Wed Apr 24 08:14:20 UTC 2024 I: starting to build hmmer2/trixie/amd64 on jenkins on '2024-04-24 08:14' Wed Apr 24 08:14:20 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_34/7844/console.log Wed Apr 24 08:14:20 UTC 2024 I: Downloading source for trixie/hmmer2=2.3.2+dfsg-12 --2024-04-24 08:14:21-- 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% 248M=0s 2024-04-24 08:14:21 (248 MB/s) - ‘hmmer2_2.3.2+dfsg-12.dsc’ saved [2236/2236] Wed Apr 24 08:14:21 UTC 2024 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 Apr 24 08:14:21 UTC 2024 I: Checking whether the package is not for us Wed Apr 24 08:14:21 UTC 2024 I: Starting 1st build on remote node infom02-amd64.debian.net. Wed Apr 24 08:14:21 UTC 2024 I: Preparing to do remote build '1' on infom02-amd64.debian.net. Wed Apr 24 08:15:35 UTC 2024 I: Deleting $TMPDIR on infom02-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue May 27 02:37:23 -12 2025 I: pbuilder-time-stamp: 1748356643 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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 gpgv: Signature made Thu Apr 11 09:03:57 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key 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/1849270/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='17f920e3d7114287ad6e619ff77b0e0b' 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='1849270' 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.J1eSeBFr/pbuilderrc_WcIi --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.J1eSeBFr/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' I: uname -a Linux infom02-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 24 13:34 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1849270/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: amd64 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 ... 19892 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} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libperl4-corelibs-perl{a} libpipeline1{a} libpkgconf3{a} libsquid-dev{a} libsquid1t64{a} libsub-override-perl{a} libtool{a} libuchardet0{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, 38 newly installed, 0 to remove and 0 not upgraded. Need to get 19.4 MB of archives. After unpacking 74.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-2+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1 amd64 1:5.45-2+b1 [105 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-2+b1 [43.1 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-3 [1180 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.39.3-6 [89.4 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.0-3 [1401 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main amd64 libelf1 amd64 0.190-1+b1 [176 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1 [109 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b2 [692 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 dh-exec amd64 0.29 [25.4 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libperl4-corelibs-perl all 0.005-1 [39.0 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-1+b2 [36.4 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libsquid1t64 amd64 1.9g+cvs20050121-15.1 [76.1 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libsquid-dev amd64 1.9g+cvs20050121-15.1 [144 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-1+b2 [29.7 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-1+b2 [26.2 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 rename all 2.02-1 [21.8 kB] Fetched 19.4 MB in 0s (61.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19892 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-2+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../02-libmagic1_1%3a5.45-2+b1_amd64.deb ... Unpacking libmagic1:amd64 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-2+b1_amd64.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-3_amd64.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.39.3-6_amd64.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.0-3_amd64.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... 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 libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../22-libelf1_0.190-1+b1_amd64.deb ... Unpacking libelf1:amd64 (0.190-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../24-libicu72_72.1-4+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-4+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b2_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_amd64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-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 .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package dh-exec. Preparing to unpack .../30-dh-exec_0.29_amd64.deb ... Unpacking dh-exec (0.29) ... Selecting previously unselected package libperl4-corelibs-perl. Preparing to unpack .../31-libperl4-corelibs-perl_0.005-1_all.deb ... Unpacking libperl4-corelibs-perl (0.005-1) ... Selecting previously unselected package libpkgconf3:amd64. Preparing to unpack .../32-libpkgconf3_1.8.1-1+b2_amd64.deb ... Unpacking libpkgconf3:amd64 (1.8.1-1+b2) ... Selecting previously unselected package libsquid1t64:amd64. Preparing to unpack .../33-libsquid1t64_1.9g+cvs20050121-15.1_amd64.deb ... Unpacking libsquid1t64:amd64 (1.9g+cvs20050121-15.1) ... Selecting previously unselected package libsquid-dev. Preparing to unpack .../34-libsquid-dev_1.9g+cvs20050121-15.1_amd64.deb ... Unpacking libsquid-dev (1.9g+cvs20050121-15.1) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../35-pkgconf-bin_1.8.1-1+b2_amd64.deb ... Unpacking pkgconf-bin (1.8.1-1+b2) ... Selecting previously unselected package pkgconf:amd64. Preparing to unpack .../36-pkgconf_1.8.1-1+b2_amd64.deb ... Unpacking pkgconf:amd64 (1.8.1-1+b2) ... Selecting previously unselected package rename. Preparing to unpack .../37-rename_2.02-1_all.deb ... Unpacking rename (2.02-1) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... Setting up libmagic-mgc (1:5.45-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libperl4-corelibs-perl (0.005-1) ... Setting up libmagic1:amd64 (1:5.45-2+b1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... 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 (1:5.45-2+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:amd64 (1.8.1-1+b2) ... Setting up autopoint (0.21-14) ... Setting up pkgconf-bin (1.8.1-1+b2) ... Setting up autoconf (2.71-3) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libelf1:amd64 (0.190-1+b1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Setting up libsquid1t64:amd64 (1.9g+cvs20050121-15.1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libsquid-dev (1.9g+cvs20050121-15.1) ... Setting up pkgconf:amd64 (1.8.1-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Setting up dh-exec (0.29) ... Processing triggers for libc-bin (2.37-18) ... 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 amd64 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 cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead 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.m4:2847: 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.m4:699: 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.m4:2920: AC_TRY_LINK is expanded from... configure.ac:289: ACX_PTHREAD is expanded from... lib/m4sugar/m4sh.m4:699: 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=x86_64-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/x86_64-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... x86_64-pc-linux-gnu checking host system type... x86_64-pc-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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 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 -fcf-protection -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 -fcf-protection -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 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' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. 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 May 27 14:38:22 2025 Linux infom02-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 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@/x86_64-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 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-dbgsym' in '../hmmer2-dbgsym_2.3.2+dfsg-12_amd64.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_amd64.deb'. dpkg-deb: building package 'hmmer2' in '../hmmer2_2.3.2+dfsg-12_amd64.deb'. dpkg-genbuildinfo --build=binary -O../hmmer2_2.3.2+dfsg-12_amd64.buildinfo dpkg-genchanges --build=binary -O../hmmer2_2.3.2+dfsg-12_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/1849270 and its subdirectories I: Current time: Tue May 27 02:38:34 -12 2025 I: pbuilder-time-stamp: 1748356714 Wed Apr 24 08:15:36 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom01-amd64.debian.net. Wed Apr 24 08:15:36 UTC 2024 I: Preparing to do remote build '2' on infom01-amd64.debian.net. Wed Apr 24 08:16:23 UTC 2024 I: Deleting $TMPDIR on infom01-amd64.debian.net. Wed Apr 24 08:16:24 UTC 2024 I: hmmer2_2.3.2+dfsg-12_amd64.changes: Format: 1.8 Date: Thu, 11 Apr 2024 09:59:24 +0200 Source: hmmer2 Binary: hmmer2 hmmer2-dbgsym hmmer2-doc libhmmer2-dev Architecture: amd64 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: 1f8096dac660cb1d22592e7e0061176c81cff20b 1325700 hmmer2-dbgsym_2.3.2+dfsg-12_amd64.deb cf021457577070ad5d9c8297f422cbbf6d82a044 78828 hmmer2-doc_2.3.2+dfsg-12_all.deb 0b093f1e88654ef3180537f86d85bd160af59a0f 5980 hmmer2_2.3.2+dfsg-12_amd64.buildinfo bc134847b175f27c982a36680b8ee131015c837b 314396 hmmer2_2.3.2+dfsg-12_amd64.deb b621d1ff7c8398af10862af7bbbe98af044b63f9 96712 libhmmer2-dev_2.3.2+dfsg-12_amd64.deb Checksums-Sha256: 746e726e0bfbc58dfc3ba237b6d9de937520d2967f2719f40816d816d88e8a59 1325700 hmmer2-dbgsym_2.3.2+dfsg-12_amd64.deb dbb6f57db9c45fb7850a91b8deb74ed54a577267d2e232fb49a343f2238ae495 78828 hmmer2-doc_2.3.2+dfsg-12_all.deb 7ebda9bcd1ea15bee9ce452d45506997ef6652910c62cb1c9489972a9c45df60 5980 hmmer2_2.3.2+dfsg-12_amd64.buildinfo 4109b4c5145d90ea2e62a56c78b8c5797d8dc9ad3593c6149d13417ecd46b20d 314396 hmmer2_2.3.2+dfsg-12_amd64.deb ab4e56fa5afef25c4c43dd666bdeb8319d8796dd6bb0d322dadde6fd28a9473b 96712 libhmmer2-dev_2.3.2+dfsg-12_amd64.deb Files: 164ac864e0d0752ebf7c449ef7a663fa 1325700 debug optional hmmer2-dbgsym_2.3.2+dfsg-12_amd64.deb 2a48f56f444afd93a54432c1d371d40a 78828 doc optional hmmer2-doc_2.3.2+dfsg-12_all.deb e189c80219e0187b29a76e5a84a0532d 5980 science optional hmmer2_2.3.2+dfsg-12_amd64.buildinfo ff8fdc7d890aa5fb827dd361b610c712 314396 science optional hmmer2_2.3.2+dfsg-12_amd64.deb bd0283277d8529a091fd8f596867e5e1 96712 libdevel optional libhmmer2-dev_2.3.2+dfsg-12_amd64.deb Wed Apr 24 08:16:25 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_34-7844.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.J1eSeBFr/hmmer2_2.3.2+dfsg-12.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.J1eSeBFr/hmmer2_2.3.2+dfsg-12.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.J1eSeBFr/hmmer2_2.3.2+dfsg-12.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.J1eSeBFr/b1/hmmer2_2.3.2+dfsg-12_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.J1eSeBFr/b2/hmmer2_2.3.2+dfsg-12_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.341s) 0.341s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.036s) 0.036s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 641ms CPU time consumed: 642ms Wed Apr 24 08:16:26 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Wed Apr 24 08:16:26 UTC 2024 I: hmmer2 from trixie built successfully and reproducibly on amd64. Wed Apr 24 08:16:27 UTC 2024 I: Submitting .buildinfo files to external archives: Wed Apr 24 08:16:27 UTC 2024 I: Submitting 8.0K b1/hmmer2_2.3.2+dfsg-12_amd64.buildinfo.asc Wed Apr 24 08:16:28 UTC 2024 I: Submitting 8.0K b2/hmmer2_2.3.2+dfsg-12_amd64.buildinfo.asc Wed Apr 24 08:16:29 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Apr 24 08:16:29 UTC 2024 I: Done submitting .buildinfo files. Wed Apr 24 08:16:29 UTC 2024 I: Removing signed hmmer2_2.3.2+dfsg-12_amd64.buildinfo.asc files: removed './b1/hmmer2_2.3.2+dfsg-12_amd64.buildinfo.asc' removed './b2/hmmer2_2.3.2+dfsg-12_amd64.buildinfo.asc'