Running as unit: rb-build-arm64_11-114729.service ==================================================================================== Wed Jul 30 02:05:04 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_11) on jenkins, called using "codethink04-arm64 codethink03-arm64" as arguments. Wed Jul 30 02:05:04 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-TKqoJ53f" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Jul 30 02:05:04 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Wed Jul 30 02:05:04 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-DA9r98' Wed Jul 30 02:05:05 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Wed Jul 30 02:05:05 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-KmE9eQ' ok, let's check if hmmer2 is building anywhere yet… ok, hmmer2 is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of hmmer2 in unstable on arm64 on jenkins now. 1st build will be done on codethink04-arm64.debian.net. 2nd build will be done on codethink03-arm64.debian.net. ============================================================================= Wed Jul 30 02:05:22 UTC 2025 I: starting to build hmmer2/unstable/arm64 on jenkins on '2025-07-30 02:05' Wed Jul 30 02:05:22 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_11/114729/console.log 1753841122 arm64 unstable hmmer2 Wed Jul 30 02:05:22 UTC 2025 I: Downloading source for unstable/hmmer2=2.3.2+dfsg-12 --2025-07-30 02:05:22-- http://deb.debian.org/debian/pool/main/h/hmmer2/hmmer2_2.3.2%2bdfsg-12.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2236 (2.2K) [text/prs.lines.tag] Saving to: ‘hmmer2_2.3.2+dfsg-12.dsc’ 0K .. 100% 275M=0s 2025-07-30 02:05:22 (275 MB/s) - ‘hmmer2_2.3.2+dfsg-12.dsc’ saved [2236/2236] --2025-07-30 02:05:22-- http://deb.debian.org/debian/pool/main/h/hmmer2/hmmer2_2.3.2%2bdfsg-12.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2236 (2.2K) [text/prs.lines.tag] Saving to: ‘hmmer2_2.3.2+dfsg-12.dsc’ 0K .. 100% 275M=0s 2025-07-30 02:05:22 (275 MB/s) - ‘hmmer2_2.3.2+dfsg-12.dsc’ saved [2236/2236] Wed Jul 30 02:05:22 UTC 2025 I: hmmer2_2.3.2+dfsg-12.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: hmmer2 Binary: hmmer2, hmmer2-doc, libhmmer2-dev Architecture: any all Version: 2.3.2+dfsg-12 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://hmmer.janelia.org/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/hmmer2 Vcs-Git: https://salsa.debian.org/med-team/hmmer2.git Testsuite: autopkgtest Testsuite-Triggers: build-essential, libperl4-corelibs-perl, libsquid-dev, pkg-config Build-Depends: debhelper-compat (= 13), libperl4-corelibs-perl, libsquid-dev, pkgconf, dh-exec, rename Package-List: hmmer2 deb science optional arch=any hmmer2-doc deb doc optional arch=all libhmmer2-dev deb libdevel optional arch=any Checksums-Sha1: 7467176def6174e90edd239558b6fcc2cb8033df 331828 hmmer2_2.3.2+dfsg.orig.tar.xz 062cd885dfd33766c3303b641a9fd2ad123990c4 21136 hmmer2_2.3.2+dfsg-12.debian.tar.xz Checksums-Sha256: f9cd50acc23743648cb7de020c249bce396c3d07e0afe7e5418620cffa07bb44 331828 hmmer2_2.3.2+dfsg.orig.tar.xz 1dd6e7702c9a6540fd8a3b53d535c98e822a7dfdbc76388f81b0cdc731e42f2a 21136 hmmer2_2.3.2+dfsg-12.debian.tar.xz Files: 4f8c9fd7c7de00fb8cfab499931ee4ba 331828 hmmer2_2.3.2+dfsg.orig.tar.xz 5d8ec6eb7213aa0fc5ec00a3be5af26b 21136 hmmer2_2.3.2+dfsg-12.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmYXp30RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtH0rQ/+Nx0cD07oRQUQX/qMb9hbDYgoC5X3s6BG t7cMJgk6/qDEClluc58uQZSVDYFLr2NDaWWf6Avh5vcwGsgiimmU99tV4eu2B2tT 5s7zx6HwEOHLtdsYDGJnPpuNUhiE1wOvzXcabZ9t8PpCRe3ZUkFkmyvSsPXrMdtX SZapCF6fbBB2AG/5JVCYJxrb4BLBxffeLl0/7YsxFaLi0Hm9k49yB9w5K7FTn+9G EmvpkpT0rHVlalEIcZNsHJ8DIfPAcN9DKRL+FxDgh1Z0TNRVQdZ7kS/72QdloAzS QPml++aDp4iI6H0s1RDHfGqJ3d5Ootz/aDktgPUmHH84+WCtTHQkQrJQuQpRfS9i UeORZNpEOpezcVR8aaYlDQTx42O+oeKC3OCYZRZkgEu64uH6zlqRijA1bfUCy/NS UglYqpYqppQBMmUDTy0d3DFk92mSM0EyWz/bN8ton0oyYXwdmjF/Jp774gZLJ5Yw xG7exdw2efasNYcMklZQ2lbrX0ClYu5mC2A+zpuGNL1TnCn3hLNh6Lx1uwZuG4xz 98NPhg6ttguogyizeEpEedDzxwUIhsDWnyr126PIynIIXj0PluqnLI2MKtwfGU6z KRFdTbBUpn83qmm7AHQWGQ0dihSVqgFne4IhuyQ4f93INpqxYKwFtDcBR8veJy8+ P8gYNfTK1/w= =SERy -----END PGP SIGNATURE----- Wed Jul 30 02:05:22 UTC 2025 I: Checking whether the package is not for us Wed Jul 30 02:05:22 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Wed Jul 30 02:05:22 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Wed Jul 30 02:05:22 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Wed Jul 30 02:05:22 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-Szukqf' ==================================================================================== Wed Jul 30 02:05:26 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "1 hmmer2 unstable /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I 2.3.2+dfsg-12" as arguments. Wed Jul 30 02:05:26 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-hbwoqqhx" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Jul 30 02:05:26 UTC 2025 I: Downloading source for unstable/hmmer2=2.3.2+dfsg-12 Reading package lists... NOTICE: 'hmmer2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/hmmer2.git Please use: git clone https://salsa.debian.org/med-team/hmmer2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 355 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main hmmer2 2.3.2+dfsg-12 (dsc) [2236 B] Get:2 http://deb.debian.org/debian unstable/main hmmer2 2.3.2+dfsg-12 (tar) [332 kB] Get:3 http://deb.debian.org/debian unstable/main hmmer2 2.3.2+dfsg-12 (diff) [21.1 kB] Fetched 355 kB in 0s (2623 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'hmmer2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/hmmer2.git Please use: git clone https://salsa.debian.org/med-team/hmmer2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 355 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main hmmer2 2.3.2+dfsg-12 (dsc) [2236 B] Get:2 http://deb.debian.org/debian unstable/main hmmer2 2.3.2+dfsg-12 (tar) [332 kB] Get:3 http://deb.debian.org/debian unstable/main hmmer2 2.3.2+dfsg-12 (diff) [21.1 kB] Fetched 355 kB in 0s (2623 kB/s) Download complete and in download only mode ============================================================================= Building hmmer2 in unstable on arm64 on codethink04-arm64 now. Date: Wed Jul 30 03:05:26 BST 2025 Date UTC: Wed Jul 30 02:05:26 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Tue Jul 29 14:05:27 -12 2025 I: pbuilder-time-stamp: 1753841127 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [hmmer2_2.3.2+dfsg-12.dsc] I: copying [./hmmer2_2.3.2+dfsg.orig.tar.xz] I: copying [./hmmer2_2.3.2+dfsg-12.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./hmmer2_2.3.2+dfsg-12.dsc: no acceptable signature found dpkg-source: info: extracting hmmer2 in hmmer2-2.3.2+dfsg dpkg-source: info: unpacking hmmer2_2.3.2+dfsg.orig.tar.xz dpkg-source: info: unpacking hmmer2_2.3.2+dfsg-12.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying version2-manpage dpkg-source: info: applying userguidepdf dpkg-source: info: applying spelling.patch dpkg-source: info: applying use_debian_packaged_biosquid.patch dpkg-source: info: applying build_libhmmer.a_with-fPIC.patch dpkg-source: info: applying add-runstatedir-option.patch dpkg-source: info: applying fixup-implicit-function-declaration.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2487435/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='d6b233b322b04cdebc76085320d382ca' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2487435' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/pbuilderrc_5LGK --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/b1 --logfile b1/build.log hmmer2_2.3.2+dfsg-12.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2487435/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libperl4-corelibs-perl, libsquid-dev, pkgconf, dh-exec, rename dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19963 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libperl4-corelibs-perl; however: Package libperl4-corelibs-perl is not installed. pbuilder-satisfydepends-dummy depends on libsquid-dev; however: Package libsquid-dev is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on dh-exec; however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on rename; however: Package rename is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libmagic-mgc{a} libmagic1t64{a} libperl4-corelibs-perl{a} libpipeline1{a} libpkgconf3{a} libsquid-dev{a} libsquid1t64{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} rename{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 37 newly installed, 0 to remove and 0 not upgraded. Need to get 11.4 MB of archives. After unpacking 46.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2 [241 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41-5 [93.8 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-2.1 [630 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2 [1611 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.2 [919 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 dh-exec arm64 0.30+b1 [25.8 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libperl4-corelibs-perl all 0.005-1 [39.0 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libsquid1t64 arm64 1.9g+cvs20050121-15.1+b2 [71.4 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libsquid-dev arm64 1.9g+cvs20050121-15.1+b2 [141 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 rename all 2.02-1 [21.8 kB] Fetched 11.4 MB in 0s (39.3 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19963 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2_arm64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_arm64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41-5_arm64.deb ... Unpacking bsdextrautils (2.41-5) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_arm64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-8_arm64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../23-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-2.1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-2.1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2_arm64.deb ... Unpacking gettext (0.23.1-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Selecting previously unselected package dh-exec. Preparing to unpack .../29-dh-exec_0.30+b1_arm64.deb ... Unpacking dh-exec (0.30+b1) ... Selecting previously unselected package libperl4-corelibs-perl. Preparing to unpack .../30-libperl4-corelibs-perl_0.005-1_all.deb ... Unpacking libperl4-corelibs-perl (0.005-1) ... Selecting previously unselected package libpkgconf3:arm64. Preparing to unpack .../31-libpkgconf3_1.8.1-4_arm64.deb ... Unpacking libpkgconf3:arm64 (1.8.1-4) ... Selecting previously unselected package libsquid1t64:arm64. Preparing to unpack .../32-libsquid1t64_1.9g+cvs20050121-15.1+b2_arm64.deb ... Unpacking libsquid1t64:arm64 (1.9g+cvs20050121-15.1+b2) ... Selecting previously unselected package libsquid-dev. Preparing to unpack .../33-libsquid-dev_1.9g+cvs20050121-15.1+b2_arm64.deb ... Unpacking libsquid-dev (1.9g+cvs20050121-15.1+b2) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../34-pkgconf-bin_1.8.1-4_arm64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../35-pkgconf_1.8.1-4_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-4) ... Selecting previously unselected package rename. Preparing to unpack .../36-rename_2.02-1_all.deb ... Unpacking rename (2.02-1) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up bsdextrautils (2.41-5) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libperl4-corelibs-perl (0.005-1) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up rename (2.02-1) ... update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20240727.1) ... Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-2.1) ... Setting up libsquid1t64:arm64 (1.9g+cvs20050121-15.1+b2) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2) ... Setting up libtool (2.5.4-4) ... Setting up libsquid-dev (1.9g+cvs20050121-15.1+b2) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.2) ... Setting up dh-exec (0.30+b1) ... Processing triggers for libc-bin (2.41-11) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/hmmer2-2.3.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../hmmer2_2.3.2+dfsg-12_source.changes dpkg-buildpackage: info: source package hmmer2 dpkg-buildpackage: info: source version 2.3.2+dfsg-12 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' dh_clean if [ -e configure_not_used ] ; then mv configure_not_used configure; fi rm -f configure.ac src/config.h make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' cp -a debian/missing-sources/configure.ac . mv configure configure_not_used dh_autoreconf configure.ac:119: warning: underquoted definition of CHECK_GNU_MAKE configure.ac:119: run info Automake 'Extending aclocal' configure.ac:119: or see https://www.gnu.org/software/automake/manual/automake.html#Extending-aclocal configure.ac:161: warning: The macro 'AC_TRY_COMPILE' is obsolete. configure.ac:161: You should run autoupdate. ./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from... configure.ac:161: the top level configure.ac:487: warning: The macro 'AC_LANG_C' is obsolete. configure.ac:487: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... configure.ac:289: ACX_PTHREAD is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:487: the top level configure.ac:487: warning: The macro 'AC_TRY_LINK' is obsolete. configure.ac:487: You should run autoupdate. ./lib/autoconf/general.m4:2918: AC_TRY_LINK is expanded from... configure.ac:289: ACX_PTHREAD is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:487: the top level make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' dh_auto_configure -- --enable-threads --enable-lfs PTHREAD_CFLAGS="-D_XOPEN_SOURCE=500" # --enable-pvm ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-threads --enable-lfs PTHREAD_CFLAGS=-D_XOPEN_SOURCE=500 configure: configuring HMMER for your system. configure: This is a full source distribution - using full config checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for ranlib... ranlib checking for ar... /usr/bin/ar checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking whether your make is GNU make... yes, it is. configure: configured for optional LFS, large file support configure: enabled POSIX multithreading support checking for pthread_setconcurrency... yes checking for pthread_attr_setscope... yes checking for pthread_join in LIBS= with CFLAGS=-D_XOPEN_SOURCE=500... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for ntohs... yes checking for ntohl... yes checking for htons... yes checking for htonl... yes configure: creating ./config.status config.status: creating src/Makefile config.status: creating testsuite/Makefile config.status: creating Makefile config.status: WARNING: 'Makefile.in' seems to ignore the --datarootdir setting config.status: creating src/config.h # avoid duplicated definition of PACKAGE_NAME (basically conflicting with biosquid when used together) sed -i -e '/^#define PACKAGE_NAME /i #ifndef PACKAGE_NAME' \ -e '/^#define PACKAGE_NAME /a #endif' \ -e '/^#define PACKAGE_VERSION /i #ifndef PACKAGE_VERSION' \ -e '/^#define PACKAGE_VERSION /a #endif' \ -e '/^#define _LARGEFILE_SOURCE /i #ifndef _LARGEFILE_SOURCE' \ -e '/^#define _LARGEFILE_SOURCE /a #endif' \ -e '/^#define _LARGEFILE64_SOURCE /i #ifndef _LARGEFILE64_SOURCE' \ -e '/^#define _LARGEFILE64_SOURCE /a #endif' \ -e '/^#define VERSION /i #ifndef VERSION' \ -e '/^#define VERSION /a #endif' \ src/config.h make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/src' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmalign.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c alphabet.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c core_algorithms.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c debug.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c display.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c emit.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c emulation.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c fast_algorithms.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c histogram.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmio.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c mathsupport.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c masks.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c misc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c modelmakers.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c plan7.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c plan9.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c postprob.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c prior.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c pvm.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c threads.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c tophits.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c trace.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmbuild.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmcalibrate.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmconvert.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmemit.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmfetch.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmindex.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmpfam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmsearch.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmalign hmmalign.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmbuild hmmbuild.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmcalibrate hmmcalibrate.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmconvert hmmconvert.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmemit hmmemit.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmfetch hmmfetch.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmindex hmmindex.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmpfam hmmpfam.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmsearch hmmsearch.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/src' make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/src' /usr/bin/ar rcv libhmmer.a alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o a - alphabet.o a - core_algorithms.o a - debug.o a - display.o a - emit.o a - emulation.o a - fast_algorithms.o a - histogram.o a - hmmio.o a - mathsupport.o a - masks.o a - misc.o a - modelmakers.o a - plan7.o a - plan9.o a - postprob.o a - prior.o a - pvm.o a - threads.o a - tophits.o a - trace.o ranlib libhmmer.a chmod 644 libhmmer.a make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/src' make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c alignalign_test.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c evd_test.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c masks_test.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c parsingviterbi_test.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c tophits_test.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c trace_test.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c viterbi_exercise.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c weeviterbi_test.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o trace_test -L../src trace_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o masks_test -L../src masks_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o parsingviterbi_test -L../src parsingviterbi_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o viterbi_exercise -L../src viterbi_exercise.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o weeviterbi_test -L../src weeviterbi_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o alignalign_test -L../src alignalign_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o tophits_test -L../src tophits_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o evd_test -L../src evd_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite' make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' dh_auto_test make -j12 check "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' (cd testsuite; make check) make[3]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite' Running test suite exercises. Warning: some tests may take several minutes to complete. ./sqc 2 exercises.sqc . ../src exercise 1 [ hmmalign] ... ok. exercise 2 [ hmmalign/h] ... ok. exercise 3 [ hmmalign/m] ... ok. exercise 4 [ hmmalign/o] ... ok. exercise 5 [ hmmalign/q] ... ok. exercise 6 [ hmmalign/informat] ... ok. exercise 7 [ hmmalign/selex] ... ok. exercise 8 [ hmmalign/a2m] ... ok. exercise 9 [ hmmalign/clustal] ... ok. exercise 10 [ hmmalign/msf] ... ok. exercise 11 [ hmmalign/phylip] ... ok. exercise 12 [ hmmalign/oneline] ... ok. exercise 13 [ hmmalign/withali] ... ok. exercise 14 [ hmmalign/mapali] ... ok. exercise 15 [ hmmbuild] ... ok. exercise 16 [ hmmbuild/h] ... ok. exercise 17 [ hmmbuild/F] ... ok. exercise 18 [ hmmbuild/n] ... ok. exercise 19 [ hmmbuild/o] ... ok. exercise 20 [ hmmbuild/A] ... ok. exercise 21 [ hmmbuild/f] ... ok. exercise 22 [ hmmbuild/g] ... ok. exercise 23 [ hmmbuild/s] ... ok. exercise 24 [ hmmbuild/fast] ... ok. exercise 25 [ hmmbuild/hand] ... ok. exercise 26 [ hmmbuild/null] ... ok. exercise 27 [ hmmbuild/pam] ... ok. exercise 28 [ hmmbuild/prior] ... ok. exercise 29 [ hmmbuild/wblosum] ... ok. exercise 30 [ hmmbuild/wgsc] ... ok. exercise 31 [ hmmbuild/wme] ... ok. exercise 32 [ hmmbuild/wpb] ... ok. exercise 33 [ hmmbuild/wvoronoi] ... ok. exercise 34 [ hmmbuild/wnone] ... ok. exercise 35 [ hmmbuild/noeff] ... ok. exercise 36 [ hmmbuild/pbswitch] ... ok. exercise 37 [ hmmbuild/amino] ... ok. exercise 38 [ hmmbuild/nucleic] ... ok. exercise 39 [ hmmbuild/archpri] ... ok. exercise 40 [ hmmbuild/binary] ... ok. exercise 41 [ hmmbuild/cfile] ... ok. exercise 42 [ hmmbuild/gapmax] ... ok. exercise 43 [ hmmbuild/idlevel] ... ok. exercise 44 [ hmmbuild/informat] ... ok. exercise 45 [ hmmbuild/pamwgt] ... ok. exercise 46 [ hmmbuild/swentry] ... ok. exercise 47 [ hmmbuild/swexit] ... ok. exercise 48 [ hmmbuild/verbose] ... ok. exercise 49 [ hmmcalibrate] ... ok. exercise 50 [ hmmcalibrate/h] ... ok. exercise 51 [ hmmcalibrate/fixed] ... ok. exercise 52 [ hmmcalibrate/mean] ... ok. exercise 53 [ hmmcalibrate/hist] ... ok. exercise 54 [ hmmcalibrate/num] ... ok. exercise 55 [ hmmcalibrate/sd] ... ok. exercise 56 [ hmmcalibrate/seed] ... ok. exercise 57 [ hmmconvert] ... ok. exercise 58 [ hmmconvert/h] ... ok. exercise 59 [ hmmconvert/F] ... ok. exercise 60 [ hmmconvert/a] ... ok. exercise 61 [ hmmconvert/A] ... ok. exercise 62 [ hmmconvert/b] ... ok. exercise 63 [ hmmconvert/p] ... ok. exercise 64 [ hmmconvert/P] ... ok. exercise 65 [ hmmemit] ... ok. exercise 66 [ hmmemit/a] ... ok. exercise 67 [ hmmemit/c] ... ok. exercise 68 [ hmmemit/h] ... ok. exercise 69 [ hmmemit/n] ... ok. exercise 70 [ hmmemit/o] ... ok. exercise 71 [ hmmemit/q] ... ok. exercise 72 [ hmmemit/seed] ... ok. exercise 73 [ hmmindex] ... ok. exercise 74 [ hmmindex/h] ... ok. exercise 75 [ hmmfetch] ... ok. exercise 76 [ hmmfetch/h] ... ok. exercise 77 [ hmmfetch/n] ... ok. exercise 78 [ hmmpfam] ... ok. exercise 79 [ hmmpfam/h] ... ok. exercise 80 [ hmmpfam/n] ... ok. exercise 81 [ hmmpfam/A] ... ok. exercise 82 [ hmmpfam/E] ... ok. exercise 83 [ hmmpfam/T] ... ok. exercise 84 [ hmmpfam/Z] ... ok. exercise 85 [ hmmpfam/acc] ... ok. exercise 86 [ hmmpfam/compat] ... ok. exercise 87 [ hmmpfam/cut_ga] ... ok. exercise 88 [ hmmpfam/cut_nc] ... ok. exercise 89 [ hmmpfam/cut_tc] ... ok. exercise 90 [ hmmpfam/domE] ... ok. exercise 91 [ hmmpfam/domT] ... ok. exercise 92 [ hmmpfam/forward] ... ok. exercise 93 [ hmmpfam/informat] ... ok. exercise 94 [ hmmpfam/null2] ... ok. exercise 95 [ hmmpfam/xnu] ... ok. exercise 96 [ hmmsearch] ... ok. exercise 97 [ hmmsearch/h] ... ok. exercise 98 [ hmmsearch/A] ... ok. exercise 99 [ hmmsearch/E] ... ok. exercise 100 [ hmmsearch/T] ... ok. exercise 101 [ hmmsearch/Z] ... ok. exercise 102 [ hmmsearch/compat] ... ok. exercise 103 [ hmmsearch/cut_ga] ... ok. exercise 104 [ hmmsearch/cut_nc] ... ok. exercise 105 [ hmmsearch/cut_tc] ... ok. exercise 106 [ hmmsearch/domE] ... ok. exercise 107 [ hmmsearch/domT] ... ok. exercise 108 [ hmmsearch/forward] ... ok. exercise 109 [ hmmsearch/informat] ... ok. exercise 110 [ hmmsearch/null2] ... ok. exercise 111 [ hmmsearch/xnu] ... ok. exercise 112 [ align_align] ... ok. exercise 113 [ evd] ... ok. exercise 114 [ masks] ... ok. exercise 115 [ parsingv] ... ok. exercise 116 [ tophits] ... ok. exercise 117 [ trace] ... ok. exercise 118 [ viterbi] ... ok. exercise 119 [ weeviterbi] ... ok. exercise 120 [ test1/conversion] ... ok. All 120 exercises at level <= 2 passed. System information: Wed Jul 30 02:06:28 2025 Linux codethink04-arm64 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux make[3]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite' make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' rm -f testsuite/*.ssi cd testsuite && make clean make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite' rm -f *.o *~ Makefile.bak core alignalign_test evd_test masks_test parsingviterbi_test tophits_test trace_test viterbi_exercise weeviterbi_test TAGS gmon.out make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite' make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' dh_auto_install -- prefix=/build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp make -j12 install DESTDIR=/build/reproducible-path/hmmer2-2.3.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/build/reproducible-path/hmmer2-2.3.2\+dfsg/debian/tmp make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' mkdir -p /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/bin mkdir -p /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1 for file in hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch ; do\ cp src/$file /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/bin/;\ done for file in hmmer hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch; do\ cp documentation/man/$file.man /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/$file.1;\ done make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' # lkajan: rename binaries and man pages like this: s/hmm/hmm2/ - except hmmer.1, rename that to hmmer2.1: rename 's/^hmm/hmm2/;' /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/bin/* cd /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/bin; rename 's/^hmm/hmm2/;' * cd /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1; rename 's/^hmm/hmm2/;' * mv /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/hmm2er.1 /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/hmmer2.1 # lkajan: resolve man page hypen issue: sed -i -e 's/--/\\-\\-/g;s/-\([[:alpha:]]\)\b/\\-\1/g;' /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/* make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' sed -e "s/@DEB_HOST_MULTIARCH@/aarch64-linux-gnu/" \ -e "s/@VERSION@/2.3.2/" debian/pkgconfig/libhmmer2.pc.in > debian/pkgconfig/libhmmer2.pc dh_install rm -f debian/pkgconfig/libhmmer2.pc make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' dh_installchangelogs -k NOTES make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' cd testsuite && make clean && cd .. make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite' rm -f *.o *~ Makefile.bak core alignalign_test evd_test masks_test parsingviterbi_test tophits_test trace_test viterbi_exercise weeviterbi_test TAGS gmon.out make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite' dh_installexamples mkdir -p /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples; cp -a testsuite/* /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/; mkdir /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/tutorial; cp -a tutorial/* /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/tutorial; sed -i "s#hmm#hmm2#g" /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/exercises.sqc sed -i "s#../tut#./tut#g" /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/exercises.sqc find /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples -name 'Makefile' | xargs sed -i "s^/build/reproducible-path/hmmer2-2.3.2+dfsg^.^g" make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package hmmer2-doc: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libhmmer2-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'libhmmer2-dev' in '../libhmmer2-dev_2.3.2+dfsg-12_arm64.deb'. dpkg-deb: building package 'hmmer2-doc' in '../hmmer2-doc_2.3.2+dfsg-12_all.deb'. dpkg-deb: building package 'hmmer2' in '../hmmer2_2.3.2+dfsg-12_arm64.deb'. dpkg-deb: building package 'hmmer2-dbgsym' in '../hmmer2-dbgsym_2.3.2+dfsg-12_arm64.deb'. dpkg-genbuildinfo --build=binary -O../hmmer2_2.3.2+dfsg-12_arm64.buildinfo dpkg-genchanges --build=binary -O../hmmer2_2.3.2+dfsg-12_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2487435 and its subdirectories I: Current time: Tue Jul 29 14:06:34 -12 2025 I: pbuilder-time-stamp: 1753841194 Wed Jul 30 02:06:34 UTC 2025 I: Signing ./b1/hmmer2_2.3.2+dfsg-12_arm64.buildinfo as hmmer2_2.3.2+dfsg-12_arm64.buildinfo.asc Wed Jul 30 02:06:34 UTC 2025 I: Signed ./b1/hmmer2_2.3.2+dfsg-12_arm64.buildinfo as ./b1/hmmer2_2.3.2+dfsg-12_arm64.buildinfo.asc Wed Jul 30 02:06:34 UTC 2025 - build #1 for hmmer2/unstable/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Wed Jul 30 02:06:34 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-hbwoqqhx, removing. /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Jul 30 02:06 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jul 30 02:05 b2 -rw-r--r-- 1 jenkins jenkins 2236 Apr 11 2024 hmmer2_2.3.2+dfsg-12.dsc -rw------- 1 jenkins jenkins 3372 Jul 30 02:05 rbuildlog.5JaI1eC /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/b1: total 1800 -rw-r--r-- 1 jenkins jenkins 60460 Jul 30 02:06 build.log -rw-r--r-- 1 jenkins jenkins 1248928 Jul 30 02:06 hmmer2-dbgsym_2.3.2+dfsg-12_arm64.deb -rw-r--r-- 1 jenkins jenkins 78828 Jul 30 02:06 hmmer2-doc_2.3.2+dfsg-12_all.deb -rw-r--r-- 1 jenkins jenkins 21136 Jul 30 02:06 hmmer2_2.3.2+dfsg-12.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2236 Jul 30 02:06 hmmer2_2.3.2+dfsg-12.dsc -rw-r--r-- 1 jenkins jenkins 5683 Jul 30 02:06 hmmer2_2.3.2+dfsg-12_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6565 Jul 30 02:06 hmmer2_2.3.2+dfsg-12_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2515 Jul 30 02:06 hmmer2_2.3.2+dfsg-12_arm64.changes -rw-r--r-- 1 jenkins jenkins 288964 Jul 30 02:06 hmmer2_2.3.2+dfsg-12_arm64.deb -rw-r--r-- 1 jenkins jenkins 1608 Jul 30 02:06 hmmer2_2.3.2+dfsg-12_source.changes -rw-r--r-- 1 jenkins jenkins 91812 Jul 30 02:06 libhmmer2-dev_2.3.2+dfsg-12_arm64.deb /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/b2: total 0 Wed Jul 30 02:06:35 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Jul 29 14:05:27 -12 2025 I: pbuilder-time-stamp: 1753841127 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [hmmer2_2.3.2+dfsg-12.dsc] I: copying [./hmmer2_2.3.2+dfsg.orig.tar.xz] I: copying [./hmmer2_2.3.2+dfsg-12.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./hmmer2_2.3.2+dfsg-12.dsc: no acceptable signature found dpkg-source: info: extracting hmmer2 in hmmer2-2.3.2+dfsg dpkg-source: info: unpacking hmmer2_2.3.2+dfsg.orig.tar.xz dpkg-source: info: unpacking hmmer2_2.3.2+dfsg-12.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying version2-manpage dpkg-source: info: applying userguidepdf dpkg-source: info: applying spelling.patch dpkg-source: info: applying use_debian_packaged_biosquid.patch dpkg-source: info: applying build_libhmmer.a_with-fPIC.patch dpkg-source: info: applying add-runstatedir-option.patch dpkg-source: info: applying fixup-implicit-function-declaration.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2487435/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='d6b233b322b04cdebc76085320d382ca' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2487435' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/pbuilderrc_5LGK --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/b1 --logfile b1/build.log hmmer2_2.3.2+dfsg-12.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2487435/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libperl4-corelibs-perl, libsquid-dev, pkgconf, dh-exec, rename dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19963 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libperl4-corelibs-perl; however: Package libperl4-corelibs-perl is not installed. pbuilder-satisfydepends-dummy depends on libsquid-dev; however: Package libsquid-dev is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on dh-exec; however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on rename; however: Package rename is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libmagic-mgc{a} libmagic1t64{a} libperl4-corelibs-perl{a} libpipeline1{a} libpkgconf3{a} libsquid-dev{a} libsquid1t64{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} rename{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 37 newly installed, 0 to remove and 0 not upgraded. Need to get 11.4 MB of archives. After unpacking 46.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2 [241 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41-5 [93.8 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-2.1 [630 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2 [1611 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.2 [919 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 dh-exec arm64 0.30+b1 [25.8 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libperl4-corelibs-perl all 0.005-1 [39.0 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libsquid1t64 arm64 1.9g+cvs20050121-15.1+b2 [71.4 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libsquid-dev arm64 1.9g+cvs20050121-15.1+b2 [141 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 rename all 2.02-1 [21.8 kB] Fetched 11.4 MB in 0s (39.3 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19963 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2_arm64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_arm64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41-5_arm64.deb ... Unpacking bsdextrautils (2.41-5) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_arm64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-8_arm64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../23-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-2.1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-2.1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2_arm64.deb ... Unpacking gettext (0.23.1-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Selecting previously unselected package dh-exec. Preparing to unpack .../29-dh-exec_0.30+b1_arm64.deb ... Unpacking dh-exec (0.30+b1) ... Selecting previously unselected package libperl4-corelibs-perl. Preparing to unpack .../30-libperl4-corelibs-perl_0.005-1_all.deb ... Unpacking libperl4-corelibs-perl (0.005-1) ... Selecting previously unselected package libpkgconf3:arm64. Preparing to unpack .../31-libpkgconf3_1.8.1-4_arm64.deb ... Unpacking libpkgconf3:arm64 (1.8.1-4) ... Selecting previously unselected package libsquid1t64:arm64. Preparing to unpack .../32-libsquid1t64_1.9g+cvs20050121-15.1+b2_arm64.deb ... Unpacking libsquid1t64:arm64 (1.9g+cvs20050121-15.1+b2) ... Selecting previously unselected package libsquid-dev. Preparing to unpack .../33-libsquid-dev_1.9g+cvs20050121-15.1+b2_arm64.deb ... Unpacking libsquid-dev (1.9g+cvs20050121-15.1+b2) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../34-pkgconf-bin_1.8.1-4_arm64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../35-pkgconf_1.8.1-4_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-4) ... Selecting previously unselected package rename. Preparing to unpack .../36-rename_2.02-1_all.deb ... Unpacking rename (2.02-1) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up bsdextrautils (2.41-5) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libperl4-corelibs-perl (0.005-1) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up rename (2.02-1) ... update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20240727.1) ... Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-2.1) ... Setting up libsquid1t64:arm64 (1.9g+cvs20050121-15.1+b2) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2) ... Setting up libtool (2.5.4-4) ... Setting up libsquid-dev (1.9g+cvs20050121-15.1+b2) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.2) ... Setting up dh-exec (0.30+b1) ... Processing triggers for libc-bin (2.41-11) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/hmmer2-2.3.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../hmmer2_2.3.2+dfsg-12_source.changes dpkg-buildpackage: info: source package hmmer2 dpkg-buildpackage: info: source version 2.3.2+dfsg-12 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' dh_clean if [ -e configure_not_used ] ; then mv configure_not_used configure; fi rm -f configure.ac src/config.h make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' cp -a debian/missing-sources/configure.ac . mv configure configure_not_used dh_autoreconf configure.ac:119: warning: underquoted definition of CHECK_GNU_MAKE configure.ac:119: run info Automake 'Extending aclocal' configure.ac:119: or see https://www.gnu.org/software/automake/manual/automake.html#Extending-aclocal configure.ac:161: warning: The macro 'AC_TRY_COMPILE' is obsolete. configure.ac:161: You should run autoupdate. ./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from... configure.ac:161: the top level configure.ac:487: warning: The macro 'AC_LANG_C' is obsolete. configure.ac:487: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... configure.ac:289: ACX_PTHREAD is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:487: the top level configure.ac:487: warning: The macro 'AC_TRY_LINK' is obsolete. configure.ac:487: You should run autoupdate. ./lib/autoconf/general.m4:2918: AC_TRY_LINK is expanded from... configure.ac:289: ACX_PTHREAD is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:487: the top level make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' dh_auto_configure -- --enable-threads --enable-lfs PTHREAD_CFLAGS="-D_XOPEN_SOURCE=500" # --enable-pvm ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-threads --enable-lfs PTHREAD_CFLAGS=-D_XOPEN_SOURCE=500 configure: configuring HMMER for your system. configure: This is a full source distribution - using full config checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for ranlib... ranlib checking for ar... /usr/bin/ar checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking whether your make is GNU make... yes, it is. configure: configured for optional LFS, large file support configure: enabled POSIX multithreading support checking for pthread_setconcurrency... yes checking for pthread_attr_setscope... yes checking for pthread_join in LIBS= with CFLAGS=-D_XOPEN_SOURCE=500... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for ntohs... yes checking for ntohl... yes checking for htons... yes checking for htonl... yes configure: creating ./config.status config.status: creating src/Makefile config.status: creating testsuite/Makefile config.status: creating Makefile config.status: WARNING: 'Makefile.in' seems to ignore the --datarootdir setting config.status: creating src/config.h # avoid duplicated definition of PACKAGE_NAME (basically conflicting with biosquid when used together) sed -i -e '/^#define PACKAGE_NAME /i #ifndef PACKAGE_NAME' \ -e '/^#define PACKAGE_NAME /a #endif' \ -e '/^#define PACKAGE_VERSION /i #ifndef PACKAGE_VERSION' \ -e '/^#define PACKAGE_VERSION /a #endif' \ -e '/^#define _LARGEFILE_SOURCE /i #ifndef _LARGEFILE_SOURCE' \ -e '/^#define _LARGEFILE_SOURCE /a #endif' \ -e '/^#define _LARGEFILE64_SOURCE /i #ifndef _LARGEFILE64_SOURCE' \ -e '/^#define _LARGEFILE64_SOURCE /a #endif' \ -e '/^#define VERSION /i #ifndef VERSION' \ -e '/^#define VERSION /a #endif' \ src/config.h make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/src' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmalign.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c alphabet.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c core_algorithms.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c debug.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c display.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c emit.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c emulation.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c fast_algorithms.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c histogram.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmio.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c mathsupport.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c masks.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c misc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c modelmakers.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c plan7.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c plan9.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c postprob.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c prior.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c pvm.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c threads.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c tophits.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c trace.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmbuild.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmcalibrate.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmconvert.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmemit.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmfetch.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmindex.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmpfam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmsearch.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmalign hmmalign.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmbuild hmmbuild.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmcalibrate hmmcalibrate.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmconvert hmmconvert.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmemit hmmemit.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmfetch hmmfetch.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmindex hmmindex.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmpfam hmmpfam.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmsearch hmmsearch.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/src' make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/src' /usr/bin/ar rcv libhmmer.a alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o a - alphabet.o a - core_algorithms.o a - debug.o a - display.o a - emit.o a - emulation.o a - fast_algorithms.o a - histogram.o a - hmmio.o a - mathsupport.o a - masks.o a - misc.o a - modelmakers.o a - plan7.o a - plan9.o a - postprob.o a - prior.o a - pvm.o a - threads.o a - tophits.o a - trace.o ranlib libhmmer.a chmod 644 libhmmer.a make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/src' make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c alignalign_test.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c evd_test.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c masks_test.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c parsingviterbi_test.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c tophits_test.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c trace_test.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c viterbi_exercise.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c weeviterbi_test.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o trace_test -L../src trace_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o masks_test -L../src masks_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o parsingviterbi_test -L../src parsingviterbi_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o viterbi_exercise -L../src viterbi_exercise.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o weeviterbi_test -L../src weeviterbi_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o alignalign_test -L../src alignalign_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o tophits_test -L../src tophits_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o evd_test -L../src evd_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite' make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' dh_auto_test make -j12 check "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' (cd testsuite; make check) make[3]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite' Running test suite exercises. Warning: some tests may take several minutes to complete. ./sqc 2 exercises.sqc . ../src exercise 1 [ hmmalign] ... ok. exercise 2 [ hmmalign/h] ... ok. exercise 3 [ hmmalign/m] ... ok. exercise 4 [ hmmalign/o] ... ok. exercise 5 [ hmmalign/q] ... ok. exercise 6 [ hmmalign/informat] ... ok. exercise 7 [ hmmalign/selex] ... ok. exercise 8 [ hmmalign/a2m] ... ok. exercise 9 [ hmmalign/clustal] ... ok. exercise 10 [ hmmalign/msf] ... ok. exercise 11 [ hmmalign/phylip] ... ok. exercise 12 [ hmmalign/oneline] ... ok. exercise 13 [ hmmalign/withali] ... ok. exercise 14 [ hmmalign/mapali] ... ok. exercise 15 [ hmmbuild] ... ok. exercise 16 [ hmmbuild/h] ... ok. exercise 17 [ hmmbuild/F] ... ok. exercise 18 [ hmmbuild/n] ... ok. exercise 19 [ hmmbuild/o] ... ok. exercise 20 [ hmmbuild/A] ... ok. exercise 21 [ hmmbuild/f] ... ok. exercise 22 [ hmmbuild/g] ... ok. exercise 23 [ hmmbuild/s] ... ok. exercise 24 [ hmmbuild/fast] ... ok. exercise 25 [ hmmbuild/hand] ... ok. exercise 26 [ hmmbuild/null] ... ok. exercise 27 [ hmmbuild/pam] ... ok. exercise 28 [ hmmbuild/prior] ... ok. exercise 29 [ hmmbuild/wblosum] ... ok. exercise 30 [ hmmbuild/wgsc] ... ok. exercise 31 [ hmmbuild/wme] ... ok. exercise 32 [ hmmbuild/wpb] ... ok. exercise 33 [ hmmbuild/wvoronoi] ... ok. exercise 34 [ hmmbuild/wnone] ... ok. exercise 35 [ hmmbuild/noeff] ... ok. exercise 36 [ hmmbuild/pbswitch] ... ok. exercise 37 [ hmmbuild/amino] ... ok. exercise 38 [ hmmbuild/nucleic] ... ok. exercise 39 [ hmmbuild/archpri] ... ok. exercise 40 [ hmmbuild/binary] ... ok. exercise 41 [ hmmbuild/cfile] ... ok. exercise 42 [ hmmbuild/gapmax] ... ok. exercise 43 [ hmmbuild/idlevel] ... ok. exercise 44 [ hmmbuild/informat] ... ok. exercise 45 [ hmmbuild/pamwgt] ... ok. exercise 46 [ hmmbuild/swentry] ... ok. exercise 47 [ hmmbuild/swexit] ... ok. exercise 48 [ hmmbuild/verbose] ... ok. exercise 49 [ hmmcalibrate] ... ok. exercise 50 [ hmmcalibrate/h] ... ok. exercise 51 [ hmmcalibrate/fixed] ... ok. exercise 52 [ hmmcalibrate/mean] ... ok. exercise 53 [ hmmcalibrate/hist] ... ok. exercise 54 [ hmmcalibrate/num] ... ok. exercise 55 [ hmmcalibrate/sd] ... ok. exercise 56 [ hmmcalibrate/seed] ... ok. exercise 57 [ hmmconvert] ... ok. exercise 58 [ hmmconvert/h] ... ok. exercise 59 [ hmmconvert/F] ... ok. exercise 60 [ hmmconvert/a] ... ok. exercise 61 [ hmmconvert/A] ... ok. exercise 62 [ hmmconvert/b] ... ok. exercise 63 [ hmmconvert/p] ... ok. exercise 64 [ hmmconvert/P] ... ok. exercise 65 [ hmmemit] ... ok. exercise 66 [ hmmemit/a] ... ok. exercise 67 [ hmmemit/c] ... ok. exercise 68 [ hmmemit/h] ... ok. exercise 69 [ hmmemit/n] ... ok. exercise 70 [ hmmemit/o] ... ok. exercise 71 [ hmmemit/q] ... ok. exercise 72 [ hmmemit/seed] ... ok. exercise 73 [ hmmindex] ... ok. exercise 74 [ hmmindex/h] ... ok. exercise 75 [ hmmfetch] ... ok. exercise 76 [ hmmfetch/h] ... ok. exercise 77 [ hmmfetch/n] ... ok. exercise 78 [ hmmpfam] ... ok. exercise 79 [ hmmpfam/h] ... ok. exercise 80 [ hmmpfam/n] ... ok. exercise 81 [ hmmpfam/A] ... ok. exercise 82 [ hmmpfam/E] ... ok. exercise 83 [ hmmpfam/T] ... ok. exercise 84 [ hmmpfam/Z] ... ok. exercise 85 [ hmmpfam/acc] ... ok. exercise 86 [ hmmpfam/compat] ... ok. exercise 87 [ hmmpfam/cut_ga] ... ok. exercise 88 [ hmmpfam/cut_nc] ... ok. exercise 89 [ hmmpfam/cut_tc] ... ok. exercise 90 [ hmmpfam/domE] ... ok. exercise 91 [ hmmpfam/domT] ... ok. exercise 92 [ hmmpfam/forward] ... ok. exercise 93 [ hmmpfam/informat] ... ok. exercise 94 [ hmmpfam/null2] ... ok. exercise 95 [ hmmpfam/xnu] ... ok. exercise 96 [ hmmsearch] ... ok. exercise 97 [ hmmsearch/h] ... ok. exercise 98 [ hmmsearch/A] ... ok. exercise 99 [ hmmsearch/E] ... ok. exercise 100 [ hmmsearch/T] ... ok. exercise 101 [ hmmsearch/Z] ... ok. exercise 102 [ hmmsearch/compat] ... ok. exercise 103 [ hmmsearch/cut_ga] ... ok. exercise 104 [ hmmsearch/cut_nc] ... ok. exercise 105 [ hmmsearch/cut_tc] ... ok. exercise 106 [ hmmsearch/domE] ... ok. exercise 107 [ hmmsearch/domT] ... ok. exercise 108 [ hmmsearch/forward] ... ok. exercise 109 [ hmmsearch/informat] ... ok. exercise 110 [ hmmsearch/null2] ... ok. exercise 111 [ hmmsearch/xnu] ... ok. exercise 112 [ align_align] ... ok. exercise 113 [ evd] ... ok. exercise 114 [ masks] ... ok. exercise 115 [ parsingv] ... ok. exercise 116 [ tophits] ... ok. exercise 117 [ trace] ... ok. exercise 118 [ viterbi] ... ok. exercise 119 [ weeviterbi] ... ok. exercise 120 [ test1/conversion] ... ok. All 120 exercises at level <= 2 passed. System information: Wed Jul 30 02:06:28 2025 Linux codethink04-arm64 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux make[3]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite' make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' rm -f testsuite/*.ssi cd testsuite && make clean make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite' rm -f *.o *~ Makefile.bak core alignalign_test evd_test masks_test parsingviterbi_test tophits_test trace_test viterbi_exercise weeviterbi_test TAGS gmon.out make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite' make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' dh_auto_install -- prefix=/build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp make -j12 install DESTDIR=/build/reproducible-path/hmmer2-2.3.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/build/reproducible-path/hmmer2-2.3.2\+dfsg/debian/tmp make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' mkdir -p /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/bin mkdir -p /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1 for file in hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch ; do\ cp src/$file /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/bin/;\ done for file in hmmer hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch; do\ cp documentation/man/$file.man /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/$file.1;\ done make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' # lkajan: rename binaries and man pages like this: s/hmm/hmm2/ - except hmmer.1, rename that to hmmer2.1: rename 's/^hmm/hmm2/;' /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/bin/* cd /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/bin; rename 's/^hmm/hmm2/;' * cd /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1; rename 's/^hmm/hmm2/;' * mv /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/hmm2er.1 /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/hmmer2.1 # lkajan: resolve man page hypen issue: sed -i -e 's/--/\\-\\-/g;s/-\([[:alpha:]]\)\b/\\-\1/g;' /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/* make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' sed -e "s/@DEB_HOST_MULTIARCH@/aarch64-linux-gnu/" \ -e "s/@VERSION@/2.3.2/" debian/pkgconfig/libhmmer2.pc.in > debian/pkgconfig/libhmmer2.pc dh_install rm -f debian/pkgconfig/libhmmer2.pc make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' dh_installchangelogs -k NOTES make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' cd testsuite && make clean && cd .. make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite' rm -f *.o *~ Makefile.bak core alignalign_test evd_test masks_test parsingviterbi_test tophits_test trace_test viterbi_exercise weeviterbi_test TAGS gmon.out make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite' dh_installexamples mkdir -p /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples; cp -a testsuite/* /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/; mkdir /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/tutorial; cp -a tutorial/* /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/tutorial; sed -i "s#hmm#hmm2#g" /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/exercises.sqc sed -i "s#../tut#./tut#g" /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/exercises.sqc find /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples -name 'Makefile' | xargs sed -i "s^/build/reproducible-path/hmmer2-2.3.2+dfsg^.^g" make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package hmmer2-doc: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libhmmer2-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'libhmmer2-dev' in '../libhmmer2-dev_2.3.2+dfsg-12_arm64.deb'. dpkg-deb: building package 'hmmer2-doc' in '../hmmer2-doc_2.3.2+dfsg-12_all.deb'. dpkg-deb: building package 'hmmer2' in '../hmmer2_2.3.2+dfsg-12_arm64.deb'. dpkg-deb: building package 'hmmer2-dbgsym' in '../hmmer2-dbgsym_2.3.2+dfsg-12_arm64.deb'. dpkg-genbuildinfo --build=binary -O../hmmer2_2.3.2+dfsg-12_arm64.buildinfo dpkg-genchanges --build=binary -O../hmmer2_2.3.2+dfsg-12_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2487435 and its subdirectories I: Current time: Tue Jul 29 14:06:34 -12 2025 I: pbuilder-time-stamp: 1753841194 Wed Jul 30 02:06:36 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Wed Jul 30 02:06:36 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Wed Jul 30 02:06:36 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Wed Jul 30 02:06:36 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-OcrD5U' ==================================================================================== Tue Sep 1 08:29:37 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink03-arm64, called using "2 hmmer2 unstable /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I 2.3.2+dfsg-12" as arguments. Tue Sep 1 08:29:37 UTC 2026 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-fBHBMH8O" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Sep 1 08:29:37 UTC 2026 I: Downloading source for unstable/hmmer2=2.3.2+dfsg-12 Reading package lists... NOTICE: 'hmmer2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/hmmer2.git Please use: git clone https://salsa.debian.org/med-team/hmmer2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 355 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main hmmer2 2.3.2+dfsg-12 (dsc) [2236 B] Get:2 http://deb.debian.org/debian unstable/main hmmer2 2.3.2+dfsg-12 (tar) [332 kB] Get:3 http://deb.debian.org/debian unstable/main hmmer2 2.3.2+dfsg-12 (diff) [21.1 kB] Fetched 355 kB in 0s (17.4 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'hmmer2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/hmmer2.git Please use: git clone https://salsa.debian.org/med-team/hmmer2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 355 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main hmmer2 2.3.2+dfsg-12 (dsc) [2236 B] Get:2 http://deb.debian.org/debian unstable/main hmmer2 2.3.2+dfsg-12 (tar) [332 kB] Get:3 http://deb.debian.org/debian unstable/main hmmer2 2.3.2+dfsg-12 (diff) [21.1 kB] Fetched 355 kB in 0s (17.4 MB/s) Download complete and in download only mode ============================================================================= Re-Building hmmer2 in unstable on arm64 on codethink03-arm64 now. Date: Tue Sep 1 09:29:37 BST 2026 Date UTC: Tue Sep 1 08:29:37 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/pbuilderrc_Jmpf + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' hmmer2 = debian-installer -o hmmer2 = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' hmmer2 = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/pbuilderrc_Jmpf --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/b2 --logfile b2/build.log hmmer2_2.3.2+dfsg-12.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Tue Sep 1 22:29:37 +14 2026 I: pbuilder-time-stamp: 1788251377 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [hmmer2_2.3.2+dfsg-12.dsc] I: copying [./hmmer2_2.3.2+dfsg.orig.tar.xz] I: copying [./hmmer2_2.3.2+dfsg-12.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./hmmer2_2.3.2+dfsg-12.dsc: no acceptable signature found dpkg-source: info: extracting hmmer2 in hmmer2-2.3.2+dfsg dpkg-source: info: unpacking hmmer2_2.3.2+dfsg.orig.tar.xz dpkg-source: info: unpacking hmmer2_2.3.2+dfsg-12.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying version2-manpage dpkg-source: info: applying userguidepdf dpkg-source: info: applying spelling.patch dpkg-source: info: applying use_debian_packaged_biosquid.patch dpkg-source: info: applying build_libhmmer.a_with-fPIC.patch dpkg-source: info: applying add-runstatedir-option.patch dpkg-source: info: applying fixup-implicit-function-declaration.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2166518/tmp/hooks/D01_modify_environment starting debug: Running on codethink03-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Sep 1 08:29 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2166518/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2166518/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=8f08320311854f728c16fa819b9495fc LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2166518 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/pbuilderrc_Jmpf --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/b2 --logfile b2/build.log hmmer2_2.3.2+dfsg-12.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2166518/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libperl4-corelibs-perl, libsquid-dev, pkgconf, dh-exec, rename dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19963 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libperl4-corelibs-perl; however: Package libperl4-corelibs-perl is not installed. pbuilder-satisfydepends-dummy depends on libsquid-dev; however: Package libsquid-dev is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on dh-exec; however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on rename; however: Package rename is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libmagic-mgc{a} libmagic1t64{a} libperl4-corelibs-perl{a} libpipeline1{a} libpkgconf3{a} libsquid-dev{a} libsquid1t64{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} rename{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 37 newly installed, 0 to remove and 0 not upgraded. Need to get 11.4 MB of archives. After unpacking 46.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2 [241 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41-5 [93.8 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-2.1 [630 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2 [1611 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.2 [919 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 dh-exec arm64 0.30+b1 [25.8 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libperl4-corelibs-perl all 0.005-1 [39.0 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libsquid1t64 arm64 1.9g+cvs20050121-15.1+b2 [71.4 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libsquid-dev arm64 1.9g+cvs20050121-15.1+b2 [141 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 rename all 2.02-1 [21.8 kB] Fetched 11.4 MB in 0s (84.2 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19963 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2_arm64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_arm64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41-5_arm64.deb ... Unpacking bsdextrautils (2.41-5) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_arm64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-8_arm64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../23-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-2.1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-2.1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2_arm64.deb ... Unpacking gettext (0.23.1-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Selecting previously unselected package dh-exec. Preparing to unpack .../29-dh-exec_0.30+b1_arm64.deb ... Unpacking dh-exec (0.30+b1) ... Selecting previously unselected package libperl4-corelibs-perl. Preparing to unpack .../30-libperl4-corelibs-perl_0.005-1_all.deb ... Unpacking libperl4-corelibs-perl (0.005-1) ... Selecting previously unselected package libpkgconf3:arm64. Preparing to unpack .../31-libpkgconf3_1.8.1-4_arm64.deb ... Unpacking libpkgconf3:arm64 (1.8.1-4) ... Selecting previously unselected package libsquid1t64:arm64. Preparing to unpack .../32-libsquid1t64_1.9g+cvs20050121-15.1+b2_arm64.deb ... Unpacking libsquid1t64:arm64 (1.9g+cvs20050121-15.1+b2) ... Selecting previously unselected package libsquid-dev. Preparing to unpack .../33-libsquid-dev_1.9g+cvs20050121-15.1+b2_arm64.deb ... Unpacking libsquid-dev (1.9g+cvs20050121-15.1+b2) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../34-pkgconf-bin_1.8.1-4_arm64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../35-pkgconf_1.8.1-4_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-4) ... Selecting previously unselected package rename. Preparing to unpack .../36-rename_2.02-1_all.deb ... Unpacking rename (2.02-1) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up bsdextrautils (2.41-5) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libperl4-corelibs-perl (0.005-1) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up rename (2.02-1) ... update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20240727.1) ... Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-2.1) ... Setting up libsquid1t64:arm64 (1.9g+cvs20050121-15.1+b2) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2) ... Setting up libtool (2.5.4-4) ... Setting up libsquid-dev (1.9g+cvs20050121-15.1+b2) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.2) ... Setting up dh-exec (0.30+b1) ... Processing triggers for libc-bin (2.41-11) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2166518/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/2166518/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/hmmer2-2.3.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../hmmer2_2.3.2+dfsg-12_source.changes dpkg-buildpackage: info: source package hmmer2 dpkg-buildpackage: info: source version 2.3.2+dfsg-12 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' dh_clean if [ -e configure_not_used ] ; then mv configure_not_used configure; fi rm -f configure.ac src/config.h make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' cp -a debian/missing-sources/configure.ac . mv configure configure_not_used dh_autoreconf configure.ac:119: warning: underquoted definition of CHECK_GNU_MAKE configure.ac:119: run info Automake 'Extending aclocal' configure.ac:119: or see https://www.gnu.org/software/automake/manual/automake.html#Extending-aclocal configure.ac:161: warning: The macro 'AC_TRY_COMPILE' is obsolete. configure.ac:161: You should run autoupdate. ./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from... configure.ac:161: the top level configure.ac:487: warning: The macro 'AC_LANG_C' is obsolete. configure.ac:487: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... configure.ac:289: ACX_PTHREAD is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:487: the top level configure.ac:487: warning: The macro 'AC_TRY_LINK' is obsolete. configure.ac:487: You should run autoupdate. ./lib/autoconf/general.m4:2918: AC_TRY_LINK is expanded from... configure.ac:289: ACX_PTHREAD is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:487: the top level make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' dh_auto_configure -- --enable-threads --enable-lfs PTHREAD_CFLAGS="-D_XOPEN_SOURCE=500" # --enable-pvm ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-threads --enable-lfs PTHREAD_CFLAGS=-D_XOPEN_SOURCE=500 configure: configuring HMMER for your system. configure: This is a full source distribution - using full config checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for ranlib... ranlib checking for ar... /usr/bin/ar checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking whether your make is GNU make... yes, it is. configure: configured for optional LFS, large file support configure: enabled POSIX multithreading support checking for pthread_setconcurrency... yes checking for pthread_attr_setscope... yes checking for pthread_join in LIBS= with CFLAGS=-D_XOPEN_SOURCE=500... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for ntohs... yes checking for ntohl... yes checking for htons... yes checking for htonl... yes configure: creating ./config.status config.status: creating src/Makefile config.status: creating testsuite/Makefile config.status: creating Makefile config.status: WARNING: 'Makefile.in' seems to ignore the --datarootdir setting config.status: creating src/config.h # avoid duplicated definition of PACKAGE_NAME (basically conflicting with biosquid when used together) sed -i -e '/^#define PACKAGE_NAME /i #ifndef PACKAGE_NAME' \ -e '/^#define PACKAGE_NAME /a #endif' \ -e '/^#define PACKAGE_VERSION /i #ifndef PACKAGE_VERSION' \ -e '/^#define PACKAGE_VERSION /a #endif' \ -e '/^#define _LARGEFILE_SOURCE /i #ifndef _LARGEFILE_SOURCE' \ -e '/^#define _LARGEFILE_SOURCE /a #endif' \ -e '/^#define _LARGEFILE64_SOURCE /i #ifndef _LARGEFILE64_SOURCE' \ -e '/^#define _LARGEFILE64_SOURCE /a #endif' \ -e '/^#define VERSION /i #ifndef VERSION' \ -e '/^#define VERSION /a #endif' \ src/config.h make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/src' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmalign.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c alphabet.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c core_algorithms.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c debug.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c display.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c emit.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c emulation.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c fast_algorithms.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c histogram.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmio.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c mathsupport.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c masks.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c misc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c modelmakers.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c plan7.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c plan9.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c postprob.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c prior.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c pvm.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c threads.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c tophits.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c trace.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmbuild.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmcalibrate.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmconvert.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmemit.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmfetch.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmindex.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmpfam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmsearch.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmalign hmmalign.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmbuild hmmbuild.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmcalibrate hmmcalibrate.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmconvert hmmconvert.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmemit hmmemit.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmfetch hmmfetch.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmindex hmmindex.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmpfam hmmpfam.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmsearch hmmsearch.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/src' make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/src' /usr/bin/ar rcv libhmmer.a alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o a - alphabet.o a - core_algorithms.o a - debug.o a - display.o a - emit.o a - emulation.o a - fast_algorithms.o a - histogram.o a - hmmio.o a - mathsupport.o a - masks.o a - misc.o a - modelmakers.o a - plan7.o a - plan9.o a - postprob.o a - prior.o a - pvm.o a - threads.o a - tophits.o a - trace.o ranlib libhmmer.a chmod 644 libhmmer.a make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/src' make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c alignalign_test.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c evd_test.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c masks_test.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c parsingviterbi_test.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c tophits_test.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c trace_test.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c viterbi_exercise.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c weeviterbi_test.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o weeviterbi_test -L../src weeviterbi_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o trace_test -L../src trace_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o masks_test -L../src masks_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o parsingviterbi_test -L../src parsingviterbi_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o viterbi_exercise -L../src viterbi_exercise.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o alignalign_test -L../src alignalign_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o tophits_test -L../src tophits_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o evd_test -L../src evd_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite' make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' dh_auto_test make -j12 check "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' (cd testsuite; make check) make[3]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite' Running test suite exercises. Warning: some tests may take several minutes to complete. ./sqc 2 exercises.sqc . ../src exercise 1 [ hmmalign] ... ok. exercise 2 [ hmmalign/h] ... ok. exercise 3 [ hmmalign/m] ... ok. exercise 4 [ hmmalign/o] ... ok. exercise 5 [ hmmalign/q] ... ok. exercise 6 [ hmmalign/informat] ... ok. exercise 7 [ hmmalign/selex] ... ok. exercise 8 [ hmmalign/a2m] ... ok. exercise 9 [ hmmalign/clustal] ... ok. exercise 10 [ hmmalign/msf] ... ok. exercise 11 [ hmmalign/phylip] ... ok. exercise 12 [ hmmalign/oneline] ... ok. exercise 13 [ hmmalign/withali] ... ok. exercise 14 [ hmmalign/mapali] ... ok. exercise 15 [ hmmbuild] ... ok. exercise 16 [ hmmbuild/h] ... ok. exercise 17 [ hmmbuild/F] ... ok. exercise 18 [ hmmbuild/n] ... ok. exercise 19 [ hmmbuild/o] ... ok. exercise 20 [ hmmbuild/A] ... ok. exercise 21 [ hmmbuild/f] ... ok. exercise 22 [ hmmbuild/g] ... ok. exercise 23 [ hmmbuild/s] ... ok. exercise 24 [ hmmbuild/fast] ... ok. exercise 25 [ hmmbuild/hand] ... ok. exercise 26 [ hmmbuild/null] ... ok. exercise 27 [ hmmbuild/pam] ... ok. exercise 28 [ hmmbuild/prior] ... ok. exercise 29 [ hmmbuild/wblosum] ... ok. exercise 30 [ hmmbuild/wgsc] ... ok. exercise 31 [ hmmbuild/wme] ... ok. exercise 32 [ hmmbuild/wpb] ... ok. exercise 33 [ hmmbuild/wvoronoi] ... ok. exercise 34 [ hmmbuild/wnone] ... ok. exercise 35 [ hmmbuild/noeff] ... ok. exercise 36 [ hmmbuild/pbswitch] ... ok. exercise 37 [ hmmbuild/amino] ... ok. exercise 38 [ hmmbuild/nucleic] ... ok. exercise 39 [ hmmbuild/archpri] ... ok. exercise 40 [ hmmbuild/binary] ... ok. exercise 41 [ hmmbuild/cfile] ... ok. exercise 42 [ hmmbuild/gapmax] ... ok. exercise 43 [ hmmbuild/idlevel] ... ok. exercise 44 [ hmmbuild/informat] ... ok. exercise 45 [ hmmbuild/pamwgt] ... ok. exercise 46 [ hmmbuild/swentry] ... ok. exercise 47 [ hmmbuild/swexit] ... ok. exercise 48 [ hmmbuild/verbose] ... ok. exercise 49 [ hmmcalibrate] ... ok. exercise 50 [ hmmcalibrate/h] ... ok. exercise 51 [ hmmcalibrate/fixed] ... ok. exercise 52 [ hmmcalibrate/mean] ... ok. exercise 53 [ hmmcalibrate/hist] ... ok. exercise 54 [ hmmcalibrate/num] ... ok. exercise 55 [ hmmcalibrate/sd] ... ok. exercise 56 [ hmmcalibrate/seed] ... ok. exercise 57 [ hmmconvert] ... ok. exercise 58 [ hmmconvert/h] ... ok. exercise 59 [ hmmconvert/F] ... ok. exercise 60 [ hmmconvert/a] ... ok. exercise 61 [ hmmconvert/A] ... ok. exercise 62 [ hmmconvert/b] ... ok. exercise 63 [ hmmconvert/p] ... ok. exercise 64 [ hmmconvert/P] ... ok. exercise 65 [ hmmemit] ... ok. exercise 66 [ hmmemit/a] ... ok. exercise 67 [ hmmemit/c] ... ok. exercise 68 [ hmmemit/h] ... ok. exercise 69 [ hmmemit/n] ... ok. exercise 70 [ hmmemit/o] ... ok. exercise 71 [ hmmemit/q] ... ok. exercise 72 [ hmmemit/seed] ... ok. exercise 73 [ hmmindex] ... ok. exercise 74 [ hmmindex/h] ... ok. exercise 75 [ hmmfetch] ... ok. exercise 76 [ hmmfetch/h] ... ok. exercise 77 [ hmmfetch/n] ... ok. exercise 78 [ hmmpfam] ... ok. exercise 79 [ hmmpfam/h] ... ok. exercise 80 [ hmmpfam/n] ... ok. exercise 81 [ hmmpfam/A] ... ok. exercise 82 [ hmmpfam/E] ... ok. exercise 83 [ hmmpfam/T] ... ok. exercise 84 [ hmmpfam/Z] ... ok. exercise 85 [ hmmpfam/acc] ... ok. exercise 86 [ hmmpfam/compat] ... ok. exercise 87 [ hmmpfam/cut_ga] ... ok. exercise 88 [ hmmpfam/cut_nc] ... ok. exercise 89 [ hmmpfam/cut_tc] ... ok. exercise 90 [ hmmpfam/domE] ... ok. exercise 91 [ hmmpfam/domT] ... ok. exercise 92 [ hmmpfam/forward] ... ok. exercise 93 [ hmmpfam/informat] ... ok. exercise 94 [ hmmpfam/null2] ... ok. exercise 95 [ hmmpfam/xnu] ... ok. exercise 96 [ hmmsearch] ... ok. exercise 97 [ hmmsearch/h] ... ok. exercise 98 [ hmmsearch/A] ... ok. exercise 99 [ hmmsearch/E] ... ok. exercise 100 [ hmmsearch/T] ... ok. exercise 101 [ hmmsearch/Z] ... ok. exercise 102 [ hmmsearch/compat] ... ok. exercise 103 [ hmmsearch/cut_ga] ... ok. exercise 104 [ hmmsearch/cut_nc] ... ok. exercise 105 [ hmmsearch/cut_tc] ... ok. exercise 106 [ hmmsearch/domE] ... ok. exercise 107 [ hmmsearch/domT] ... ok. exercise 108 [ hmmsearch/forward] ... ok. exercise 109 [ hmmsearch/informat] ... ok. exercise 110 [ hmmsearch/null2] ... ok. exercise 111 [ hmmsearch/xnu] ... ok. exercise 112 [ align_align] ... ok. exercise 113 [ evd] ... ok. exercise 114 [ masks] ... ok. exercise 115 [ parsingv] ... ok. exercise 116 [ tophits] ... ok. exercise 117 [ trace] ... ok. exercise 118 [ viterbi] ... ok. exercise 119 [ weeviterbi] ... ok. exercise 120 [ test1/conversion] ... ok. All 120 exercises at level <= 2 passed. System information: Tue Sep 1 08:30:16 2026 Linux i-capture-the-hostname 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux make[3]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite' make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' rm -f testsuite/*.ssi cd testsuite && make clean make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite' rm -f *.o *~ Makefile.bak core alignalign_test evd_test masks_test parsingviterbi_test tophits_test trace_test viterbi_exercise weeviterbi_test TAGS gmon.out make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite' make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' dh_auto_install -- prefix=/build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp make -j12 install DESTDIR=/build/reproducible-path/hmmer2-2.3.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/build/reproducible-path/hmmer2-2.3.2\+dfsg/debian/tmp make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' mkdir -p /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/bin mkdir -p /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1 for file in hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch ; do\ cp src/$file /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/bin/;\ done for file in hmmer hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch; do\ cp documentation/man/$file.man /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/$file.1;\ done make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' # lkajan: rename binaries and man pages like this: s/hmm/hmm2/ - except hmmer.1, rename that to hmmer2.1: rename 's/^hmm/hmm2/;' /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/bin/* cd /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/bin; rename 's/^hmm/hmm2/;' * cd /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1; rename 's/^hmm/hmm2/;' * mv /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/hmm2er.1 /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/hmmer2.1 # lkajan: resolve man page hypen issue: sed -i -e 's/--/\\-\\-/g;s/-\([[:alpha:]]\)\b/\\-\1/g;' /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/* make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' sed -e "s/@DEB_HOST_MULTIARCH@/aarch64-linux-gnu/" \ -e "s/@VERSION@/2.3.2/" debian/pkgconfig/libhmmer2.pc.in > debian/pkgconfig/libhmmer2.pc dh_install rm -f debian/pkgconfig/libhmmer2.pc make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' dh_installchangelogs -k NOTES make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' cd testsuite && make clean && cd .. make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite' rm -f *.o *~ Makefile.bak core alignalign_test evd_test masks_test parsingviterbi_test tophits_test trace_test viterbi_exercise weeviterbi_test TAGS gmon.out make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite' dh_installexamples mkdir -p /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples; cp -a testsuite/* /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/; mkdir /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/tutorial; cp -a tutorial/* /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/tutorial; sed -i "s#hmm#hmm2#g" /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/exercises.sqc sed -i "s#../tut#./tut#g" /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/exercises.sqc find /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples -name 'Makefile' | xargs sed -i "s^/build/reproducible-path/hmmer2-2.3.2+dfsg^.^g" make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libhmmer2-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package hmmer2-doc: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'hmmer2' in '../hmmer2_2.3.2+dfsg-12_arm64.deb'. dpkg-deb: building package 'hmmer2-doc' in '../hmmer2-doc_2.3.2+dfsg-12_all.deb'. dpkg-deb: building package 'libhmmer2-dev' in '../libhmmer2-dev_2.3.2+dfsg-12_arm64.deb'. dpkg-deb: building package 'hmmer2-dbgsym' in '../hmmer2-dbgsym_2.3.2+dfsg-12_arm64.deb'. dpkg-genbuildinfo --build=binary -O../hmmer2_2.3.2+dfsg-12_arm64.buildinfo dpkg-genchanges --build=binary -O../hmmer2_2.3.2+dfsg-12_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2166518/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2166518/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2166518 and its subdirectories I: Current time: Tue Sep 1 22:30:28 +14 2026 I: pbuilder-time-stamp: 1788251428 + false + set +x Tue Sep 1 08:30:28 UTC 2026 I: Signing ./b2/hmmer2_2.3.2+dfsg-12_arm64.buildinfo as hmmer2_2.3.2+dfsg-12_arm64.buildinfo.asc Tue Sep 1 08:30:28 UTC 2026 I: Signed ./b2/hmmer2_2.3.2+dfsg-12_arm64.buildinfo as ./b2/hmmer2_2.3.2+dfsg-12_arm64.buildinfo.asc Tue Sep 1 08:30:28 UTC 2026 - build #2 for hmmer2/unstable/arm64 on codethink03-arm64 done. Starting cleanup. All cleanup done. Tue Sep 1 08:30:28 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-fBHBMH8O, removing. /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I: total 80 drwxr-xr-x 2 jenkins jenkins 4096 Jul 30 02:06 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jul 30 02:07 b2 -rw-r--r-- 1 jenkins jenkins 2236 Apr 11 2024 hmmer2_2.3.2+dfsg-12.dsc -rw------- 1 jenkins jenkins 64133 Jul 30 02:06 rbuildlog.5JaI1eC /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/b1: total 1808 -rw-r--r-- 1 jenkins jenkins 60460 Jul 30 02:06 build.log -rw-r--r-- 1 jenkins jenkins 1248928 Jul 30 02:06 hmmer2-dbgsym_2.3.2+dfsg-12_arm64.deb -rw-r--r-- 1 jenkins jenkins 78828 Jul 30 02:06 hmmer2-doc_2.3.2+dfsg-12_all.deb -rw-r--r-- 1 jenkins jenkins 21136 Jul 30 02:06 hmmer2_2.3.2+dfsg-12.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2236 Jul 30 02:06 hmmer2_2.3.2+dfsg-12.dsc -rw-r--r-- 1 jenkins jenkins 5683 Jul 30 02:06 hmmer2_2.3.2+dfsg-12_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6565 Jul 30 02:06 hmmer2_2.3.2+dfsg-12_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2515 Jul 30 02:06 hmmer2_2.3.2+dfsg-12_arm64.changes -rw-r--r-- 1 jenkins jenkins 288964 Jul 30 02:06 hmmer2_2.3.2+dfsg-12_arm64.deb -rw-r--r-- 1 jenkins jenkins 1608 Jul 30 02:06 hmmer2_2.3.2+dfsg-12_source.changes -rw-r--r-- 1 jenkins jenkins 91812 Jul 30 02:06 libhmmer2-dev_2.3.2+dfsg-12_arm64.deb /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/b2: total 1792 -rw-r--r-- 1 jenkins jenkins 62410 Jul 30 02:07 build.log -rw-r--r-- 1 jenkins jenkins 1248928 Jul 30 02:07 hmmer2-dbgsym_2.3.2+dfsg-12_arm64.deb -rw-r--r-- 1 jenkins jenkins 78828 Jul 30 02:07 hmmer2-doc_2.3.2+dfsg-12_all.deb -rw-r--r-- 1 jenkins jenkins 21136 Jul 30 02:07 hmmer2_2.3.2+dfsg-12.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2236 Jul 30 02:07 hmmer2_2.3.2+dfsg-12.dsc -rw-r--r-- 1 jenkins jenkins 5683 Jul 30 02:07 hmmer2_2.3.2+dfsg-12_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6565 Jul 30 02:07 hmmer2_2.3.2+dfsg-12_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2515 Jul 30 02:07 hmmer2_2.3.2+dfsg-12_arm64.changes -rw-r--r-- 1 jenkins jenkins 288964 Jul 30 02:07 hmmer2_2.3.2+dfsg-12_arm64.deb -rw-r--r-- 1 jenkins jenkins 1608 Jul 30 02:07 hmmer2_2.3.2+dfsg-12_source.changes -rw-r--r-- 1 jenkins jenkins 91812 Jul 30 02:07 libhmmer2-dev_2.3.2+dfsg-12_arm64.deb Wed Jul 30 02:07:32 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Wed Jul 30 02:07:36 UTC 2025 I: hmmer2_2.3.2+dfsg-12_arm64.changes: Format: 1.8 Date: Thu, 11 Apr 2024 09:59:24 +0200 Source: hmmer2 Binary: hmmer2 hmmer2-dbgsym hmmer2-doc libhmmer2-dev Architecture: arm64 all Version: 2.3.2+dfsg-12 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: hmmer2 - profile hidden Markov models for protein sequence analysis hmmer2-doc - profile hidden Markov models for protein sequence analysis (docs) libhmmer2-dev - profile hidden Markov models for protein sequence analysis (devel Changes: hmmer2 (2.3.2+dfsg-12) unstable; urgency=medium . * Drop -fcf-protection=full option in autoplgtest which works on amd64+i386 only and makes the test fail on other architectures * Drop emeritus Laszlo Kajan from Uploaders (thanks for all your work Laszlo) * Standards-Version: 4.7.0 (routine-update) * Use secure URI in Homepage field. * Remove patch hardening.patch that is missing from debian/patches/series. * DEP3 + Forwarded: No Checksums-Sha1: c885750f9a2cf7b3b4830528fdca6ce76d6444fe 1248928 hmmer2-dbgsym_2.3.2+dfsg-12_arm64.deb cf021457577070ad5d9c8297f422cbbf6d82a044 78828 hmmer2-doc_2.3.2+dfsg-12_all.deb 7c109417b6515bd08b3ca84b6cb0762afcd509aa 5683 hmmer2_2.3.2+dfsg-12_arm64.buildinfo dab6f7432e53e12de758776b0522907ada9ecc91 288964 hmmer2_2.3.2+dfsg-12_arm64.deb d28a783841646009a654e77264be96a082cb2813 91812 libhmmer2-dev_2.3.2+dfsg-12_arm64.deb Checksums-Sha256: 5e5459e6e47d5f06cbdce18d5168b63a6530775dda3084ecab1b1f6b6933cce3 1248928 hmmer2-dbgsym_2.3.2+dfsg-12_arm64.deb dbb6f57db9c45fb7850a91b8deb74ed54a577267d2e232fb49a343f2238ae495 78828 hmmer2-doc_2.3.2+dfsg-12_all.deb b9c807778bbc1a6e81fe419c6829125968e34a5b2de6a670c0fae627f6c60ee0 5683 hmmer2_2.3.2+dfsg-12_arm64.buildinfo 50185b591e173a3b434b63b5e369744454099504eee566fb2225354c6dd3a85a 288964 hmmer2_2.3.2+dfsg-12_arm64.deb 54afd800b7e3308aa46e0e062474ba0167a9fe2ff3e8e0e364b097228cdbd878 91812 libhmmer2-dev_2.3.2+dfsg-12_arm64.deb Files: af3190e50822afde881d72b3904e87de 1248928 debug optional hmmer2-dbgsym_2.3.2+dfsg-12_arm64.deb 2a48f56f444afd93a54432c1d371d40a 78828 doc optional hmmer2-doc_2.3.2+dfsg-12_all.deb 7889dd7c52844da5c4dacb613390d1cb 5683 science optional hmmer2_2.3.2+dfsg-12_arm64.buildinfo b2941a3e1194c68c2e15c1d85f80e038 288964 science optional hmmer2_2.3.2+dfsg-12_arm64.deb 2e38cfa4393d81cf76dab0944c48d2fd 91812 libdevel optional libhmmer2-dev_2.3.2+dfsg-12_arm64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/hmmer2_2.3.2+dfsg-12.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/hmmer2_2.3.2+dfsg-12.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/hmmer2_2.3.2+dfsg-12.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/hmmer2_2.3.2+dfsg-12.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/arm64/hmmer2_2.3.2+dfsg-12_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/hmmer2_2.3.2+dfsg-12.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-07-30 02:06:35.455059262 +0000 +++ b2/build.log 2025-07-30 02:07:32.363125843 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jul 29 14:05:27 -12 2025 -I: pbuilder-time-stamp: 1753841127 +I: Current time: Tue Sep 1 22:29:37 +14 2026 +I: pbuilder-time-stamp: 1788251377 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying fixup-implicit-function-declaration.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2487435/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2166518/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Sep 1 08:29 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2166518/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2166518/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='d6b233b322b04cdebc76085320d382ca' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='2487435' - PS1='# ' - PS2='> ' + INVOCATION_ID=8f08320311854f728c16fa819b9495fc + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2166518 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/pbuilderrc_5LGK --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/b1 --logfile b1/build.log hmmer2_2.3.2+dfsg-12.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/pbuilderrc_Jmpf --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/b2 --logfile b2/build.log hmmer2_2.3.2+dfsg-12.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2487435/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2166518/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -158,7 +190,7 @@ Get: 35 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 rename all 2.02-1 [21.8 kB] -Fetched 11.4 MB in 0s (39.3 MB/s) +Fetched 11.4 MB in 0s (84.2 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19963 files and directories currently installed.) @@ -322,7 +354,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/hmmer2-2.3.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../hmmer2_2.3.2+dfsg-12_source.changes +I: user script /srv/workspace/pbuilder/2166518/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2166518/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/hmmer2-2.3.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../hmmer2_2.3.2+dfsg-12_source.changes dpkg-buildpackage: info: source package hmmer2 dpkg-buildpackage: info: source version 2.3.2+dfsg-12 dpkg-buildpackage: info: source distribution unstable @@ -499,11 +535,11 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c trace_test.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c viterbi_exercise.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c weeviterbi_test.c +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o weeviterbi_test -L../src weeviterbi_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o trace_test -L../src trace_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o masks_test -L../src masks_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o parsingviterbi_test -L../src parsingviterbi_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o viterbi_exercise -L../src viterbi_exercise.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o weeviterbi_test -L../src weeviterbi_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o alignalign_test -L../src alignalign_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o tophits_test -L../src tophits_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o evd_test -L../src evd_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm @@ -646,8 +682,8 @@ System information: -Wed Jul 30 02:06:28 2025 -Linux codethink04-arm64 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux +Tue Sep 1 08:30:16 2026 +Linux i-capture-the-hostname 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux make[3]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite' make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg' rm -f testsuite/*.ssi @@ -724,13 +760,13 @@ diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol -dpkg-gencontrol: warning: Depends field of package hmmer2-doc: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libhmmer2-dev: substitution variable ${shlibs:Depends} used, but is not defined +dpkg-gencontrol: warning: Depends field of package hmmer2-doc: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb -dpkg-deb: building package 'libhmmer2-dev' in '../libhmmer2-dev_2.3.2+dfsg-12_arm64.deb'. -dpkg-deb: building package 'hmmer2-doc' in '../hmmer2-doc_2.3.2+dfsg-12_all.deb'. dpkg-deb: building package 'hmmer2' in '../hmmer2_2.3.2+dfsg-12_arm64.deb'. +dpkg-deb: building package 'hmmer2-doc' in '../hmmer2-doc_2.3.2+dfsg-12_all.deb'. +dpkg-deb: building package 'libhmmer2-dev' in '../libhmmer2-dev_2.3.2+dfsg-12_arm64.deb'. dpkg-deb: building package 'hmmer2-dbgsym' in '../hmmer2-dbgsym_2.3.2+dfsg-12_arm64.deb'. dpkg-genbuildinfo --build=binary -O../hmmer2_2.3.2+dfsg-12_arm64.buildinfo dpkg-genchanges --build=binary -O../hmmer2_2.3.2+dfsg-12_arm64.changes @@ -739,12 +775,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2166518/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2166518/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/2487435 and its subdirectories -I: Current time: Tue Jul 29 14:06:34 -12 2025 -I: pbuilder-time-stamp: 1753841194 +I: removing directory /srv/workspace/pbuilder/2166518 and its subdirectories +I: Current time: Tue Sep 1 22:30:28 +14 2026 +I: pbuilder-time-stamp: 1788251428 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/hmmer2_2.3.2+dfsg-12.diff: 75.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/hmmer2_2.3.2+dfsg-12.diff.gz b2/build.log: 83.6% -- replaced with stdout Compressing the 1st log... b1/build.log: 84.2% -- replaced with stdout Wed Jul 30 02:07:37 UTC 2025 I: diffoscope 302 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_hmmer2_unstable_arm64_1753841257 + touch /var/log/reproducible-builds/diffoscope_stamp_hmmer2_unstable_arm64_1753841257 + RESULT=0 + systemd-run '--description=diffoscope on hmmer2/2.3.2+dfsg-12 in unstable/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_11-114729 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I --run-session -c jenkins-reproducible-unstable-diffoscope-45c95a89-cd2f-4604-9c9c-006c8088d476 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/dbd-tmp-R9CXZSc ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/hmmer2_2.3.2+dfsg-12.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/hmmer2_2.3.2+dfsg-12.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/hmmer2_2.3.2+dfsg-12.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/b1/hmmer2_2.3.2+dfsg-12_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/b2/hmmer2_2.3.2+dfsg-12_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_11-114729.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/hmmer2_2.3.2+dfsg-12.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/hmmer2_2.3.2+dfsg-12.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/hmmer2_2.3.2+dfsg-12.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/b1/hmmer2_2.3.2+dfsg-12_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.Ll3J1h8I/b2/hmmer2_2.3.2+dfsg-12_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 167ms CPU time consumed: 169ms _ ____ | |__ _ __ ___ _ __ ___ ___ _ _|___ \ | '_ \| '_ ` _ \| '_ ` _ \ / _ \ '__|__) | | | | | | | | | | | | | | | __/ | / __/ |_| |_|_| |_| |_|_| |_| |_|\___|_| |_____| Wed Jul 30 02:07:37 UTC 2025 I: diffoscope 302 found no differences in the changes files, and a .buildinfo file also exists. Wed Jul 30 02:07:37 UTC 2025 I: hmmer2 from unstable built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-07-30 02:07:38] INFO: Starting at 2025-07-30 02:07:38.309516 [2025-07-30 02:07:38] INFO: Generating the pages of 1 package(s) [2025-07-30 02:07:38] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/arm64/hmmer2 didn't produce a buildlog, even though it has been built. [2025-07-30 02:07:38] INFO: Finished at 2025-07-30 02:07:38.546265, took: 0:00:00.236752 Wed Jul 30 02:07:38 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/hmmer2.html Wed Jul 30 02:07:38 UTC 2025 I: Removing signed hmmer2_2.3.2+dfsg-12_arm64.buildinfo.asc files: removed './b1/hmmer2_2.3.2+dfsg-12_arm64.buildinfo.asc' removed './b2/hmmer2_2.3.2+dfsg-12_arm64.buildinfo.asc' 1753841258 arm64 unstable hmmer2 Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/hmmer2_2.3.2+dfsg-12.rbuild.log: 81.1% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/hmmer2_2.3.2+dfsg-12.rbuild.log.gz [2025-07-30 02:07:38] INFO: Starting at 2025-07-30 02:07:38.804850 [2025-07-30 02:07:38] INFO: Generating the pages of 1 package(s) [2025-07-30 02:07:39] INFO: Finished at 2025-07-30 02:07:39.036724, took: 0:00:00.231879 All cleanup done. Wed Jul 30 02:07:39 UTC 2025 - total duration: 0h 2m 33s. Wed Jul 30 02:07:39 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-TKqoJ53f, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 2min 34.529s CPU time consumed: 4.488s