwiabWH2SLUw+RV3MavwrzHrv8N1MCb FJUyqUzeQaENSuImLOnvOoTFyNvoisGvlO2OMM8GbHLnYC4jKZKPxQFSRiUNCeXa wcVwxJub9jPQTIuk3jDS3+liUyjqGRSI6VuBCGctEDLVCvGO5TZnCcRUW18VESOX HIfYF7gXDsebx1/bfBYqvJrgpy5peMUlKKMbiRx9VKMoJ/d5b6+VpWZanZFwQOP1 LfXIALkmNWql2TgB3GAgBpd6opCEk14o2CT5OX287L3Xrfu7rczcxhvclxG0lZf3 QnK5hgmzm1k= =hV00 -----END PGP SIGNATURE----- gpgv: Signature made Fri Oct 15 13:43:15 2021 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify signature ./primer3_2.5.0-1.dsc dpkg-source: info: extracting primer3 in /<> dpkg-source: info: unpacking primer3_2.5.0.orig.tar.gz dpkg-source: info: unpacking primer3_2.5.0-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening.patch dpkg-source: info: applying primer_thermodynamic_parameters_path_2_etc.patch dpkg-source: info: applying p3test_fix_exit_status.patch dpkg-source: info: applying set_prefix.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-24051775 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-24051775 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-24051775 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 -b -rfakeroot dpkg-buildpackage: info: source package primer3 dpkg-buildpackage: info: source version 2.5.0-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j4 clean make[1]: Entering directory '/<>/src' no windows rm -f *.o primer3_core ntdpal ntthal oligotm long_seq_tm_test primer3_masker *~ libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libmasker.a libprimer3.so.1.0.0 libdpal.a.so.1.0.0 libthal.a.so.1.0.0 libthalpara.a.so.1.0.0 liboligotm.so.1.2.0 libmasker.a.so.1.0.0 example.for example.rev example.int core ../*~ cd ../test/; make clean make[2]: Entering directory '/<>/test' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. echo; echo; echo 'CLEAN UP TEST DIRECTORIES'; echo; echo; CLEAN UP TEST DIRECTORIES rm -rf primer_list_tmp/* rm -rf primer1_list_tmp/* rm -rf primer1_th_list_tmp/* rm -rf th-w-other-tasks_list_tmp/* rm -f primer_global_err/*.tmp primer_global_err/*.tmp2 primer_global_err/*.bak rm -f *.tmp *.bak *.tmp.err *~ rm -f hyb_probe_only.for hyb_probe_only.int rm -f right_only.for right_only.rev left_only.for rm -f pcr_primers_and_io.int pcr_primers_and_io.rev pcr_primers_and_io.for rm -f pcr_primers.rev pcr_primers.for rm -f pick_primer_list_and_file_flag_th_[1-4].for pick_primer_list_and_file_flag_th_[1-4].rev rm -f pick_primer_list_and_file_flag_th_[1-4].int rm -f syntax[0-1][0-9].for syntax[0-1][0-9].int syntax[0-1][0-9].rev rm -f oligotm.*.valg # valgrind output from oligotm_test.pl --valgrind rm -f ntdpal.*.valg # valgrind output from dpal_test.pl --valgrind rm -f ntthal.*.valg # valgrind output from thal_test.pl --valgrind rm -f masker.*.valg # valgrind output from thal_test.pl --valgrind rm -f oligotm.*.valg.* # valgrind output from oligotm_test.pl --valgrind rm -f ntdpal.*.valg.* # valgrind output from dpal_test.pl --valgrind rm -f ntthal.*.valg.* # valgrind output from thal_test.pl --valgrind rm -f masker.*.valg.* # valgrind output from masker_test.pl --valgrind rm -f *.vg */*.vg # valgrind output from p3test{,z}.pl --valgrind rm -f *.vg.core.* # core files from crashed valgrind test rm -f ./core # in case we crashed and left a core file make[2]: Leaving directory '/<>/test' make[1]: Leaving directory '/<>/src' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- 'CPP=$(CXX)' cd src && make -j4 "INSTALL=install --strip-program=true" CPP=\$\(CXX\) make[2]: Entering directory '/<>/src' no windows gcc -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 primer3_boulder_main.c gcc -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -o format_output.o format_output.c gcc -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -o read_boulder.o read_boulder.c gcc -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -o print_boulder.o print_boulder.c g++ -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -std=c++11 -o libprimer3.o libprimer3.cc gcc -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -o p3_seq_lib.o p3_seq_lib.c gcc -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -o dpal_primer.o dpal.c gcc -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -ffloat-store -o thal_primer.o thal.c gcc -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -ffloat-store -o thal_parameters.o thal_parameters.c gcc -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o oligotm.o oligotm.c gcc -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 masker.c gcc -c -g -Wall -o ntdpal_main.o ntdpal_main.c gcc -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -o dpal.o dpal.c gcc -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -o thal_main.o thal_main.c gcc -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -ffloat-store -o thal.o thal.c gcc -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o -lm ar rv libdpal.a dpal_primer.o ar: creating libdpal.a a - dpal_primer.o ranlib libdpal.a ar rv libthalpara.a thal_parameters.o ar: creating libthalpara.a a - thal_parameters.o ranlib libthalpara.a ar rv liboligotm.a oligotm.o ar: creating liboligotm.a a - oligotm.o ranlib liboligotm.a ar rv libmasker.a masker.o ar: creating libmasker.a a - masker.o ranlib libmasker.a gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -o ntdpal ntdpal_main.o dpal.o gcc -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -o oligotm oligotm_main.c liboligotm.a -lm ar rv libthal.a thal_primer.o ar: creating libthal.a a - thal_primer.o ranlib libthal.a ar rv libprimer3.a libprimer3.o p3_seq_lib.o ar: creating libprimer3.a a - libprimer3.o a - p3_seq_lib.o ranlib libprimer3.a g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -std=c++11 -lstdc++ -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -o primer3_core primer3_boulder_main.o format_output.o read_boulder.o print_boulder.o libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libmasker.a -lm g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -std=c++11 -lstdc++ -o primer3_masker masker_main.c libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libmasker.a -lm gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -g -o ntthal thal_main.o thal.o thal_parameters.o -lm make[2]: Leaving directory '/<>/src' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' dh_auto_test --sourcedirectory=test cd test && make -j4 test make[2]: Entering directory '/<>/test' cd ../src; make perl cmdline_test.pl perl oligotm_test.pl echo; echo; echo 'TESTING ALIGNMENT CALCS'; echo; perl dpal_test.pl ; TESTING ALIGNMENT CALCS make[3]: Entering directory '/<>/src' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. no windows make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/<>/src' echo; echo; echo 'TESTING THERMODYNAMIC ALIGNMENT CALCS'; echo; perl thal_test.pl ; TESTING THERMODYNAMIC ALIGNMENT CALCS TESTING Tm CALCULATIONS Tm tests nr 1-Error handling of too-long sequence...[OK] Default implementations + alignment... TESTING command line arguments Test 1... Error handling of too-long sequence... [OK] Test 2... 1................................... [OK] Default implementations + alignment...[OK] Test 3... [OK] Test 4... [OK] Test 5... [OK] Passed all tests - [OK] echo; echo; echo 'TESTING MASKER'; echo; perl masker_test.pl ; TESTING MASKER 50: [OK] echo; echo; echo 'TESTING primer3_core'; echo; perl p3test.pl TESTING primer3_core Default implementations...mkdir: ../test/primer_list_tmp mkdir: ../test/primer1_list_tmp mkdir: ../test/primer1_th_list_tmp mkdir: ../test/th-w-other-tasks_list_tmp p3test.pl for primer3_core version 2.5.0 p3test.pl: testing ../src/primer3_core START, Thu Jun 23 09:45:48 2022 testing fatal errors... ./primer_global_err/bad_divalent_dntp_conc_1 Testing --output and --error flags on ../src/primer3_core --strict_tags ./primer_global_err/bad_divalent_dntp_conc_1.in --output ./primer_global_err/bad_divalent_dntp_conc_1.tmp --error ./primer_global_err/bad_divalent_dntp_conc_1.tmp2 ./primer_global_err/bad_divalent_dntp_conc_2 ./primer_global_err/bad_divalent_dntp_conc_3 ./primer_global_err/bad_divalent_dntp_conc_4 ./primer_global_err/bad_dna_conc ./primer_global_err/bad_first_base_index ./primer_global_err/bad_float_1 ./primer_global_err/bad_float_2 ./primer_global_err/bad_float_3 ./primer_global_err/bad_float_4 ./primer_global_err/bad_gc_1 ./primer_global_err/bad_gc_2 ./primer_global_err/bad_gc_3 ./primer_global_err/bad_gc_int_1 ./primer_global_err/bad_gc_int_2 ./primer_global_err/bad_gc_int_3 ./primer_global_err/bad_min_three_prime_distance ./primer_global_err/bad_num_ns ./primer_global_err/bad_num_ns_int ./primer_global_err/bad_product_sizes_1 ./primer_global_err/bad_product_sizes_2 ./primer_global_err/bad_product_sizes_3 ./primer_global_err/bad_product_sizes_4 ./primer_global_err/bad_salt_conc ./primer_global_err/bad_self_any ./primer_global_err/bad_self_any_int ./primer_global_err/bad_self_end ./primer_global_err/bad_self_end_int ./primer_global_err/bad_settings0 ./primer_global_err/bad_settings1 ./primer_global_err/bad_settings2 ./primer_global_err/bad_settings3 ./primer_global_err/bad_settings4 ./primer_global_err/bad_settings5 ./primer_global_err/bad_settings6 ./primer_global_err/empty_1 ./primer_global_err/empty_product_size ./primer_global_err/gc_clamp_min_size ./primer_global_err/incorrect_task ./primer_global_err/io_gc_content_obj_fn ./primer_global_err/io_obj_fn ./primer_global_err/junction_overlap_max_size ./primer_global_err/junction_overlap_min_size ./primer_global_err/max_min_tm ./primer_global_err/max_min_tm_int ./primer_global_err/max_opt_tm ./primer_global_err/max_opt_tm_int ./primer_global_err/MAX_PRIMER_LENGTH [OK] ./primer_global_err/max_size_limit_int ./primer_global_err/max_size_min_product ./primer_global_err/max_size_min_product_int ./primer_global_err/min_opt_tm ./primer_global_err/min_opt_tm_int ./primer_global_err/mishyb_obj_fn ./primer_global_err/mispr_obj_fn ./primer_global_err/must_match_length_0 ./primer_global_err/must_match_length_1 ./primer_global_err/must_match_length_10 ./primer_global_err/must_match_length_2 ./primer_global_err/must_match_length_3 ./primer_global_err/must_match_length_4 ./primer_global_err/must_match_length_5 ./primer_global_err/must_match_length_6 ./primer_global_err/must_match_length_7 ./primer_global_err/must_match_length_8 ./primer_global_err/must_match_length_9 ./primer_global_err/no_equal ./primer_global_err/no_terminal_equal ./primer_global_err/opt_max_size ./primer_global_err/opt_max_size_int ./primer_global_err/opt_min_size ./primer_global_err/opt_min_size_int ./primer_global_err/pair_mispr ./primer_global_err/pr_gc_content_obj_fn ./primer_global_err/product_size_obj_fn ./primer_global_err/product_tm_obj_fn ./primer_global_err/repeat_lib_err ./primer_global_err/repeat_lib_err1 ./primer_global_err/repeat_lib_err2 ./primer_global_err/repeat_lib_err3 ./primer_global_err/repeat_lib_err4 ./primer_global_err/repeat_lib_err5 ./primer_global_err/repeat_lib_err6 ./primer_global_err/repeat_lib_int_err ./primer_global_err/repeat_lib_int_err1 ./primer_global_err/repeat_lib_int_err2 ./primer_global_err/repeat_lib_int_err3 ./primer_global_err/repeat_lib_int_err4 ./primer_global_err/repeat_lib_int_err5 ./primer_global_err/repeat_lib_int_err6 ./primer_global_err/seq_quality1 ./primer_global_err/seq_quality2 ./primer_global_err/seq_quality3 ./primer_global_err/seq_quality4 ./primer_global_err/too_many_product_sizes ./primer_global_err/zero_min_size ./primer_global_err/zero_num_return [OK] primer_must_use_th...0s [OK] primer_sec_struct_dpal...0s [OK] primer_task_th...[OK] Default implementations + NO alignment 1...[OK] Default implementations + NO alignment 1...[OK] Default implementations + NO alignment 2...[OK] Force _dpal_generic...1s [OK] primer_thal_args...0s [OK] primer_thal_max_seq_error...[OK] Force _dpal_long_nopath_generic 1...[OK] Default implementations + NO alignment 2...0s [OK] primer_first_base_index...0s [OK] primer_must_match...0s [OK] primer_masker...[OK] [OK] Force _dpal_long_nopath_generic 2...[OK] Force long maxgap1 functions 1...[OK] Force long maxgap1 functions 2...[OK] 2s [OK] primer_masker_formatted...2s [OK] test_compl_error...0s [OK] test_left_to_right_of_right...0s [OK] dv_conc_vs_dntp_conc...0s [OK] primer_boundary...0s [OK] primer_boundary1...0s [OK] primer_boundary_formatted...0s [OK] primer_boundary1_formatted...0s [OK] primer3_v1_1_4_default_settings...0s [OK] primer3web_v0_4_0_default_settings...0s [OK] primer3web_v3_0_0_default_settings...1s [OK] primer3web_v4_0_0_default_settings...0s [OK] primer_internal...0s [OK] primer_internal1...0s [OK] primer_internal_formatted...0s [OK] primer_internal1_formatted...0s [OK] primer_ok_regions...0s [OK] primer_ok_regions_formatted...0s [OK] primer_ok_regions2...5s [OK] primer_tm_lc_masking...0s [OK] primer_tm_lc_masking_formatted...0s [OK] primer_start_codon...0s [OK] primer_task...0s [OK] primer_task_formatted...0s [OK] primer_renewed_tasks...0s [OK] primer_new_tasks...1s [OK] primer_new_tasks_formatted...0s [OK] primer_windows_newlines...1s [OK] primer_must_overlap_point...0s [OK] primer_overlap_junction...0s [OK] primer_all_settingsfiles...0s [OK] primer_high_tm_load_set...0s [OK] primer_high_gc_load_set...0s [OK] primer_gc_end...0s [OK] primer_check...0s [OK] primer_must_use...0s [OK] primer_must_use_formatted...0s [OK] primer_syntax...0s [OK] primer_end_pathology...0s [OK] primer_num_best...0s [OK] primer_quality_boundary...0s [OK] primer...1s [OK] primer_list_files...[OK] primer1...0s [OK] primer1_list_files...[OK] primer_mispriming...1s [OK] primer_mispriming_formatted...0s [OK] primer_mispriming_boundary1...0s [OK] primer_mispriming_boundary1_formatted...0s [OK] primer_mispriming_boundary2...0s [OK] primer_mispriming_boundary2_formatted...0s [OK] primer_mispriming_long_lib...0s [OK] primer_rat...1s [OK] primer_human...0s [OK] long_seq...0s [OK] primer_position_penalty...1s [OK] primer_position_penalty_formatted...1s [OK] p3-tmpl-mispriming...0s [OK] primer_three_prime_distance...0s [OK] primer_obj_fn...2s [OK] p3_3_prime_n...0s [OK] primer_masker...1s [OK] primer_masker_formatted...2s [OK] primer_mispriming_th...8s [OK] th-w-other-tasks...13s [OK] th-w-other-tasks_list_files...[OK] primer_new_tasks_th...13s [OK] primer_sec_struct_thal...13s [OK] primer_thermod_align...33s [OK] primer_thermod_align_formatted...33s [OK] primer1_th...84s [OK] primer1_th_list_files...[OK] primer_lib_amb_codes... NOTE: this test takes _much_ longer than the others (5 to 20 minutes or more). starting primer_lib_amb_codes at Thu Jun 23 09:49:29 2022...134s [OK] Tests in p3test.pl ran for 355 s (5.91666666666667 min) DONE Thu Jun 23 09:51:43 2022 Passed all tests - [OK] echo; echo; echo "Testing completed. You must check the test output for the string FAILED"; echo; echo; Testing completed. You must check the test output for the string FAILED make[2]: Leaving directory '/<>/test' dh clean --sourcedirectory=test dh_auto_clean -O--sourcedirectory=test cd test && make -j4 clean make[2]: Entering directory '/<>/test' echo; echo; echo 'CLEAN UP TEST DIRECTORIES'; echo; echo; CLEAN UP TEST DIRECTORIES rm -rf primer_list_tmp/* rm -rf primer1_list_tmp/* rm -rf primer1_th_list_tmp/* rm -rf th-w-other-tasks_list_tmp/* rm -f primer_global_err/*.tmp primer_global_err/*.tmp2 primer_global_err/*.bak rm -f *.tmp *.bak *.tmp.err *~ rm -f hyb_probe_only.for hyb_probe_only.int rm -f right_only.for right_only.rev left_only.for rm -f pcr_primers_and_io.int pcr_primers_and_io.rev pcr_primers_and_io.for rm -f pcr_primers.rev pcr_primers.for rm -f pick_primer_list_and_file_flag_th_[1-4].for pick_primer_list_and_file_flag_th_[1-4].rev rm -f pick_primer_list_and_file_flag_th_[1-4].int rm -f syntax[0-1][0-9].for syntax[0-1][0-9].int syntax[0-1][0-9].rev rm -f oligotm.*.valg # valgrind output from oligotm_test.pl --valgrind rm -f ntdpal.*.valg # valgrind output from dpal_test.pl --valgrind rm -f ntthal.*.valg # valgrind output from thal_test.pl --valgrind rm -f masker.*.valg # valgrind output from thal_test.pl --valgrind rm -f oligotm.*.valg.* # valgrind output from oligotm_test.pl --valgrind rm -f ntdpal.*.valg.* # valgrind output from dpal_test.pl --valgrind rm -f ntthal.*.valg.* # valgrind output from thal_test.pl --valgrind rm -f masker.*.valg.* # valgrind output from masker_test.pl --valgrind rm -f *.vg */*.vg # valgrind output from p3test{,z}.pl --valgrind rm -f *.vg.core.* # core files from crashed valgrind test rm -f ./core # in case we crashed and left a core file make[2]: Leaving directory '/<>/test' dh_autoreconf_clean -O--sourcedirectory=test dh_clean -O--sourcedirectory=test make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install -- PREFIX=debian/primer3/usr cd src && make -j4 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" PREFIX=debian/primer3/usr make[2]: Entering directory '/<>/src' no windows install -d "debian/primer3/usr/bin" install -m 755 primer3_core ntdpal ntthal oligotm long_seq_tm_test primer3_masker "debian/primer3/usr/bin" make[2]: Leaving directory '/<>/src' make[1]: Leaving directory '/<>' dh_install -O--sourcedirectory=src dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src debian/rules override_dh_installexamples make[1]: Entering directory '/<>' dh_installexamples mkdir -p /<>/debian/primer3-examples/usr/share/doc/primer3/examples/test; mkdir -p /<>/debian/primer3-examples/usr/share/doc/primer3/examples/src; mkdir -p /<>/debian/primer3-examples/usr/share/doc/primer3/examples/settings_files; mkdir -p /<>/debian/primer3-examples/usr/share/doc/primer3/examples/kmer_lists; cp -aR ./test/* /<>/debian/primer3-examples/usr/share/doc/primer3/examples/test; cp -aR ./src/humrep_and_simple.txt /<>/debian/primer3-examples/usr/share/doc/primer3/examples/src; cp -a settings_files/primer*.txt /<>/debian/primer3-examples/usr/share/doc/primer3/examples/settings_files; cp -aR ./kmer_lists/*.list /<>/debian/primer3-examples/usr/share/doc/primer3/examples/kmer_lists; chmod -x /<>/debian/primer3-examples/usr/share/doc/primer3/examples/test/thal*; sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' /<>/debian/primer3-examples/usr/share/doc/primer3/examples/test/long_seq_tm_test.pl ; sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' /<>/debian/primer3-examples/usr/share/doc/primer3/examples/test/vgrep.pl ; make[1]: Leaving directory '/<>' dh_installman -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_lintian -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src debugedit: debian/primer3/usr/bin/primer3_core: Unknown DWARF DW_FORM_0x1f20 f896f03ee45375d38b86dddc53f4e8766ee4f3d9 debugedit: debian/primer3/usr/bin/ntthal: Unknown DWARF DW_FORM_0x1f20 771a36f6c1913dea58cd19570f2bd2971de057a9 debugedit: debian/primer3/usr/bin/ntdpal: Unknown DWARF DW_FORM_0x1f20 b29eb07ab12a2aba0e8a37a8b682fc7cc307c899 debugedit: debian/primer3/usr/bin/oligotm: Unknown DWARF DW_FORM_0x1f21 aaa225269b494e4dad444062f507a1980b420269 dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing primer3 (in debian/primer3); do_strip: , oemstrip: pkgstriptranslations: processing primer3-examples (in debian/primer3-examples); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/primer3/DEBIAN/control, package primer3, directory debian/primer3 pkgstripfiles: Truncating usr/share/doc/primer3/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package primer3 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'primer3' in '../primer3_2.5.0-1_amd64.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/primer3-examples/DEBIAN/control, package primer3-examples, directory debian/primer3-examples pkgstripfiles: Truncating usr/share/doc/primer3-examples/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package primer3-examples ... pkgstripfiles: No PNG files. dpkg-deb: building package 'primer3-examples' in '../primer3-examples_2.5.0-1_all.deb'. dpkg-genbuildinfo --build=binary -O../primer3_2.5.0-1_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../primer3_2.5.0-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-06-23T09:53:25Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ primer3_2.5.0-1_amd64.changes: ------------------------------ Format: 1.8 Date: Fri, 15 Oct 2021 15:20:35 +0200 Source: primer3 Binary: primer3 primer3-examples Built-For-Profiles: noudeb Architecture: all amd64 Version: 2.5.0-1 Distribution: kinetic Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: primer3 - tool to design flanking oligo nucleotides for DNA amplification primer3-examples - tool to design flanking oligo nucleotides for DNA amplification ( Changes: primer3 (2.5.0-1) unstable; urgency=medium . * Fix watchfile to detect new versions on github * New upstream version * Standards-Version: 4.6.0 (routine-update) * Apply multi-arch hints. + primer3-examples: Add Multi-Arch: foreign. * Fix PREFIX Checksums-Sha1: b1aa2d38eaad2750d50d1e4d22a0095dff752d40 30808862 primer3-examples_2.5.0-1_all.deb 1f493d0e177a3c00d537739c0ee25035d46f2d67 5833 primer3_2.5.0-1_amd64.buildinfo eb61234cfbb8f714c021587d39e0d04adb2d5f74 206100 primer3_2.5.0-1_amd64.deb Checksums-Sha256: d987f478370adeffab8b046916fe0750cf9ae050d910345912ce0cc4b0f2c983 30808862 primer3-examples_2.5.0-1_all.deb df9d119ea33362ffab31bcc82aef7f32393a01bd18fe055dd89f4e2d60dbe0b8 5833 primer3_2.5.0-1_amd64.buildinfo 7fea7e814614167e968cf8c8654b5016794953c105720925bc1b7626a3fee643 206100 primer3_2.5.0-1_amd64.deb Files: a77c88ad0436a8b261ec4c17ea98f549 30808862 science optional primer3-examples_2.5.0-1_all.deb 2ce961ec0ef8c928507a55298affbe44 5833 science optional primer3_2.5.0-1_amd64.buildinfo 5cdd84dc9581e5b96ad437e424bab8e3 206100 science optional primer3_2.5.0-1_amd64.deb /<>/primer3_2.5.0-1_amd64.changes.new could not be renamed to /<>/primer3_2.5.0-1_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: primer3 Binary: primer3 primer3-examples Architecture: all amd64 Version: 2.5.0-1 Checksums-Md5: a77c88ad0436a8b261ec4c17ea98f549 30808862 primer3-examples_2.5.0-1_all.deb 5cdd84dc9581e5b96ad437e424bab8e3 206100 primer3_2.5.0-1_amd64.deb Checksums-Sha1: b1aa2d38eaad2750d50d1e4d22a0095dff752d40 30808862 primer3-examples_2.5.0-1_all.deb eb61234cfbb8f714c021587d39e0d04adb2d5f74 206100 primer3_2.5.0-1_amd64.deb Checksums-Sha256: d987f478370adeffab8b046916fe0750cf9ae050d910345912ce0cc4b0f2c983 30808862 primer3-examples_2.5.0-1_all.deb 7fea7e814614167e968cf8c8654b5016794953c105720925bc1b7626a3fee643 206100 primer3_2.5.0-1_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Thu, 23 Jun 2022 09:53:25 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-6), autotools-dev (= 20220109.1), base-files (= 12.2ubuntu1), base-passwd (= 3.5.52build1), bash (= 5.1-6ubuntu1), binutils (= 2.38.50.20220615-4ubuntu1), binutils-common (= 2.38.50.20220615-4ubuntu1), binutils-x86-64-linux-gnu (= 2.38.50.20220615-4ubuntu1), bsdextrautils (= 2.38-4ubuntu1), bsdutils (= 1:2.38-4ubuntu1), build-essential (= 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1.4.2-0ubuntu6), sed (= 4.8-1ubuntu2), sensible-utils (= 0.0.17), sysvinit-utils (= 3.01-1ubuntu1), tar (= 1.34+dfsg-1build3), util-linux (= 2.38-4ubuntu1), util-linux-extra (= 2.38-4ubuntu1), xz-utils (= 5.2.5-2.1), zlib1g (= 1:1.2.11.dfsg-2ubuntu9) Environment: DEB_BUILD_OPTIONS="noautodbgsym parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1634304035" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ primer3-examples_2.5.0-1_all.deb -------------------------------- new Debian package, version 2.0. size 30808862 bytes: control archive=14104 bytes. 970 bytes, 21 lines control 64827 bytes, 614 lines md5sums Package: primer3-examples Source: primer3 Version: 2.5.0-1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 31289 Suggests: primer3 Section: science Priority: optional Multi-Arch: foreign Homepage: http://primer3.sourceforge.net Description: tool to design flanking oligo nucleotides for DNA amplification (examples) Primer3 picks primers for Polymerase Chain Reactions (PCRs), considering as criteria oligonucleotide melting temperature, size, GC content and primer-dimer possibilities, PCR product size, positional constraints within the source sequence, and miscellaneous other constraints. All of these criteria are user-specifiable as constraints, and some are specifiable as terms in an objective function that characterizes an optimal primer pair. . This package contains example data to test the package. drwxr-xr-x root/root 0 2021-10-15 13:20 ./ drwxr-xr-x root/root 0 2021-10-15 13:20 ./usr/ drwxr-xr-x root/root 0 2021-10-15 13:20 ./usr/share/ drwxr-xr-x root/root 0 2021-10-15 13:20 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-10-15 13:20 ./usr/share/doc/primer3-examples/ -rw-r--r-- root/root 1538 2021-10-15 13:20 ./usr/share/doc/primer3-examples/changelog.Debian.gz -rw-r--r-- root/root 2606 2021-10-15 13:20 ./usr/share/doc/primer3-examples/copyright drwxr-xr-x root/root 0 2021-10-15 13:20 ./usr/share/doc/primer3/ drwxr-xr-x root/root 0 2021-10-15 13:20 ./usr/share/doc/primer3/examples/ drwxr-xr-x root/root 0 2021-10-15 13:20 ./usr/share/doc/primer3/examples/kmer_lists/ -rw-r--r-- root/root 3444035 2019-08-17 03:54 ./usr/share/doc/primer3/examples/kmer_lists/homo_sapiens_11.list.gz -rw-r--r-- root/root 17889591 2019-08-17 03:54 ./usr/share/doc/primer3/examples/kmer_lists/homo_sapiens_16.list.gz -rw-r--r-- root/root 6792750 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drwxr-xr-x root/root 0 2021-10-15 13:20 ./usr/share/doc/primer3/examples/test/ -rw-r--r-- root/root 1964 2019-08-17 03:54 ./usr/share/doc/primer3/examples/test/Makefile.gz -rw-r--r-- root/root 2160 2019-08-17 03:54 ./usr/share/doc/primer3/examples/test/cmd_test3_output -rw-r--r-- root/root 33 2019-08-17 03:54 ./usr/share/doc/primer3/examples/test/cmd_test4_output -rw-r--r-- root/root 2160 2019-08-17 03:54 ./usr/share/doc/primer3/examples/test/cmd_test5_output -rw-r--r-- root/root 4249 2019-08-17 03:54 ./usr/share/doc/primer3/examples/test/cmdline_test.pl.gz -rw-r--r-- root/root 1147 2019-08-17 03:54 ./usr/share/doc/primer3/examples/test/dpal_input.gz -rw-r--r-- root/root 974 2019-08-17 03:54 ./usr/share/doc/primer3/examples/test/dpal_long_input.gz -rw-r--r-- root/root 65 2019-08-17 03:54 ./usr/share/doc/primer3/examples/test/dpal_long_score_output -rw-r--r-- root/root 1320 2019-08-17 03:54 ./usr/share/doc/primer3/examples/test/dpal_output.gz -rw-r--r-- root/root 1754 2019-08-17 03:54 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drwxr-xr-x root/root 0 2021-10-15 13:20 ./usr/share/lintian/ drwxr-xr-x root/root 0 2021-10-15 13:20 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 137 2021-10-15 13:20 ./usr/share/lintian/overrides/primer3-examples primer3_2.5.0-1_amd64.deb ------------------------- new Debian package, version 2.0. size 206100 bytes: control archive=1373 bytes. 1387 bytes, 34 lines conffiles 938 bytes, 19 lines control 981 bytes, 15 lines md5sums Package: primer3 Version: 2.5.0-1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 735 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libstdc++6 (>= 11) Suggests: ncbi-epcr Enhances: emboss Section: science Priority: optional Homepage: http://primer3.sourceforge.net Description: tool to design flanking oligo nucleotides for DNA amplification Primer3 picks primers for Polymerase Chain Reactions (PCRs), considering as criteria oligonucleotide melting temperature, size, GC content and primer-dimer possibilities, PCR product size, positional constraints within the source sequence, and miscellaneous other constraints. 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+------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 210016 Build-Time: 466 Distribution: kinetic Host Architecture: amd64 Install-Time: 5 Job: primer3_2.5.0-1.dsc Machine Architecture: amd64 Package: primer3 Package-Time: 472 Source-Version: 2.5.0-1 Space: 210016 Status: successful Version: 2.5.0-1 -------------------------------------------------------------------------------- Finished at 2022-06-23T09:53:25Z Build needed 00:07:52, 210016k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24051775 Scanning for processes to kill in build PACKAGEBUILD-24051775