Running as unit: rb-build-arm64_7-68107.service ==================================================================================== Wed Apr 23 06:12:07 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_7) on jenkins, called using "codethink04-arm64 codethink03-arm64" as arguments. Wed Apr 23 06:12:07 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-z0jgsj0J" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Apr 23 06:12:07 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Wed Apr 23 06:12:07 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-CgOA1N' Wed Apr 23 06:12:08 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Wed Apr 23 06:12:08 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-k5lziK' ok, let's check if libpsortb is building anywhere yet… ok, libpsortb is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of libpsortb 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 Apr 23 06:12:25 UTC 2025 I: starting to build libpsortb/unstable/arm64 on jenkins on '2025-04-23 06:12' Wed Apr 23 06:12:25 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_7/68107/console.log 1745388745 arm64 unstable libpsortb Wed Apr 23 06:12:25 UTC 2025 I: Downloading source for unstable/libpsortb=1.0+dfsg-7 --2025-04-23 06:12:25-- http://deb.debian.org/debian/pool/main/libp/libpsortb/libpsortb_1.0%2bdfsg-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2350 (2.3K) [text/prs.lines.tag] Saving to: ‘libpsortb_1.0+dfsg-7.dsc’ 0K .. 100% 334M=0s 2025-04-23 06:12:25 (334 MB/s) - ‘libpsortb_1.0+dfsg-7.dsc’ saved [2350/2350] --2025-04-23 06:12:25-- http://deb.debian.org/debian/pool/main/libp/libpsortb/libpsortb_1.0%2bdfsg-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2350 (2.3K) [text/prs.lines.tag] Saving to: ‘libpsortb_1.0+dfsg-7.dsc’ 0K .. 100% 334M=0s 2025-04-23 06:12:25 (334 MB/s) - ‘libpsortb_1.0+dfsg-7.dsc’ saved [2350/2350] Wed Apr 23 06:12:25 UTC 2025 I: libpsortb_1.0+dfsg-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libpsortb Binary: libmodhmm0, libmodhmm-dev, libsvmloc0, libsvmloc-dev Architecture: any Version: 1.0+dfsg-7 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://www.psort.org/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/libpsortb Vcs-Git: https://salsa.debian.org/med-team/libpsortb.git Build-Depends: debhelper-compat (= 13), d-shlibs, libsvm-dev, libsquid-dev, libhmmer2-dev, pkgconf Package-List: libmodhmm-dev deb libdevel optional arch=any libmodhmm0 deb libs optional arch=any libsvmloc-dev deb libdevel optional arch=any libsvmloc0 deb libs optional arch=any Checksums-Sha1: 44d3705f46372837f5ecdf8fa2ad0273a6c38433 95644 libpsortb_1.0+dfsg.orig.tar.xz b13c9071a55d1fe8f0fe968c8271e74a977871a7 10220 libpsortb_1.0+dfsg-7.debian.tar.xz Checksums-Sha256: 5021b7ac656b33b8f0aa8c2e0403056a5459e1b92c17008b3ff442e262b3e2e5 95644 libpsortb_1.0+dfsg.orig.tar.xz 2a17d0a360424c133b6ca22f3d7fc70d8eb437015bf79b38802ec2136360e1af 10220 libpsortb_1.0+dfsg-7.debian.tar.xz Files: f9c6cf32032da4c9e88b609fba9bb02d 95644 libpsortb_1.0+dfsg.orig.tar.xz ef1736bb4ae38302866e97128937776e 10220 libpsortb_1.0+dfsg-7.debian.tar.xz Dgit: 9bafca52917fb0f97fdcfae9782dc8bea37d31de debian archive/debian/1.0+dfsg-7 https://git.dgit.debian.org/libpsortb -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmbLNAUUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdpbTBAAue6pNuR0IsU/ogBxhLroVEpbYERU GL9QIn6xm2CGbnpQTlMVPMJkJ+969D0sAMAsy51CZ0saoP9mgAxL9h3AXNHjsJ3i CLqmi5miQe+/BpDM4EOWN2AxcL9FRYS9oi5WPvdtG9jcMWJhhm03MgB67Nz5iuJi h/5nYHeZ2Ed17ckYQMVCX+qP1xaeAdElX93+rLLaNZCV/dY82Kc8cLzaLCO+aRWf 7hJvJhXmDeCG5Go2CZhYOATgFo3LyvPf6QJqq1gUjEtcPlo8Qz9y04zVVntDtJ9w P2hTd9Dra8xrOgF5Q1hyqGVCalS+Oe6fYU9k4vhzx8EqiDvbX1Z3A1LbzJML+Oja HQHvEnkYL8pcCtj2wSCZsdgkX5QWB/zgRIVoUNTccxEqSUEpHi58wXtbCevv22cr 74HZVSyOlJSzDz5dEPz0stzspItEF9a2KsO9ZHhSl+54vf2bCV4l4kyt+6neIv9p 6J542LXdkj51N0hyV2d0p7SQp+duydfJWSA2+6vFBioZqFV3rfHBaDqfP/CkcOuK /57X8hzxkUV4GkvBwR/u1AEF8HVBP9B/d3k9YMF7GeotxdmMrTVVTwdI7Gzr5ikh wx1htA3IoR3lNGbe1MsEvx6YW4PkO9qkwS9ixvOfsS62dRttp1sM6qADhJVUP1OY qpapCM//shZ/aQU= =RFu7 -----END PGP SIGNATURE----- Wed Apr 23 06:12:25 UTC 2025 I: Checking whether the package is not for us Wed Apr 23 06:12:25 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Wed Apr 23 06:12:25 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Wed Apr 23 06:12:25 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Wed Apr 23 06:12:25 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-MEFkCC' ==================================================================================== Wed Apr 23 06:12:27 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "1 libpsortb unstable /srv/reproducible-results/rbuild-debian/r-b-build.REw1aXKj 1.0+dfsg-7" as arguments. Wed Apr 23 06:12:27 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-x5qZppC0" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Apr 23 06:12:27 UTC 2025 I: Downloading source for unstable/libpsortb=1.0+dfsg-7 Reading package lists... NOTICE: 'libpsortb' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libpsortb.git Please use: git clone https://salsa.debian.org/med-team/libpsortb.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 108 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main libpsortb 1.0+dfsg-7 (dsc) [2350 B] Get:2 http://deb.debian.org/debian unstable/main libpsortb 1.0+dfsg-7 (tar) [95.6 kB] Get:3 http://deb.debian.org/debian unstable/main libpsortb 1.0+dfsg-7 (diff) [10.2 kB] Fetched 108 kB in 0s (3770 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'libpsortb' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libpsortb.git Please use: git clone https://salsa.debian.org/med-team/libpsortb.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 108 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main libpsortb 1.0+dfsg-7 (dsc) [2350 B] Get:2 http://deb.debian.org/debian unstable/main libpsortb 1.0+dfsg-7 (tar) [95.6 kB] Get:3 http://deb.debian.org/debian unstable/main libpsortb 1.0+dfsg-7 (diff) [10.2 kB] Fetched 108 kB in 0s (3770 kB/s) Download complete and in download only mode ============================================================================= Building libpsortb in unstable on arm64 on codethink04-arm64 now. Date: Wed Apr 23 07:12:27 BST 2025 Date UTC: Wed Apr 23 06:12:27 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 Apr 22 18:12:27 -12 2025 I: pbuilder-time-stamp: 1745388747 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 [libpsortb_1.0+dfsg-7.dsc] I: copying [./libpsortb_1.0+dfsg.orig.tar.xz] I: copying [./libpsortb_1.0+dfsg-7.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./libpsortb_1.0+dfsg-7.dsc: unsupported subcommand dpkg-source: info: extracting libpsortb in libpsortb-1.0+dfsg dpkg-source: info: unpacking libpsortb_1.0+dfsg.orig.tar.xz dpkg-source: info: unpacking libpsortb_1.0+dfsg-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libs.patch dpkg-source: info: applying use_debian_packaged_libsvm.patch dpkg-source: info: applying remove_unused_debug_functions.patch dpkg-source: info: applying fix-implicit-declaration.patch dpkg-source: info: applying gcc14.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2862450/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='ec750af594d948edbe1404d0bbd0b048' 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='2862450' 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.REw1aXKj/pbuilderrc_A5zV --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.REw1aXKj/b1 --logfile b1/build.log libpsortb_1.0+dfsg-7.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 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2862450/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), d-shlibs, libsvm-dev, libsquid-dev, libhmmer2-dev, pkgconf dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19953 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 d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on libsvm-dev; however: Package libsvm-dev is not installed. pbuilder-satisfydepends-dummy depends on libsquid-dev; however: Package libsquid-dev is not installed. pbuilder-satisfydepends-dummy depends on libhmmer2-dev; however: Package libhmmer2-dev is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf 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} d-shlibs{a} debhelper{a} dh-autoreconf{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} libhmmer2-dev{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpkgconf3{a} libsquid-dev{a} libsquid1t64{a} libsvm-dev{a} libsvm3{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} pkgconf{a} pkgconf-bin{a} po-debconf{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 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 0.23.1-1 [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 1.23.0-7 [1129 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41-4 [93.9 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 2.13.0-1 [1404 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 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 d-shlibs all 0.109 [11.1 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 23 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.4 [629 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.2 [919 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libhmmer2-dev arm64 2.3.2+dfsg-12+b2 [92.3 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 libsvm3 arm64 3.24+ds-6.1 [38.6 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libsvm-dev arm64 3.24+ds-6.1 [59.7 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Fetched 11.4 MB in 0s (97.9 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 ... 19953 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_0.23.1-1_arm64.deb ... Unpacking gettext-base (0.23.1-1) ... 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_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41-4_arm64.deb ... Unpacking bsdextrautils (2.41-4) ... 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_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... 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_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../15-d-shlibs_0.109_all.deb ... Unpacking d-shlibs (0.109) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-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 .../20-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 .../21-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 .../22-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../24-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.4_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-1_arm64.deb ... Unpacking gettext (0.23.1-1) ... 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_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Selecting previously unselected package libhmmer2-dev:arm64. Preparing to unpack .../30-libhmmer2-dev_2.3.2+dfsg-12+b2_arm64.deb ... Unpacking libhmmer2-dev:arm64 (2.3.2+dfsg-12+b2) ... 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 libsvm3:arm64. Preparing to unpack .../34-libsvm3_3.24+ds-6.1_arm64.deb ... Unpacking libsvm3:arm64 (3.24+ds-6.1) ... Selecting previously unselected package libsvm-dev:arm64. Preparing to unpack .../35-libsvm-dev_3.24+ds-6.1_arm64.deb ... Unpacking libsvm-dev:arm64 (3.24+ds-6.1) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../36-pkgconf-bin_1.8.1-4_arm64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../37-pkgconf_1.8.1-4_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-4) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up bsdextrautils (2.41-4) ... 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 libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-8) ... 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 (0.23.1-1) ... Setting up d-shlibs (0.109) ... 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 libhmmer2-dev:arm64 (2.3.2+dfsg-12+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up libsquid1t64:arm64 (1.9g+cvs20050121-15.1+b2) ... Setting up libsvm3:arm64 (3.24+ds-6.1) ... 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 (0.23.1-1) ... 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 libsvm-dev:arm64 (3.24+ds-6.1) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.2) ... Processing triggers for libc-bin (2.41-7) ... 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/libpsortb-1.0+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 > ../libpsortb_1.0+dfsg-7_source.changes dpkg-buildpackage: info: source package libpsortb dpkg-buildpackage: info: source version 1.0+dfsg-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: Consider adding 'AC_CONFIG_MACRO_DIRS([m4])' to configure.ac, libtoolize: and rerunning libtoolize and aclocal. libtoolize: Consider adding '-I m4' to ACLOCAL_AMFLAGS in Makefile.am. configure.ac:7: warning: The macro 'AC_CONFIG_HEADER' is obsolete. configure.ac:7: You should run autoupdate. ./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from... configure.ac:7: the top level configure.ac:17: warning: The macro 'AC_PROG_LIBTOOL' is obsolete. configure.ac:17: You should run autoupdate. aclocal.m4:122: AC_PROG_LIBTOOL is expanded from... configure.ac:17: the top level configure.ac:47: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.ac:47: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.ac:47: the top level configure.ac:55: warning: The macro 'AC_HEADER_TIME' is obsolete. configure.ac:55: You should run autoupdate. ./lib/autoconf/headers.m4:702: AC_HEADER_TIME is expanded from... configure.ac:55: the top level configure.ac:12: installing './compile' configure.ac:17: installing './config.guess' configure.ac:17: installing './config.sub' configure.ac:8: installing './install-sh' configure.ac:8: installing './missing' modhmm0.92b/Makefile.am: installing './depcomp' dh_auto_configure ./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 checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes checking for g++... g++ 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 g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc 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 whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ranlib... ranlib checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/time.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for main in -lm... yes checking for egrep... (cached) /usr/bin/grep -E checking for float.h... yes checking for limits.h... yes checking for memory.h... yes checking for netinet/in.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for _Bool... yes checking for stdbool.h that conforms to C99 or later... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking whether struct tm is in sys/time.h or time.h... time.h checking for declarations of fseeko and ftello... yes checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking whether lstat correctly handles trailing slash... yes checking whether stat accepts an empty string... no checking for strftime... yes checking for vprintf... yes checking for working strtod... yes checking for atexit... yes checking for floor... yes checking for memmove... yes checking for memset... yes checking for pow... yes checking for sqrt... yes checking for strchr... yes checking for strcspn... yes checking for strerror... yes checking for strpbrk... yes checking for strrchr... yes checking for strspn... yes checking for strstr... yes checking for strtol... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating svmloc/Makefile config.status: creating modhmm0.92b/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' make all-recursive make[2]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' Making all in svmloc make[3]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o binding.lo binding.cpp /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o svmloc.lo svmloc.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c svmloc.cpp -fPIC -DPIC -o .libs/svmloc.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c binding.cpp -fPIC -DPIC -o .libs/binding.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c binding.cpp -o binding.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c svmloc.cpp -o svmloc.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -version-info 0:0:0 -lsvm -Wl,-z,relro -Wl,-z,now -o libsvmloc.la -rpath /usr/lib/aarch64-linux-gnu binding.lo svmloc.lo -lm libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o .libs/binding.o .libs/svmloc.o -lsvm -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -Werror=format-security -mbranch-protection=standard -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libsvmloc.so.0 -o .libs/libsvmloc.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libsvmloc.so.0" && ln -s "libsvmloc.so.0.0.0" "libsvmloc.so.0") libtool: link: (cd ".libs" && rm -f "libsvmloc.so" && ln -s "libsvmloc.so.0.0.0" "libsvmloc.so") libtool: link: ar cr .libs/libsvmloc.a binding.o svmloc.o libtool: link: ranlib .libs/libsvmloc.a libtool: link: ( cd ".libs" && rm -f "libsvmloc.la" && ln -s "../libsvmloc.la" "libsvmloc.la" ) make[3]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' Making all in modhmm0.92b make[3]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o core_algorithms_multialpha.lo core_algorithms_multialpha.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o debug_funcs.lo debug_funcs.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o hmmsearch.lo hmmsearch.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o readhmm.lo readhmm.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o readhmm_multialpha.lo readhmm_multialpha.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o readseqs_multialpha.lo readseqs_multialpha.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o std_calculation_funcs.lo std_calculation_funcs.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o std_funcs.lo std_funcs.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o training_algorithms_multialpha.lo training_algorithms_multialpha.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c debug_funcs.c -fPIC -DPIC -o .libs/debug_funcs.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readseqs_multialpha.c -fPIC -DPIC -o .libs/readseqs_multialpha.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c training_algorithms_multialpha.c -fPIC -DPIC -o .libs/training_algorithms_multialpha.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readhmm_multialpha.c -fPIC -DPIC -o .libs/readhmm_multialpha.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readhmm.c -fPIC -DPIC -o .libs/readhmm.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c hmmsearch.c -fPIC -DPIC -o .libs/hmmsearch.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c std_calculation_funcs.c -fPIC -DPIC -o .libs/std_calculation_funcs.o debug_funcs.c:7:76: warning: 'struct hmm_multi_s' declared inside parameter list will not be visible outside of this definition or declaration 7 | int read_multi_prior_file_multi(struct emission_dirichlet_s *em_di, struct hmm_multi_s *hmmp, FILE *priorfile, int alphabet); | ^~~~~~~~~~~ debug_funcs.c:7:40: warning: 'struct emission_dirichlet_s' declared inside parameter list will not be visible outside of this definition or declaration 7 | int read_multi_prior_file_multi(struct emission_dirichlet_s *em_di, struct hmm_multi_s *hmmp, FILE *priorfile, int alphabet); | ^~~~~~~~~~~~~~~~~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c std_funcs.c -fPIC -DPIC -o .libs/std_funcs.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c core_algorithms_multialpha.c -fPIC -DPIC -o .libs/core_algorithms_multialpha.o readseqs_multialpha.c: In function 'get_sequence_std_multi': readseqs_multialpha.c:121:55: warning: unknown escape sequence: '\s' 121 | if(line[0] == '<' || line[0] == '#' || line[0] == '\s' || line[0] == '\n' || line[0] == '/') { | ^~~~ readseqs_multialpha.c: In function 'get_sequences_msa_std_multi': readseqs_multialpha.c:372:18: warning: unknown escape sequence: '\s' 372 | else if(i == '\s' && i == '\n') { | ^~~~ readseqs_multialpha.c: In function 'get_sequence_std_multi': readseqs_multialpha.c:286:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 286 | fgets(line, MAX_LINE, seqfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c: In function 'msa_baum_welch_dirichlet_multi': training_algorithms_multialpha.c:701:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 701 | alphabet = (int)hmmp->alphabet; | ^ training_algorithms_multialpha.c:710:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 710 | alphabet = (int)hmmp->alphabet_2; | ^ training_algorithms_multialpha.c:719:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 719 | alphabet = (int)hmmp->alphabet_3; | ^ training_algorithms_multialpha.c:728:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 728 | alphabet = (int)hmmp->alphabet_4; | ^ readseqs_multialpha.c: In function 'get_sequences_msa_std_multi': readseqs_multialpha.c:625:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 625 | fgets(line, MAX_LINE, seqfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readseqs_multialpha.c:754:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 754 | fgets(line, MAX_LINE, seqfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readseqs_multialpha.c:874:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 874 | fgets(line, MAX_LINE, seqfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readseqs_multialpha.c:995:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 995 | fgets(line, MAX_LINE, seqfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c: In function 'readhmm_multialpha': readhmm_multialpha.c:326:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 326 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c: In function 'extended_msa_baum_welch_dirichlet_multi': training_algorithms_multialpha.c:1639:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1639 | alphabet = (int)hmmp->alphabet; | ^ training_algorithms_multialpha.c:1646:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1646 | alphabet = (int)hmmp->alphabet_2; | ^ readhmm_multialpha.c: In function 'read_module_multi': readhmm_multialpha.c:1039:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1039 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1074:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1074 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1108:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1108 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1137:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1137 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1140:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1140 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1166:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1166 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1169:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1169 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1195:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1195 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1199:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1199 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1226:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1226 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1233:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1233 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c:1653:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1653 | alphabet = (int)hmmp->alphabet_3; | ^ training_algorithms_multialpha.c:1660:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1660 | alphabet = (int)hmmp->alphabet_4; | ^ training_algorithms_multialpha.c:1784:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1784 | alphabet = (int)hmmp->alphabet; | ^ training_algorithms_multialpha.c:1791:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1791 | alphabet = (int)hmmp->alphabet_2; | ^ training_algorithms_multialpha.c:1798:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1798 | alphabet = (int)hmmp->alphabet_3; | ^ training_algorithms_multialpha.c:1805:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1805 | alphabet = (int)hmmp->alphabet_4; | ^ readhmm.c: In function 'readhmm': readhmm.c:69:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm.c: In function 'readanhmm': readhmm.c:342:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 342 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c: In function 'add_to_E_multi': readhmm.c: In function 'read_module': readhmm.c:745:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 745 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm.c:780:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 780 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm.c:815:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 815 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm.c:844:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 844 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm.c:848:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 848 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c:3589:43: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 3589 | (char*)alphabet); | ^ training_algorithms_multialpha.c:3593:49: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 3593 | (char*)alphabet); | ^ readhmm.c: In function 'read_prior_files': readhmm.c:1225:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1225 | fgets(ps, 2048, priorfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c:3618:36: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 3618 | (char*)alphabet); | ^ training_algorithms_multialpha.c:3622:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 3622 | (char*)alphabet); | ^ hmmsearch.c: In function 'get_nullmodel_score_multi': hmmsearch.c:656:42: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] 656 | printf("Could not find letter %s when scoring null model\n", &seq[l]); | ~^ ~~~~~~~ | | | | char * struct letter_s * hmmsearch.c:674:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] 674 | printf("Could not find letter %s when scoring null model\n", &seq_2[l]); | ~^ ~~~~~~~~~ | | | | char * struct letter_s * hmmsearch.c:693:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] 693 | printf("Could not find letter %s when scoring null model\n", &seq_3[l]); | ~^ ~~~~~~~~~ | | | | char * struct letter_s * hmmsearch.c:712:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] 712 | printf("Could not find letter %s when scoring null model\n", &seq[l]); | ~^ ~~~~~~~ | | | | char * struct letter_s * std_calculation_funcs.c: In function 'update_labelings': std_calculation_funcs.c:1295:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1295 | cur_address = (int)((cur_rowp+v)->labeling); | ^ std_calculation_funcs.c:1309:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1309 | if((int)((cur_rowp+w)->labeling) == cur_address && (cur_rowp + w)->is_updated == NO) { | ^ std_calculation_funcs.c: In function 'deallocate_row_labelings': std_calculation_funcs.c:1425:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1425 | cur_address = (int)((prev_rowp+v)->labeling); | ^ std_calculation_funcs.c:1430:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1430 | if((int)((prev_rowp+w)->labeling) == cur_address) { | ^ std_funcs.c: In function 'get_replacement_letter_index_single': std_funcs.c:680:62: warning: comparison between pointer and integer 680 | if(((replacement_letters->letters + a_index)->letter)[0] == c) { | ^~ std_funcs.c: In function 'get_nr_alphabets': std_funcs.c:2726:10: warning: 'fgets' writing 4000 bytes into a region of size 1000 overflows the destination [-Wstringop-overflow=] 2726 | if(fgets(s, MAX_LINE, hmmfile) != NULL) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ std_funcs.c:2719:8: note: destination object 's' of size 1000 2719 | char s[1000]; | ^ In file included from /usr/include/stdio.h:970, from std_funcs.c:1: /usr/include/aarch64-linux-gnu/bits/stdio2.h:305:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' 305 | fgets (__fortify_clang_overload_arg (char *, __restrict, __s), int __n, | ^~~~~ std_funcs.c:2733:8: warning: 'fgets' writing 4000 bytes into a region of size 1000 overflows the destination [-Wstringop-overflow=] 2733 | if(fgets(s, MAX_LINE, hmmfile) != NULL) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ std_funcs.c:2719:8: note: destination object 's' of size 1000 2719 | char s[1000]; | ^ /usr/include/aarch64-linux-gnu/bits/stdio2.h:305:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' 305 | fgets (__fortify_clang_overload_arg (char *, __restrict, __s), int __n, | ^~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c hmmsearch.c -o hmmsearch.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c debug_funcs.c -o debug_funcs.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readseqs_multialpha.c -o readseqs_multialpha.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readhmm.c -o readhmm.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c std_calculation_funcs.c -o std_calculation_funcs.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readhmm_multialpha.c -o readhmm_multialpha.o >/dev/null 2>&1 In function 'fgets', inlined from 'get_nr_alphabets' at std_funcs.c:2726:10: /usr/include/aarch64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'get_nr_alphabets' at std_funcs.c:2733:8: /usr/include/aarch64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c std_funcs.c -o std_funcs.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c core_algorithms_multialpha.c -o core_algorithms_multialpha.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c training_algorithms_multialpha.c -o training_algorithms_multialpha.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -version-info 0:0:0 -Wl,-z,relro -Wl,-z,now -o libmodhmm.la -rpath /usr/lib/aarch64-linux-gnu core_algorithms_multialpha.lo debug_funcs.lo hmmsearch.lo readhmm.lo readhmm_multialpha.lo readseqs_multialpha.lo std_calculation_funcs.lo std_funcs.lo training_algorithms_multialpha.lo -lm libtool: link: gcc -shared -fPIC -DPIC .libs/core_algorithms_multialpha.o .libs/debug_funcs.o .libs/hmmsearch.o .libs/readhmm.o .libs/readhmm_multialpha.o .libs/readseqs_multialpha.o .libs/std_calculation_funcs.o .libs/std_funcs.o .libs/training_algorithms_multialpha.o -lm -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -Werror=format-security -mbranch-protection=standard -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libmodhmm.so.0 -o .libs/libmodhmm.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libmodhmm.so.0" && ln -s "libmodhmm.so.0.0.0" "libmodhmm.so.0") libtool: link: (cd ".libs" && rm -f "libmodhmm.so" && ln -s "libmodhmm.so.0.0.0" "libmodhmm.so") libtool: link: ar cr .libs/libmodhmm.a core_algorithms_multialpha.o debug_funcs.o hmmsearch.o readhmm.o readhmm_multialpha.o readseqs_multialpha.o std_calculation_funcs.o std_funcs.o training_algorithms_multialpha.o libtool: link: ranlib .libs/libmodhmm.a libtool: link: ( cd ".libs" && rm -f "libmodhmm.la" && ln -s "../libmodhmm.la" "libmodhmm.la" ) make[3]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' make[3]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[3]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[2]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' dh_auto_test make -j12 check "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' Making check in svmloc make[2]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' Making check in modhmm0.92b make[2]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' make[2]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[2]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' dh_auto_install make -j1 install DESTDIR=/build/reproducible-path/libpsortb-1.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' Making install in svmloc make[3]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' make[4]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' /usr/bin/mkdir -p '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libsvmloc.la '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libsvmloc.so.0.0.0 /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.so.0.0.0 libtool: install: (cd /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libsvmloc.so.0.0.0 libsvmloc.so.0 || { rm -f libsvmloc.so.0 && ln -s libsvmloc.so.0.0.0 libsvmloc.so.0; }; }) libtool: install: (cd /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libsvmloc.so.0.0.0 libsvmloc.so || { rm -f libsvmloc.so && ln -s libsvmloc.so.0.0.0 libsvmloc.so; }; }) libtool: install: /usr/bin/install -c .libs/libsvmloc.lai /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.la libtool: install: /usr/bin/install -c .libs/libsvmloc.a /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.a libtool: install: chmod 644 /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.a libtool: install: ranlib /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' make[3]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' Making install in modhmm0.92b make[3]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' make[4]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' /usr/bin/mkdir -p '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libmodhmm.la '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libmodhmm.so.0.0.0 /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.so.0.0.0 libtool: install: (cd /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libmodhmm.so.0.0.0 libmodhmm.so.0 || { rm -f libmodhmm.so.0 && ln -s libmodhmm.so.0.0.0 libmodhmm.so.0; }; }) libtool: install: (cd /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libmodhmm.so.0.0.0 libmodhmm.so || { rm -f libmodhmm.so && ln -s libmodhmm.so.0.0.0 libmodhmm.so; }; }) libtool: install: /usr/bin/install -c .libs/libmodhmm.lai /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.la libtool: install: /usr/bin/install -c .libs/libmodhmm.a /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.a libtool: install: chmod 644 /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.a libtool: install: ranlib /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' make[3]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' make[3]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[4]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[3]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[2]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ debian/tmp/usr/lib/*/libmodhmm.so Library package automatic movement utility set -e install -d -m 755 debian/libmodhmm-dev/usr/lib/aarch64-linux-gnu install -d -m 755 debian/libmodhmm0/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.a debian/libmodhmm-dev/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.so debian/libmodhmm-dev/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.so.0 debian/libmodhmm0/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.so.0.0.0 debian/libmodhmm0/usr/lib/aarch64-linux-gnu PKGDEV=libmodhmm-dev PKGSHL=libmodhmm0 d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ debian/tmp/usr/lib/*/libsvmloc.so Library package automatic movement utility --> libsvm-dev package exists. set -e install -d -m 755 debian/libsvmloc-dev/usr/lib/aarch64-linux-gnu install -d -m 755 debian/libsvmloc0/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.a debian/libsvmloc-dev/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.so debian/libsvmloc-dev/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.so.0 debian/libsvmloc0/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.so.0.0.0 debian/libsvmloc0/usr/lib/aarch64-linux-gnu PKGDEV=libsvmloc-dev PKGSHL=libsvmloc0 find debian -name "lib*.la" -delete make[1]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' dh_installdocs dh_installchangelogs 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 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 dh_md5sums dh_builddeb dpkg-deb: building package 'libmodhmm0' in '../libmodhmm0_1.0+dfsg-7_arm64.deb'. dpkg-deb: building package 'libmodhmm0-dbgsym' in '../libmodhmm0-dbgsym_1.0+dfsg-7_arm64.deb'. dpkg-deb: building package 'libmodhmm-dev' in '../libmodhmm-dev_1.0+dfsg-7_arm64.deb'. dpkg-deb: building package 'libsvmloc0' in '../libsvmloc0_1.0+dfsg-7_arm64.deb'. dpkg-deb: building package 'libsvmloc0-dbgsym' in '../libsvmloc0-dbgsym_1.0+dfsg-7_arm64.deb'. dpkg-deb: building package 'libsvmloc-dev' in '../libsvmloc-dev_1.0+dfsg-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libpsortb_1.0+dfsg-7_arm64.buildinfo dpkg-genchanges --build=binary -O../libpsortb_1.0+dfsg-7_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/2862450 and its subdirectories I: Current time: Tue Apr 22 18:13:17 -12 2025 I: pbuilder-time-stamp: 1745388797 Wed Apr 23 06:13:17 UTC 2025 I: Signing ./b1/libpsortb_1.0+dfsg-7_arm64.buildinfo as libpsortb_1.0+dfsg-7_arm64.buildinfo.asc Wed Apr 23 06:13:17 UTC 2025 I: Signed ./b1/libpsortb_1.0+dfsg-7_arm64.buildinfo as ./b1/libpsortb_1.0+dfsg-7_arm64.buildinfo.asc Wed Apr 23 06:13:17 UTC 2025 - build #1 for libpsortb/unstable/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Wed Apr 23 06:13:17 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-x5qZppC0, removing. /srv/reproducible-results/rbuild-debian/r-b-build.REw1aXKj: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Apr 23 06:13 b1 drwxr-xr-x 2 jenkins jenkins 4096 Apr 23 06:12 b2 -rw-r--r-- 1 jenkins jenkins 2350 Aug 25 2024 libpsortb_1.0+dfsg-7.dsc -rw------- 1 jenkins jenkins 3493 Apr 23 06:12 rbuildlog.3n04bey /srv/reproducible-results/rbuild-debian/r-b-build.REw1aXKj/b1: total 584 -rw-r--r-- 1 jenkins jenkins 69045 Apr 23 06:13 build.log -rw-r--r-- 1 jenkins jenkins 70280 Apr 23 06:13 libmodhmm-dev_1.0+dfsg-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 211280 Apr 23 06:13 libmodhmm0-dbgsym_1.0+dfsg-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 68124 Apr 23 06:13 libmodhmm0_1.0+dfsg-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 10220 Apr 23 06:13 libpsortb_1.0+dfsg-7.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2350 Apr 23 06:13 libpsortb_1.0+dfsg-7.dsc -rw-r--r-- 1 jenkins jenkins 6660 Apr 23 06:13 libpsortb_1.0+dfsg-7_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 7542 Apr 23 06:13 libpsortb_1.0+dfsg-7_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2918 Apr 23 06:13 libpsortb_1.0+dfsg-7_arm64.changes -rw-r--r-- 1 jenkins jenkins 1338 Apr 23 06:13 libpsortb_1.0+dfsg-7_source.changes -rw-r--r-- 1 jenkins jenkins 12028 Apr 23 06:13 libsvmloc-dev_1.0+dfsg-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 98660 Apr 23 06:13 libsvmloc0-dbgsym_1.0+dfsg-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 12828 Apr 23 06:13 libsvmloc0_1.0+dfsg-7_arm64.deb /srv/reproducible-results/rbuild-debian/r-b-build.REw1aXKj/b2: total 0 Wed Apr 23 06:13:18 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Apr 22 18:12:27 -12 2025 I: pbuilder-time-stamp: 1745388747 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 [libpsortb_1.0+dfsg-7.dsc] I: copying [./libpsortb_1.0+dfsg.orig.tar.xz] I: copying [./libpsortb_1.0+dfsg-7.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./libpsortb_1.0+dfsg-7.dsc: unsupported subcommand dpkg-source: info: extracting libpsortb in libpsortb-1.0+dfsg dpkg-source: info: unpacking libpsortb_1.0+dfsg.orig.tar.xz dpkg-source: info: unpacking libpsortb_1.0+dfsg-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libs.patch dpkg-source: info: applying use_debian_packaged_libsvm.patch dpkg-source: info: applying remove_unused_debug_functions.patch dpkg-source: info: applying fix-implicit-declaration.patch dpkg-source: info: applying gcc14.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2862450/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='ec750af594d948edbe1404d0bbd0b048' 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='2862450' 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.REw1aXKj/pbuilderrc_A5zV --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.REw1aXKj/b1 --logfile b1/build.log libpsortb_1.0+dfsg-7.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 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2862450/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), d-shlibs, libsvm-dev, libsquid-dev, libhmmer2-dev, pkgconf dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19953 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 d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on libsvm-dev; however: Package libsvm-dev is not installed. pbuilder-satisfydepends-dummy depends on libsquid-dev; however: Package libsquid-dev is not installed. pbuilder-satisfydepends-dummy depends on libhmmer2-dev; however: Package libhmmer2-dev is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf 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} d-shlibs{a} debhelper{a} dh-autoreconf{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} libhmmer2-dev{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpkgconf3{a} libsquid-dev{a} libsquid1t64{a} libsvm-dev{a} libsvm3{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} pkgconf{a} pkgconf-bin{a} po-debconf{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 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 0.23.1-1 [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 1.23.0-7 [1129 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41-4 [93.9 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 2.13.0-1 [1404 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 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 d-shlibs all 0.109 [11.1 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 23 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.4 [629 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.2 [919 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libhmmer2-dev arm64 2.3.2+dfsg-12+b2 [92.3 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 libsvm3 arm64 3.24+ds-6.1 [38.6 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libsvm-dev arm64 3.24+ds-6.1 [59.7 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Fetched 11.4 MB in 0s (97.9 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 ... 19953 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_0.23.1-1_arm64.deb ... Unpacking gettext-base (0.23.1-1) ... 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_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41-4_arm64.deb ... Unpacking bsdextrautils (2.41-4) ... 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_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... 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_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../15-d-shlibs_0.109_all.deb ... Unpacking d-shlibs (0.109) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-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 .../20-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 .../21-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 .../22-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../24-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.4_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-1_arm64.deb ... Unpacking gettext (0.23.1-1) ... 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_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Selecting previously unselected package libhmmer2-dev:arm64. Preparing to unpack .../30-libhmmer2-dev_2.3.2+dfsg-12+b2_arm64.deb ... Unpacking libhmmer2-dev:arm64 (2.3.2+dfsg-12+b2) ... 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 libsvm3:arm64. Preparing to unpack .../34-libsvm3_3.24+ds-6.1_arm64.deb ... Unpacking libsvm3:arm64 (3.24+ds-6.1) ... Selecting previously unselected package libsvm-dev:arm64. Preparing to unpack .../35-libsvm-dev_3.24+ds-6.1_arm64.deb ... Unpacking libsvm-dev:arm64 (3.24+ds-6.1) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../36-pkgconf-bin_1.8.1-4_arm64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../37-pkgconf_1.8.1-4_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-4) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up bsdextrautils (2.41-4) ... 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 libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-8) ... 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 (0.23.1-1) ... Setting up d-shlibs (0.109) ... 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 libhmmer2-dev:arm64 (2.3.2+dfsg-12+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up libsquid1t64:arm64 (1.9g+cvs20050121-15.1+b2) ... Setting up libsvm3:arm64 (3.24+ds-6.1) ... 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 (0.23.1-1) ... 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 libsvm-dev:arm64 (3.24+ds-6.1) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.2) ... Processing triggers for libc-bin (2.41-7) ... 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/libpsortb-1.0+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 > ../libpsortb_1.0+dfsg-7_source.changes dpkg-buildpackage: info: source package libpsortb dpkg-buildpackage: info: source version 1.0+dfsg-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: Consider adding 'AC_CONFIG_MACRO_DIRS([m4])' to configure.ac, libtoolize: and rerunning libtoolize and aclocal. libtoolize: Consider adding '-I m4' to ACLOCAL_AMFLAGS in Makefile.am. configure.ac:7: warning: The macro 'AC_CONFIG_HEADER' is obsolete. configure.ac:7: You should run autoupdate. ./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from... configure.ac:7: the top level configure.ac:17: warning: The macro 'AC_PROG_LIBTOOL' is obsolete. configure.ac:17: You should run autoupdate. aclocal.m4:122: AC_PROG_LIBTOOL is expanded from... configure.ac:17: the top level configure.ac:47: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.ac:47: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.ac:47: the top level configure.ac:55: warning: The macro 'AC_HEADER_TIME' is obsolete. configure.ac:55: You should run autoupdate. ./lib/autoconf/headers.m4:702: AC_HEADER_TIME is expanded from... configure.ac:55: the top level configure.ac:12: installing './compile' configure.ac:17: installing './config.guess' configure.ac:17: installing './config.sub' configure.ac:8: installing './install-sh' configure.ac:8: installing './missing' modhmm0.92b/Makefile.am: installing './depcomp' dh_auto_configure ./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 checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes checking for g++... g++ 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 g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc 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 whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ranlib... ranlib checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/time.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for main in -lm... yes checking for egrep... (cached) /usr/bin/grep -E checking for float.h... yes checking for limits.h... yes checking for memory.h... yes checking for netinet/in.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for _Bool... yes checking for stdbool.h that conforms to C99 or later... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking whether struct tm is in sys/time.h or time.h... time.h checking for declarations of fseeko and ftello... yes checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking whether lstat correctly handles trailing slash... yes checking whether stat accepts an empty string... no checking for strftime... yes checking for vprintf... yes checking for working strtod... yes checking for atexit... yes checking for floor... yes checking for memmove... yes checking for memset... yes checking for pow... yes checking for sqrt... yes checking for strchr... yes checking for strcspn... yes checking for strerror... yes checking for strpbrk... yes checking for strrchr... yes checking for strspn... yes checking for strstr... yes checking for strtol... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating svmloc/Makefile config.status: creating modhmm0.92b/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' make all-recursive make[2]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' Making all in svmloc make[3]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o binding.lo binding.cpp /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o svmloc.lo svmloc.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c svmloc.cpp -fPIC -DPIC -o .libs/svmloc.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c binding.cpp -fPIC -DPIC -o .libs/binding.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c binding.cpp -o binding.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c svmloc.cpp -o svmloc.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -version-info 0:0:0 -lsvm -Wl,-z,relro -Wl,-z,now -o libsvmloc.la -rpath /usr/lib/aarch64-linux-gnu binding.lo svmloc.lo -lm libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o .libs/binding.o .libs/svmloc.o -lsvm -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -Werror=format-security -mbranch-protection=standard -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libsvmloc.so.0 -o .libs/libsvmloc.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libsvmloc.so.0" && ln -s "libsvmloc.so.0.0.0" "libsvmloc.so.0") libtool: link: (cd ".libs" && rm -f "libsvmloc.so" && ln -s "libsvmloc.so.0.0.0" "libsvmloc.so") libtool: link: ar cr .libs/libsvmloc.a binding.o svmloc.o libtool: link: ranlib .libs/libsvmloc.a libtool: link: ( cd ".libs" && rm -f "libsvmloc.la" && ln -s "../libsvmloc.la" "libsvmloc.la" ) make[3]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' Making all in modhmm0.92b make[3]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o core_algorithms_multialpha.lo core_algorithms_multialpha.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o debug_funcs.lo debug_funcs.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o hmmsearch.lo hmmsearch.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o readhmm.lo readhmm.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o readhmm_multialpha.lo readhmm_multialpha.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o readseqs_multialpha.lo readseqs_multialpha.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o std_calculation_funcs.lo std_calculation_funcs.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o std_funcs.lo std_funcs.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o training_algorithms_multialpha.lo training_algorithms_multialpha.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c debug_funcs.c -fPIC -DPIC -o .libs/debug_funcs.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readseqs_multialpha.c -fPIC -DPIC -o .libs/readseqs_multialpha.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c training_algorithms_multialpha.c -fPIC -DPIC -o .libs/training_algorithms_multialpha.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readhmm_multialpha.c -fPIC -DPIC -o .libs/readhmm_multialpha.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readhmm.c -fPIC -DPIC -o .libs/readhmm.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c hmmsearch.c -fPIC -DPIC -o .libs/hmmsearch.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c std_calculation_funcs.c -fPIC -DPIC -o .libs/std_calculation_funcs.o debug_funcs.c:7:76: warning: 'struct hmm_multi_s' declared inside parameter list will not be visible outside of this definition or declaration 7 | int read_multi_prior_file_multi(struct emission_dirichlet_s *em_di, struct hmm_multi_s *hmmp, FILE *priorfile, int alphabet); | ^~~~~~~~~~~ debug_funcs.c:7:40: warning: 'struct emission_dirichlet_s' declared inside parameter list will not be visible outside of this definition or declaration 7 | int read_multi_prior_file_multi(struct emission_dirichlet_s *em_di, struct hmm_multi_s *hmmp, FILE *priorfile, int alphabet); | ^~~~~~~~~~~~~~~~~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c std_funcs.c -fPIC -DPIC -o .libs/std_funcs.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c core_algorithms_multialpha.c -fPIC -DPIC -o .libs/core_algorithms_multialpha.o readseqs_multialpha.c: In function 'get_sequence_std_multi': readseqs_multialpha.c:121:55: warning: unknown escape sequence: '\s' 121 | if(line[0] == '<' || line[0] == '#' || line[0] == '\s' || line[0] == '\n' || line[0] == '/') { | ^~~~ readseqs_multialpha.c: In function 'get_sequences_msa_std_multi': readseqs_multialpha.c:372:18: warning: unknown escape sequence: '\s' 372 | else if(i == '\s' && i == '\n') { | ^~~~ readseqs_multialpha.c: In function 'get_sequence_std_multi': readseqs_multialpha.c:286:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 286 | fgets(line, MAX_LINE, seqfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c: In function 'msa_baum_welch_dirichlet_multi': training_algorithms_multialpha.c:701:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 701 | alphabet = (int)hmmp->alphabet; | ^ training_algorithms_multialpha.c:710:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 710 | alphabet = (int)hmmp->alphabet_2; | ^ training_algorithms_multialpha.c:719:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 719 | alphabet = (int)hmmp->alphabet_3; | ^ training_algorithms_multialpha.c:728:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 728 | alphabet = (int)hmmp->alphabet_4; | ^ readseqs_multialpha.c: In function 'get_sequences_msa_std_multi': readseqs_multialpha.c:625:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 625 | fgets(line, MAX_LINE, seqfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readseqs_multialpha.c:754:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 754 | fgets(line, MAX_LINE, seqfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readseqs_multialpha.c:874:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 874 | fgets(line, MAX_LINE, seqfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readseqs_multialpha.c:995:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 995 | fgets(line, MAX_LINE, seqfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c: In function 'readhmm_multialpha': readhmm_multialpha.c:326:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 326 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c: In function 'extended_msa_baum_welch_dirichlet_multi': training_algorithms_multialpha.c:1639:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1639 | alphabet = (int)hmmp->alphabet; | ^ training_algorithms_multialpha.c:1646:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1646 | alphabet = (int)hmmp->alphabet_2; | ^ readhmm_multialpha.c: In function 'read_module_multi': readhmm_multialpha.c:1039:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1039 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1074:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1074 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1108:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1108 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1137:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1137 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1140:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1140 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1166:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1166 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1169:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1169 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1195:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1195 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1199:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1199 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1226:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1226 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1233:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1233 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c:1653:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1653 | alphabet = (int)hmmp->alphabet_3; | ^ training_algorithms_multialpha.c:1660:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1660 | alphabet = (int)hmmp->alphabet_4; | ^ training_algorithms_multialpha.c:1784:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1784 | alphabet = (int)hmmp->alphabet; | ^ training_algorithms_multialpha.c:1791:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1791 | alphabet = (int)hmmp->alphabet_2; | ^ training_algorithms_multialpha.c:1798:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1798 | alphabet = (int)hmmp->alphabet_3; | ^ training_algorithms_multialpha.c:1805:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1805 | alphabet = (int)hmmp->alphabet_4; | ^ readhmm.c: In function 'readhmm': readhmm.c:69:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm.c: In function 'readanhmm': readhmm.c:342:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 342 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c: In function 'add_to_E_multi': readhmm.c: In function 'read_module': readhmm.c:745:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 745 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm.c:780:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 780 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm.c:815:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 815 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm.c:844:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 844 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm.c:848:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 848 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c:3589:43: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 3589 | (char*)alphabet); | ^ training_algorithms_multialpha.c:3593:49: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 3593 | (char*)alphabet); | ^ readhmm.c: In function 'read_prior_files': readhmm.c:1225:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1225 | fgets(ps, 2048, priorfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c:3618:36: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 3618 | (char*)alphabet); | ^ training_algorithms_multialpha.c:3622:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 3622 | (char*)alphabet); | ^ hmmsearch.c: In function 'get_nullmodel_score_multi': hmmsearch.c:656:42: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] 656 | printf("Could not find letter %s when scoring null model\n", &seq[l]); | ~^ ~~~~~~~ | | | | char * struct letter_s * hmmsearch.c:674:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] 674 | printf("Could not find letter %s when scoring null model\n", &seq_2[l]); | ~^ ~~~~~~~~~ | | | | char * struct letter_s * hmmsearch.c:693:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] 693 | printf("Could not find letter %s when scoring null model\n", &seq_3[l]); | ~^ ~~~~~~~~~ | | | | char * struct letter_s * hmmsearch.c:712:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] 712 | printf("Could not find letter %s when scoring null model\n", &seq[l]); | ~^ ~~~~~~~ | | | | char * struct letter_s * std_calculation_funcs.c: In function 'update_labelings': std_calculation_funcs.c:1295:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1295 | cur_address = (int)((cur_rowp+v)->labeling); | ^ std_calculation_funcs.c:1309:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1309 | if((int)((cur_rowp+w)->labeling) == cur_address && (cur_rowp + w)->is_updated == NO) { | ^ std_calculation_funcs.c: In function 'deallocate_row_labelings': std_calculation_funcs.c:1425:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1425 | cur_address = (int)((prev_rowp+v)->labeling); | ^ std_calculation_funcs.c:1430:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1430 | if((int)((prev_rowp+w)->labeling) == cur_address) { | ^ std_funcs.c: In function 'get_replacement_letter_index_single': std_funcs.c:680:62: warning: comparison between pointer and integer 680 | if(((replacement_letters->letters + a_index)->letter)[0] == c) { | ^~ std_funcs.c: In function 'get_nr_alphabets': std_funcs.c:2726:10: warning: 'fgets' writing 4000 bytes into a region of size 1000 overflows the destination [-Wstringop-overflow=] 2726 | if(fgets(s, MAX_LINE, hmmfile) != NULL) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ std_funcs.c:2719:8: note: destination object 's' of size 1000 2719 | char s[1000]; | ^ In file included from /usr/include/stdio.h:970, from std_funcs.c:1: /usr/include/aarch64-linux-gnu/bits/stdio2.h:305:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' 305 | fgets (__fortify_clang_overload_arg (char *, __restrict, __s), int __n, | ^~~~~ std_funcs.c:2733:8: warning: 'fgets' writing 4000 bytes into a region of size 1000 overflows the destination [-Wstringop-overflow=] 2733 | if(fgets(s, MAX_LINE, hmmfile) != NULL) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ std_funcs.c:2719:8: note: destination object 's' of size 1000 2719 | char s[1000]; | ^ /usr/include/aarch64-linux-gnu/bits/stdio2.h:305:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' 305 | fgets (__fortify_clang_overload_arg (char *, __restrict, __s), int __n, | ^~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c hmmsearch.c -o hmmsearch.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c debug_funcs.c -o debug_funcs.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readseqs_multialpha.c -o readseqs_multialpha.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readhmm.c -o readhmm.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c std_calculation_funcs.c -o std_calculation_funcs.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readhmm_multialpha.c -o readhmm_multialpha.o >/dev/null 2>&1 In function 'fgets', inlined from 'get_nr_alphabets' at std_funcs.c:2726:10: /usr/include/aarch64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'get_nr_alphabets' at std_funcs.c:2733:8: /usr/include/aarch64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c std_funcs.c -o std_funcs.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c core_algorithms_multialpha.c -o core_algorithms_multialpha.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c training_algorithms_multialpha.c -o training_algorithms_multialpha.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -version-info 0:0:0 -Wl,-z,relro -Wl,-z,now -o libmodhmm.la -rpath /usr/lib/aarch64-linux-gnu core_algorithms_multialpha.lo debug_funcs.lo hmmsearch.lo readhmm.lo readhmm_multialpha.lo readseqs_multialpha.lo std_calculation_funcs.lo std_funcs.lo training_algorithms_multialpha.lo -lm libtool: link: gcc -shared -fPIC -DPIC .libs/core_algorithms_multialpha.o .libs/debug_funcs.o .libs/hmmsearch.o .libs/readhmm.o .libs/readhmm_multialpha.o .libs/readseqs_multialpha.o .libs/std_calculation_funcs.o .libs/std_funcs.o .libs/training_algorithms_multialpha.o -lm -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -Werror=format-security -mbranch-protection=standard -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libmodhmm.so.0 -o .libs/libmodhmm.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libmodhmm.so.0" && ln -s "libmodhmm.so.0.0.0" "libmodhmm.so.0") libtool: link: (cd ".libs" && rm -f "libmodhmm.so" && ln -s "libmodhmm.so.0.0.0" "libmodhmm.so") libtool: link: ar cr .libs/libmodhmm.a core_algorithms_multialpha.o debug_funcs.o hmmsearch.o readhmm.o readhmm_multialpha.o readseqs_multialpha.o std_calculation_funcs.o std_funcs.o training_algorithms_multialpha.o libtool: link: ranlib .libs/libmodhmm.a libtool: link: ( cd ".libs" && rm -f "libmodhmm.la" && ln -s "../libmodhmm.la" "libmodhmm.la" ) make[3]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' make[3]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[3]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[2]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' dh_auto_test make -j12 check "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' Making check in svmloc make[2]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' Making check in modhmm0.92b make[2]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' make[2]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[2]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' dh_auto_install make -j1 install DESTDIR=/build/reproducible-path/libpsortb-1.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' Making install in svmloc make[3]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' make[4]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' /usr/bin/mkdir -p '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libsvmloc.la '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libsvmloc.so.0.0.0 /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.so.0.0.0 libtool: install: (cd /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libsvmloc.so.0.0.0 libsvmloc.so.0 || { rm -f libsvmloc.so.0 && ln -s libsvmloc.so.0.0.0 libsvmloc.so.0; }; }) libtool: install: (cd /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libsvmloc.so.0.0.0 libsvmloc.so || { rm -f libsvmloc.so && ln -s libsvmloc.so.0.0.0 libsvmloc.so; }; }) libtool: install: /usr/bin/install -c .libs/libsvmloc.lai /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.la libtool: install: /usr/bin/install -c .libs/libsvmloc.a /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.a libtool: install: chmod 644 /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.a libtool: install: ranlib /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' make[3]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' Making install in modhmm0.92b make[3]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' make[4]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' /usr/bin/mkdir -p '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libmodhmm.la '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libmodhmm.so.0.0.0 /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.so.0.0.0 libtool: install: (cd /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libmodhmm.so.0.0.0 libmodhmm.so.0 || { rm -f libmodhmm.so.0 && ln -s libmodhmm.so.0.0.0 libmodhmm.so.0; }; }) libtool: install: (cd /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libmodhmm.so.0.0.0 libmodhmm.so || { rm -f libmodhmm.so && ln -s libmodhmm.so.0.0.0 libmodhmm.so; }; }) libtool: install: /usr/bin/install -c .libs/libmodhmm.lai /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.la libtool: install: /usr/bin/install -c .libs/libmodhmm.a /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.a libtool: install: chmod 644 /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.a libtool: install: ranlib /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' make[3]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' make[3]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[4]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[3]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[2]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ debian/tmp/usr/lib/*/libmodhmm.so Library package automatic movement utility set -e install -d -m 755 debian/libmodhmm-dev/usr/lib/aarch64-linux-gnu install -d -m 755 debian/libmodhmm0/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.a debian/libmodhmm-dev/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.so debian/libmodhmm-dev/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.so.0 debian/libmodhmm0/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.so.0.0.0 debian/libmodhmm0/usr/lib/aarch64-linux-gnu PKGDEV=libmodhmm-dev PKGSHL=libmodhmm0 d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ debian/tmp/usr/lib/*/libsvmloc.so Library package automatic movement utility --> libsvm-dev package exists. set -e install -d -m 755 debian/libsvmloc-dev/usr/lib/aarch64-linux-gnu install -d -m 755 debian/libsvmloc0/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.a debian/libsvmloc-dev/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.so debian/libsvmloc-dev/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.so.0 debian/libsvmloc0/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.so.0.0.0 debian/libsvmloc0/usr/lib/aarch64-linux-gnu PKGDEV=libsvmloc-dev PKGSHL=libsvmloc0 find debian -name "lib*.la" -delete make[1]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' dh_installdocs dh_installchangelogs 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 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 dh_md5sums dh_builddeb dpkg-deb: building package 'libmodhmm0' in '../libmodhmm0_1.0+dfsg-7_arm64.deb'. dpkg-deb: building package 'libmodhmm0-dbgsym' in '../libmodhmm0-dbgsym_1.0+dfsg-7_arm64.deb'. dpkg-deb: building package 'libmodhmm-dev' in '../libmodhmm-dev_1.0+dfsg-7_arm64.deb'. dpkg-deb: building package 'libsvmloc0' in '../libsvmloc0_1.0+dfsg-7_arm64.deb'. dpkg-deb: building package 'libsvmloc0-dbgsym' in '../libsvmloc0-dbgsym_1.0+dfsg-7_arm64.deb'. dpkg-deb: building package 'libsvmloc-dev' in '../libsvmloc-dev_1.0+dfsg-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libpsortb_1.0+dfsg-7_arm64.buildinfo dpkg-genchanges --build=binary -O../libpsortb_1.0+dfsg-7_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/2862450 and its subdirectories I: Current time: Tue Apr 22 18:13:17 -12 2025 I: pbuilder-time-stamp: 1745388797 Wed Apr 23 06:13:19 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Wed Apr 23 06:13:19 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Wed Apr 23 06:13:19 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Wed Apr 23 06:13:19 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-p1Yick' ==================================================================================== Tue May 26 12:36:20 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink03-arm64, called using "2 libpsortb unstable /srv/reproducible-results/rbuild-debian/r-b-build.REw1aXKj 1.0+dfsg-7" as arguments. Tue May 26 12:36:20 UTC 2026 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-Wam1zcQa" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue May 26 12:36:20 UTC 2026 I: Downloading source for unstable/libpsortb=1.0+dfsg-7 Reading package lists... NOTICE: 'libpsortb' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libpsortb.git Please use: git clone https://salsa.debian.org/med-team/libpsortb.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 108 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main libpsortb 1.0+dfsg-7 (dsc) [2350 B] Get:2 http://deb.debian.org/debian unstable/main libpsortb 1.0+dfsg-7 (tar) [95.6 kB] Get:3 http://deb.debian.org/debian unstable/main libpsortb 1.0+dfsg-7 (diff) [10.2 kB] Fetched 108 kB in 0s (5048 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'libpsortb' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libpsortb.git Please use: git clone https://salsa.debian.org/med-team/libpsortb.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 108 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main libpsortb 1.0+dfsg-7 (dsc) [2350 B] Get:2 http://deb.debian.org/debian unstable/main libpsortb 1.0+dfsg-7 (tar) [95.6 kB] Get:3 http://deb.debian.org/debian unstable/main libpsortb 1.0+dfsg-7 (diff) [10.2 kB] Fetched 108 kB in 0s (5048 kB/s) Download complete and in download only mode ============================================================================= Re-Building libpsortb in unstable on arm64 on codethink03-arm64 now. Date: Tue May 26 13:36:21 BST 2026 Date UTC: Tue May 26 12:36:21 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.REw1aXKj + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.REw1aXKj/pbuilderrc_GxbO + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' libpsortb = debian-installer -o libpsortb = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' libpsortb = u-boot ']' + case "${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.REw1aXKj/pbuilderrc_GxbO --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.REw1aXKj/b2 --logfile b2/build.log libpsortb_1.0+dfsg-7.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: Wed May 27 02:36:21 +14 2026 I: pbuilder-time-stamp: 1779798981 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 [libpsortb_1.0+dfsg-7.dsc] I: copying [./libpsortb_1.0+dfsg.orig.tar.xz] I: copying [./libpsortb_1.0+dfsg-7.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./libpsortb_1.0+dfsg-7.dsc: unsupported subcommand dpkg-source: info: extracting libpsortb in libpsortb-1.0+dfsg dpkg-source: info: unpacking libpsortb_1.0+dfsg.orig.tar.xz dpkg-source: info: unpacking libpsortb_1.0+dfsg-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libs.patch dpkg-source: info: applying use_debian_packaged_libsvm.patch dpkg-source: info: applying remove_unused_debug_functions.patch dpkg-source: info: applying fix-implicit-declaration.patch dpkg-source: info: applying gcc14.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/311063/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 May 26 12:36 /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/311063/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/311063/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=aa83499a673740709b80967b42d0b778 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=311063 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.REw1aXKj/pbuilderrc_GxbO --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.REw1aXKj/b2 --logfile b2/build.log libpsortb_1.0+dfsg-7.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 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/311063/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), d-shlibs, libsvm-dev, libsquid-dev, libhmmer2-dev, pkgconf dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19953 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 d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on libsvm-dev; however: Package libsvm-dev is not installed. pbuilder-satisfydepends-dummy depends on libsquid-dev; however: Package libsquid-dev is not installed. pbuilder-satisfydepends-dummy depends on libhmmer2-dev; however: Package libhmmer2-dev is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf 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} d-shlibs{a} debhelper{a} dh-autoreconf{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} libhmmer2-dev{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpkgconf3{a} libsquid-dev{a} libsquid1t64{a} libsvm-dev{a} libsvm3{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} pkgconf{a} pkgconf-bin{a} po-debconf{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 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 0.23.1-1 [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 1.23.0-7 [1129 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41-4 [93.9 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 2.13.0-1 [1404 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 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 d-shlibs all 0.109 [11.1 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 23 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.4 [629 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.2 [919 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libhmmer2-dev arm64 2.3.2+dfsg-12+b2 [92.3 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 libsvm3 arm64 3.24+ds-6.1 [38.6 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libsvm-dev arm64 3.24+ds-6.1 [59.7 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Fetched 11.4 MB in 0s (49.9 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 ... 19953 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_0.23.1-1_arm64.deb ... Unpacking gettext-base (0.23.1-1) ... 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_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41-4_arm64.deb ... Unpacking bsdextrautils (2.41-4) ... 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_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... 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_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../15-d-shlibs_0.109_all.deb ... Unpacking d-shlibs (0.109) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-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 .../20-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 .../21-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 .../22-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../24-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.4_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-1_arm64.deb ... Unpacking gettext (0.23.1-1) ... 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_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Selecting previously unselected package libhmmer2-dev:arm64. Preparing to unpack .../30-libhmmer2-dev_2.3.2+dfsg-12+b2_arm64.deb ... Unpacking libhmmer2-dev:arm64 (2.3.2+dfsg-12+b2) ... 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 libsvm3:arm64. Preparing to unpack .../34-libsvm3_3.24+ds-6.1_arm64.deb ... Unpacking libsvm3:arm64 (3.24+ds-6.1) ... Selecting previously unselected package libsvm-dev:arm64. Preparing to unpack .../35-libsvm-dev_3.24+ds-6.1_arm64.deb ... Unpacking libsvm-dev:arm64 (3.24+ds-6.1) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../36-pkgconf-bin_1.8.1-4_arm64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../37-pkgconf_1.8.1-4_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-4) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up bsdextrautils (2.41-4) ... 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 libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-8) ... 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 (0.23.1-1) ... Setting up d-shlibs (0.109) ... 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 libhmmer2-dev:arm64 (2.3.2+dfsg-12+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up libsquid1t64:arm64 (1.9g+cvs20050121-15.1+b2) ... Setting up libsvm3:arm64 (3.24+ds-6.1) ... 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 (0.23.1-1) ... 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 libsvm-dev:arm64 (3.24+ds-6.1) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.2) ... Processing triggers for libc-bin (2.41-7) ... 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/311063/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/311063/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/libpsortb-1.0+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 > ../libpsortb_1.0+dfsg-7_source.changes dpkg-buildpackage: info: source package libpsortb dpkg-buildpackage: info: source version 1.0+dfsg-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: Consider adding 'AC_CONFIG_MACRO_DIRS([m4])' to configure.ac, libtoolize: and rerunning libtoolize and aclocal. libtoolize: Consider adding '-I m4' to ACLOCAL_AMFLAGS in Makefile.am. configure.ac:7: warning: The macro 'AC_CONFIG_HEADER' is obsolete. configure.ac:7: You should run autoupdate. ./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from... configure.ac:7: the top level configure.ac:17: warning: The macro 'AC_PROG_LIBTOOL' is obsolete. configure.ac:17: You should run autoupdate. aclocal.m4:122: AC_PROG_LIBTOOL is expanded from... configure.ac:17: the top level configure.ac:47: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.ac:47: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.ac:47: the top level configure.ac:55: warning: The macro 'AC_HEADER_TIME' is obsolete. configure.ac:55: You should run autoupdate. ./lib/autoconf/headers.m4:702: AC_HEADER_TIME is expanded from... configure.ac:55: the top level configure.ac:12: installing './compile' configure.ac:17: installing './config.guess' configure.ac:17: installing './config.sub' configure.ac:8: installing './install-sh' configure.ac:8: installing './missing' modhmm0.92b/Makefile.am: installing './depcomp' dh_auto_configure ./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 checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes checking for g++... g++ 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 g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc 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 whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ranlib... ranlib checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/time.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for main in -lm... yes checking for egrep... (cached) /usr/bin/grep -E checking for float.h... yes checking for limits.h... yes checking for memory.h... yes checking for netinet/in.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for _Bool... yes checking for stdbool.h that conforms to C99 or later... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking whether struct tm is in sys/time.h or time.h... time.h checking for declarations of fseeko and ftello... yes checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking whether lstat correctly handles trailing slash... yes checking whether stat accepts an empty string... no checking for strftime... yes checking for vprintf... yes checking for working strtod... yes checking for atexit... yes checking for floor... yes checking for memmove... yes checking for memset... yes checking for pow... yes checking for sqrt... yes checking for strchr... yes checking for strcspn... yes checking for strerror... yes checking for strpbrk... yes checking for strrchr... yes checking for strspn... yes checking for strstr... yes checking for strtol... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating svmloc/Makefile config.status: creating modhmm0.92b/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' make all-recursive make[2]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' Making all in svmloc make[3]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o binding.lo binding.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o svmloc.lo svmloc.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c binding.cpp -fPIC -DPIC -o .libs/binding.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c svmloc.cpp -fPIC -DPIC -o .libs/svmloc.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c binding.cpp -o binding.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c svmloc.cpp -o svmloc.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -version-info 0:0:0 -lsvm -Wl,-z,relro -Wl,-z,now -o libsvmloc.la -rpath /usr/lib/aarch64-linux-gnu binding.lo svmloc.lo -lm libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o .libs/binding.o .libs/svmloc.o -lsvm -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -Werror=format-security -mbranch-protection=standard -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libsvmloc.so.0 -o .libs/libsvmloc.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libsvmloc.so.0" && ln -s "libsvmloc.so.0.0.0" "libsvmloc.so.0") libtool: link: (cd ".libs" && rm -f "libsvmloc.so" && ln -s "libsvmloc.so.0.0.0" "libsvmloc.so") libtool: link: ar cr .libs/libsvmloc.a binding.o svmloc.o libtool: link: ranlib .libs/libsvmloc.a libtool: link: ( cd ".libs" && rm -f "libsvmloc.la" && ln -s "../libsvmloc.la" "libsvmloc.la" ) make[3]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' Making all in modhmm0.92b make[3]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o core_algorithms_multialpha.lo core_algorithms_multialpha.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o debug_funcs.lo debug_funcs.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o hmmsearch.lo hmmsearch.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o readhmm.lo readhmm.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o readhmm_multialpha.lo readhmm_multialpha.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o readseqs_multialpha.lo readseqs_multialpha.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o std_calculation_funcs.lo std_calculation_funcs.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o std_funcs.lo std_funcs.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o training_algorithms_multialpha.lo training_algorithms_multialpha.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c debug_funcs.c -fPIC -DPIC -o .libs/debug_funcs.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c core_algorithms_multialpha.c -fPIC -DPIC -o .libs/core_algorithms_multialpha.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readhmm_multialpha.c -fPIC -DPIC -o .libs/readhmm_multialpha.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c hmmsearch.c -fPIC -DPIC -o .libs/hmmsearch.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readseqs_multialpha.c -fPIC -DPIC -o .libs/readseqs_multialpha.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readhmm.c -fPIC -DPIC -o .libs/readhmm.o debug_funcs.c:7:76: warning: 'struct hmm_multi_s' declared inside parameter list will not be visible outside of this definition or declaration 7 | int read_multi_prior_file_multi(struct emission_dirichlet_s *em_di, struct hmm_multi_s *hmmp, FILE *priorfile, int alphabet); | ^~~~~~~~~~~ debug_funcs.c:7:40: warning: 'struct emission_dirichlet_s' declared inside parameter list will not be visible outside of this definition or declaration 7 | int read_multi_prior_file_multi(struct emission_dirichlet_s *em_di, struct hmm_multi_s *hmmp, FILE *priorfile, int alphabet); | ^~~~~~~~~~~~~~~~~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c std_calculation_funcs.c -fPIC -DPIC -o .libs/std_calculation_funcs.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c training_algorithms_multialpha.c -fPIC -DPIC -o .libs/training_algorithms_multialpha.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c std_funcs.c -fPIC -DPIC -o .libs/std_funcs.o hmmsearch.c: In function 'get_nullmodel_score_multi': hmmsearch.c:656:42: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] 656 | printf("Could not find letter %s when scoring null model\n", &seq[l]); | ~^ ~~~~~~~ | | | | char * struct letter_s * hmmsearch.c:674:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] 674 | printf("Could not find letter %s when scoring null model\n", &seq_2[l]); | ~^ ~~~~~~~~~ | | | | char * struct letter_s * hmmsearch.c:693:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] 693 | printf("Could not find letter %s when scoring null model\n", &seq_3[l]); | ~^ ~~~~~~~~~ | | | | char * struct letter_s * hmmsearch.c:712:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] 712 | printf("Could not find letter %s when scoring null model\n", &seq[l]); | ~^ ~~~~~~~ | | | | char * struct letter_s * readseqs_multialpha.c: In function 'get_sequence_std_multi': readhmm_multialpha.c: In function 'readhmm_multialpha': readseqs_multialpha.c:121:55: warning: unknown escape sequence: '\s' 121 | if(line[0] == '<' || line[0] == '#' || line[0] == '\s' || line[0] == '\n' || line[0] == '/') { | ^~~~ readhmm_multialpha.c:326:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 326 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readseqs_multialpha.c: In function 'get_sequences_msa_std_multi': readseqs_multialpha.c:372:18: warning: unknown escape sequence: '\s' 372 | else if(i == '\s' && i == '\n') { | ^~~~ readhmm_multialpha.c: In function 'read_module_multi': readhmm_multialpha.c:1039:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1039 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1074:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1074 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1108:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1108 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1137:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1137 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1140:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1140 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1166:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1166 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1169:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1169 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1195:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1195 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1199:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1199 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1226:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1226 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1233:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1233 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ std_funcs.c: In function 'get_replacement_letter_index_single': readhmm.c: In function 'readhmm': readhmm.c:69:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm.c: In function 'readanhmm': std_calculation_funcs.c: In function 'update_labelings': readseqs_multialpha.c: In function 'get_sequence_std_multi': readseqs_multialpha.c:286:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 286 | fgets(line, MAX_LINE, seqfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ std_calculation_funcs.c:1295:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1295 | cur_address = (int)((cur_rowp+v)->labeling); | ^ std_calculation_funcs.c:1309:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1309 | if((int)((cur_rowp+w)->labeling) == cur_address && (cur_rowp + w)->is_updated == NO) { | ^ std_calculation_funcs.c: In function 'deallocate_row_labelings': std_calculation_funcs.c:1425:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1425 | cur_address = (int)((prev_rowp+v)->labeling); | ^ std_calculation_funcs.c:1430:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1430 | if((int)((prev_rowp+w)->labeling) == cur_address) { | ^ readhmm.c:342:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 342 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ std_funcs.c:680:62: warning: comparison between pointer and integer 680 | if(((replacement_letters->letters + a_index)->letter)[0] == c) { | ^~ readhmm.c: In function 'read_module': readhmm.c:745:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 745 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm.c:780:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 780 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm.c:815:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 815 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm.c:844:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 844 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm.c:848:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 848 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c: In function 'msa_baum_welch_dirichlet_multi': training_algorithms_multialpha.c:701:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 701 | alphabet = (int)hmmp->alphabet; | ^ readhmm.c: In function 'read_prior_files': readseqs_multialpha.c: In function 'get_sequences_msa_std_multi': readseqs_multialpha.c:625:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 625 | fgets(line, MAX_LINE, seqfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readseqs_multialpha.c:754:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 754 | fgets(line, MAX_LINE, seqfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readseqs_multialpha.c:874:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 874 | fgets(line, MAX_LINE, seqfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readseqs_multialpha.c:995:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 995 | fgets(line, MAX_LINE, seqfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readhmm.c:1225:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1225 | fgets(ps, 2048, priorfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c:710:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 710 | alphabet = (int)hmmp->alphabet_2; | ^ training_algorithms_multialpha.c:719:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 719 | alphabet = (int)hmmp->alphabet_3; | ^ training_algorithms_multialpha.c:728:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 728 | alphabet = (int)hmmp->alphabet_4; | ^ training_algorithms_multialpha.c: In function 'extended_msa_baum_welch_dirichlet_multi': training_algorithms_multialpha.c:1639:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1639 | alphabet = (int)hmmp->alphabet; | ^ training_algorithms_multialpha.c:1646:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1646 | alphabet = (int)hmmp->alphabet_2; | ^ training_algorithms_multialpha.c:1653:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1653 | alphabet = (int)hmmp->alphabet_3; | ^ training_algorithms_multialpha.c:1660:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1660 | alphabet = (int)hmmp->alphabet_4; | ^ training_algorithms_multialpha.c:1784:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1784 | alphabet = (int)hmmp->alphabet; | ^ training_algorithms_multialpha.c:1791:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1791 | alphabet = (int)hmmp->alphabet_2; | ^ training_algorithms_multialpha.c:1798:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1798 | alphabet = (int)hmmp->alphabet_3; | ^ training_algorithms_multialpha.c:1805:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1805 | alphabet = (int)hmmp->alphabet_4; | ^ training_algorithms_multialpha.c: In function 'add_to_E_multi': training_algorithms_multialpha.c:3589:43: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 3589 | (char*)alphabet); | ^ training_algorithms_multialpha.c:3593:49: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 3593 | (char*)alphabet); | ^ training_algorithms_multialpha.c:3618:36: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 3618 | (char*)alphabet); | ^ training_algorithms_multialpha.c:3622:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 3622 | (char*)alphabet); | ^ std_funcs.c: In function 'get_nr_alphabets': std_funcs.c:2726:10: warning: 'fgets' writing 4000 bytes into a region of size 1000 overflows the destination [-Wstringop-overflow=] 2726 | if(fgets(s, MAX_LINE, hmmfile) != NULL) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ std_funcs.c:2719:8: note: destination object 's' of size 1000 2719 | char s[1000]; | ^ In file included from /usr/include/stdio.h:970, from std_funcs.c:1: /usr/include/aarch64-linux-gnu/bits/stdio2.h:305:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' 305 | fgets (__fortify_clang_overload_arg (char *, __restrict, __s), int __n, | ^~~~~ std_funcs.c:2733:8: warning: 'fgets' writing 4000 bytes into a region of size 1000 overflows the destination [-Wstringop-overflow=] 2733 | if(fgets(s, MAX_LINE, hmmfile) != NULL) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ std_funcs.c:2719:8: note: destination object 's' of size 1000 2719 | char s[1000]; | ^ /usr/include/aarch64-linux-gnu/bits/stdio2.h:305:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' 305 | fgets (__fortify_clang_overload_arg (char *, __restrict, __s), int __n, | ^~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c hmmsearch.c -o hmmsearch.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c debug_funcs.c -o debug_funcs.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readhmm_multialpha.c -o readhmm_multialpha.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readseqs_multialpha.c -o readseqs_multialpha.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readhmm.c -o readhmm.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c std_calculation_funcs.c -o std_calculation_funcs.o >/dev/null 2>&1 In function 'fgets', inlined from 'get_nr_alphabets' at std_funcs.c:2726:10: /usr/include/aarch64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'get_nr_alphabets' at std_funcs.c:2733:8: /usr/include/aarch64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c core_algorithms_multialpha.c -o core_algorithms_multialpha.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c std_funcs.c -o std_funcs.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c training_algorithms_multialpha.c -o training_algorithms_multialpha.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -version-info 0:0:0 -Wl,-z,relro -Wl,-z,now -o libmodhmm.la -rpath /usr/lib/aarch64-linux-gnu core_algorithms_multialpha.lo debug_funcs.lo hmmsearch.lo readhmm.lo readhmm_multialpha.lo readseqs_multialpha.lo std_calculation_funcs.lo std_funcs.lo training_algorithms_multialpha.lo -lm libtool: link: gcc -shared -fPIC -DPIC .libs/core_algorithms_multialpha.o .libs/debug_funcs.o .libs/hmmsearch.o .libs/readhmm.o .libs/readhmm_multialpha.o .libs/readseqs_multialpha.o .libs/std_calculation_funcs.o .libs/std_funcs.o .libs/training_algorithms_multialpha.o -lm -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -Werror=format-security -mbranch-protection=standard -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libmodhmm.so.0 -o .libs/libmodhmm.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libmodhmm.so.0" && ln -s "libmodhmm.so.0.0.0" "libmodhmm.so.0") libtool: link: (cd ".libs" && rm -f "libmodhmm.so" && ln -s "libmodhmm.so.0.0.0" "libmodhmm.so") libtool: link: ar cr .libs/libmodhmm.a core_algorithms_multialpha.o debug_funcs.o hmmsearch.o readhmm.o readhmm_multialpha.o readseqs_multialpha.o std_calculation_funcs.o std_funcs.o training_algorithms_multialpha.o libtool: link: ranlib .libs/libmodhmm.a libtool: link: ( cd ".libs" && rm -f "libmodhmm.la" && ln -s "../libmodhmm.la" "libmodhmm.la" ) make[3]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' make[3]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[3]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[2]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' dh_auto_test make -j12 check "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' Making check in svmloc make[2]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' Making check in modhmm0.92b make[2]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' make[2]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[2]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' dh_auto_install make -j1 install DESTDIR=/build/reproducible-path/libpsortb-1.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' Making install in svmloc make[3]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' make[4]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' /usr/bin/mkdir -p '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' /bin/sh ../libtool --mode=install /usr/bin/install -c libsvmloc.la '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libsvmloc.so.0.0.0 /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.so.0.0.0 libtool: install: (cd /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libsvmloc.so.0.0.0 libsvmloc.so.0 || { rm -f libsvmloc.so.0 && ln -s libsvmloc.so.0.0.0 libsvmloc.so.0; }; }) libtool: install: (cd /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libsvmloc.so.0.0.0 libsvmloc.so || { rm -f libsvmloc.so && ln -s libsvmloc.so.0.0.0 libsvmloc.so; }; }) libtool: install: /usr/bin/install -c .libs/libsvmloc.lai /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.la libtool: install: /usr/bin/install -c .libs/libsvmloc.a /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.a libtool: install: chmod 644 /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.a libtool: install: ranlib /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' make[3]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' Making install in modhmm0.92b make[3]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' make[4]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' /usr/bin/mkdir -p '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' /bin/sh ../libtool --mode=install /usr/bin/install -c libmodhmm.la '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libmodhmm.so.0.0.0 /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.so.0.0.0 libtool: install: (cd /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libmodhmm.so.0.0.0 libmodhmm.so.0 || { rm -f libmodhmm.so.0 && ln -s libmodhmm.so.0.0.0 libmodhmm.so.0; }; }) libtool: install: (cd /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libmodhmm.so.0.0.0 libmodhmm.so || { rm -f libmodhmm.so && ln -s libmodhmm.so.0.0.0 libmodhmm.so; }; }) libtool: install: /usr/bin/install -c .libs/libmodhmm.lai /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.la libtool: install: /usr/bin/install -c .libs/libmodhmm.a /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.a libtool: install: chmod 644 /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.a libtool: install: ranlib /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' make[3]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' make[3]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[4]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[3]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[2]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ debian/tmp/usr/lib/*/libmodhmm.so Library package automatic movement utility set -e install -d -m 755 debian/libmodhmm-dev/usr/lib/aarch64-linux-gnu install -d -m 755 debian/libmodhmm0/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.a debian/libmodhmm-dev/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.so debian/libmodhmm-dev/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.so.0 debian/libmodhmm0/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.so.0.0.0 debian/libmodhmm0/usr/lib/aarch64-linux-gnu PKGDEV=libmodhmm-dev PKGSHL=libmodhmm0 d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ debian/tmp/usr/lib/*/libsvmloc.so Library package automatic movement utility --> libsvm-dev package exists. set -e install -d -m 755 debian/libsvmloc-dev/usr/lib/aarch64-linux-gnu install -d -m 755 debian/libsvmloc0/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.a debian/libsvmloc-dev/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.so debian/libsvmloc-dev/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.so.0 debian/libsvmloc0/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.so.0.0.0 debian/libsvmloc0/usr/lib/aarch64-linux-gnu PKGDEV=libsvmloc-dev PKGSHL=libsvmloc0 find debian -name "lib*.la" -delete make[1]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' dh_installdocs dh_installchangelogs 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 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 dh_md5sums dh_builddeb dpkg-deb: building package 'libmodhmm-dev' in '../libmodhmm-dev_1.0+dfsg-7_arm64.deb'. dpkg-deb: building package 'libmodhmm0' in '../libmodhmm0_1.0+dfsg-7_arm64.deb'. dpkg-deb: building package 'libsvmloc-dev' in '../libsvmloc-dev_1.0+dfsg-7_arm64.deb'. dpkg-deb: building package 'libmodhmm0-dbgsym' in '../libmodhmm0-dbgsym_1.0+dfsg-7_arm64.deb'. dpkg-deb: building package 'libsvmloc0' in '../libsvmloc0_1.0+dfsg-7_arm64.deb'. dpkg-deb: building package 'libsvmloc0-dbgsym' in '../libsvmloc0-dbgsym_1.0+dfsg-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libpsortb_1.0+dfsg-7_arm64.buildinfo dpkg-genchanges --build=binary -O../libpsortb_1.0+dfsg-7_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/311063/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/311063/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/311063 and its subdirectories I: Current time: Wed May 27 02:38:13 +14 2026 I: pbuilder-time-stamp: 1779799093 + false + set +x Tue May 26 12:38:13 UTC 2026 I: Signing ./b2/libpsortb_1.0+dfsg-7_arm64.buildinfo as libpsortb_1.0+dfsg-7_arm64.buildinfo.asc Tue May 26 12:38:13 UTC 2026 I: Signed ./b2/libpsortb_1.0+dfsg-7_arm64.buildinfo as ./b2/libpsortb_1.0+dfsg-7_arm64.buildinfo.asc Tue May 26 12:38:14 UTC 2026 - build #2 for libpsortb/unstable/arm64 on codethink03-arm64 done. Starting cleanup. All cleanup done. Tue May 26 12:38:14 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-Wam1zcQa, removing. /srv/reproducible-results/rbuild-debian/r-b-build.REw1aXKj: total 88 drwxr-xr-x 2 jenkins jenkins 4096 Apr 23 06:13 b1 drwxr-xr-x 2 jenkins jenkins 4096 Apr 23 06:15 b2 -rw-r--r-- 1 jenkins jenkins 2350 Aug 25 2024 libpsortb_1.0+dfsg-7.dsc -rw------- 1 jenkins jenkins 72839 Apr 23 06:13 rbuildlog.3n04bey /srv/reproducible-results/rbuild-debian/r-b-build.REw1aXKj/b1: total 604 -rw-r--r-- 1 jenkins jenkins 69045 Apr 23 06:13 build.log -rw-r--r-- 1 jenkins jenkins 70280 Apr 23 06:13 libmodhmm-dev_1.0+dfsg-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 211280 Apr 23 06:13 libmodhmm0-dbgsym_1.0+dfsg-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 68124 Apr 23 06:13 libmodhmm0_1.0+dfsg-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 10220 Apr 23 06:13 libpsortb_1.0+dfsg-7.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2350 Apr 23 06:13 libpsortb_1.0+dfsg-7.dsc -rw-r--r-- 1 jenkins jenkins 6660 Apr 23 06:13 libpsortb_1.0+dfsg-7_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 7542 Apr 23 06:13 libpsortb_1.0+dfsg-7_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2918 Apr 23 06:13 libpsortb_1.0+dfsg-7_arm64.changes -rw-r--r-- 1 jenkins jenkins 1338 Apr 23 06:13 libpsortb_1.0+dfsg-7_source.changes -rw-r--r-- 1 jenkins jenkins 12028 Apr 23 06:13 libsvmloc-dev_1.0+dfsg-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 98660 Apr 23 06:13 libsvmloc0-dbgsym_1.0+dfsg-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 12828 Apr 23 06:13 libsvmloc0_1.0+dfsg-7_arm64.deb /srv/reproducible-results/rbuild-debian/r-b-build.REw1aXKj/b2: total 588 -rw-r--r-- 1 jenkins jenkins 70950 Apr 23 06:15 build.log -rw-r--r-- 1 jenkins jenkins 70280 Apr 23 06:15 libmodhmm-dev_1.0+dfsg-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 211280 Apr 23 06:15 libmodhmm0-dbgsym_1.0+dfsg-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 68124 Apr 23 06:15 libmodhmm0_1.0+dfsg-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 10220 Apr 23 06:15 libpsortb_1.0+dfsg-7.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2350 Apr 23 06:15 libpsortb_1.0+dfsg-7.dsc -rw-r--r-- 1 jenkins jenkins 6660 Apr 23 06:15 libpsortb_1.0+dfsg-7_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 7542 Apr 23 06:15 libpsortb_1.0+dfsg-7_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2918 Apr 23 06:15 libpsortb_1.0+dfsg-7_arm64.changes -rw-r--r-- 1 jenkins jenkins 1338 Apr 23 06:15 libpsortb_1.0+dfsg-7_source.changes -rw-r--r-- 1 jenkins jenkins 12028 Apr 23 06:15 libsvmloc-dev_1.0+dfsg-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 98660 Apr 23 06:15 libsvmloc0-dbgsym_1.0+dfsg-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 12828 Apr 23 06:15 libsvmloc0_1.0+dfsg-7_arm64.deb Wed Apr 23 06:15:15 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Wed Apr 23 06:15:16 UTC 2025 I: libpsortb_1.0+dfsg-7_arm64.changes: Format: 1.8 Date: Sun, 25 Aug 2024 15:12:08 +0200 Source: libpsortb Binary: libmodhmm-dev libmodhmm0 libmodhmm0-dbgsym libsvmloc-dev libsvmloc0 libsvmloc0-dbgsym Architecture: arm64 Version: 1.0+dfsg-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: libmodhmm-dev - library for constructing, training and scoring hidden Markov mode libmodhmm0 - library for constructing, training and scoring hidden Markov mode libsvmloc-dev - PSORTb adapted library for svm machine-learning library (dev) libsvmloc0 - PSORTb adapted library for svm machine-learning library Closes: 1075198 Changes: libpsortb (1.0+dfsg-7) unstable; urgency=medium . * gcc14.patch: new: fix multiple issues caught by gcc14. (Closes: #1075198) * d/control: add myself to uploaders. Checksums-Sha1: 3491a9584e78ed3662e559392efcb1f20152e034 70280 libmodhmm-dev_1.0+dfsg-7_arm64.deb 831d19e42818be5e40f39e8a9ba2d7e7c112f938 211280 libmodhmm0-dbgsym_1.0+dfsg-7_arm64.deb 6943881458285d8b10176a1e281ecc53f2f6c937 68124 libmodhmm0_1.0+dfsg-7_arm64.deb 711ec596061689e433d251b68207998b87f71381 6660 libpsortb_1.0+dfsg-7_arm64.buildinfo a06b374d7cf2b4f0ad05d03b28f411e15098ef33 12028 libsvmloc-dev_1.0+dfsg-7_arm64.deb 88b6e850e438149b30d29c0be9aefb349e119a7d 98660 libsvmloc0-dbgsym_1.0+dfsg-7_arm64.deb dfffc3ac3495f3e618f42b53162105c0159ddf3b 12828 libsvmloc0_1.0+dfsg-7_arm64.deb Checksums-Sha256: a93d40bae4c1eb92dd742b8024ab3c705176c5000e49917b49e448c0ad8f331f 70280 libmodhmm-dev_1.0+dfsg-7_arm64.deb 26324061f28247c388cca7478a4de198312c21b86d4674f46d16cbe7454920d7 211280 libmodhmm0-dbgsym_1.0+dfsg-7_arm64.deb d1b7031258cf9d112262535644be429d84838f4d69ad76b37e01d5e44245694b 68124 libmodhmm0_1.0+dfsg-7_arm64.deb e16d940bb663ced6c10fb687e82d7a031423dca64f8d36f81fcdc5ac0b806262 6660 libpsortb_1.0+dfsg-7_arm64.buildinfo 5a7cc3bdb9ef624b0682adde612eca30ac85c15214d557645fe96f38bcfe69b8 12028 libsvmloc-dev_1.0+dfsg-7_arm64.deb 192c36a68b53289f1998b3eb7fecee985cb49a01b98b32ae4e693b14ba98f308 98660 libsvmloc0-dbgsym_1.0+dfsg-7_arm64.deb 9ec68373f5c32ebed4d5154a2c7aa21b7708a741721d8930a5e9315789c6a3a8 12828 libsvmloc0_1.0+dfsg-7_arm64.deb Files: 34734a7515538167fba98200f7b1f8d5 70280 libdevel optional libmodhmm-dev_1.0+dfsg-7_arm64.deb 133d42bdcfd31b5c4a9453c53d27297a 211280 debug optional libmodhmm0-dbgsym_1.0+dfsg-7_arm64.deb 55fdb7961f0668e49d58b01779c2d682 68124 libs optional libmodhmm0_1.0+dfsg-7_arm64.deb ffd2f14c2eb84c9f234b12e19b8606d4 6660 science optional libpsortb_1.0+dfsg-7_arm64.buildinfo 5f0f5857f729e7b61f90454dcfcf4d45 12028 libdevel optional libsvmloc-dev_1.0+dfsg-7_arm64.deb 89568fd4ba715dacdff19034a057a5cf 98660 debug optional libsvmloc0-dbgsym_1.0+dfsg-7_arm64.deb 8bac4aca045857648541c30c51482cb7 12828 libs optional libsvmloc0_1.0+dfsg-7_arm64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/libpsortb_1.0+dfsg-7.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/libpsortb_1.0+dfsg-7.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/libpsortb_1.0+dfsg-7.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/libpsortb_1.0+dfsg-7.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/arm64/libpsortb_1.0+dfsg-7_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/libpsortb_1.0+dfsg-7.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-04-23 06:13:18.585736664 +0000 +++ b2/build.log 2025-04-23 06:15:15.131254543 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Apr 22 18:12:27 -12 2025 -I: pbuilder-time-stamp: 1745388747 +I: Current time: Wed May 27 02:36:21 +14 2026 +I: pbuilder-time-stamp: 1779798981 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -28,52 +28,84 @@ dpkg-source: info: applying gcc14.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2862450/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/311063/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 May 26 12:36 /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/311063/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/311063/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='ec750af594d948edbe1404d0bbd0b048' - 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='2862450' - PS1='# ' - PS2='> ' + INVOCATION_ID=aa83499a673740709b80967b42d0b778 + 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=311063 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.REw1aXKj/pbuilderrc_A5zV --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.REw1aXKj/b1 --logfile b1/build.log libpsortb_1.0+dfsg-7.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.REw1aXKj/pbuilderrc_GxbO --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.REw1aXKj/b2 --logfile b2/build.log libpsortb_1.0+dfsg-7.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 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2862450/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/311063/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -157,7 +189,7 @@ Get: 36 http://deb.debian.org/debian unstable/main arm64 libsvm-dev arm64 3.24+ds-6.1 [59.7 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] -Fetched 11.4 MB in 0s (97.9 MB/s) +Fetched 11.4 MB in 0s (49.9 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 ... 19953 files and directories currently installed.) @@ -324,7 +356,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/libpsortb-1.0+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 > ../libpsortb_1.0+dfsg-7_source.changes +I: user script /srv/workspace/pbuilder/311063/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/311063/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libpsortb-1.0+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 > ../libpsortb_1.0+dfsg-7_source.changes dpkg-buildpackage: info: source package libpsortb dpkg-buildpackage: info: source version 1.0+dfsg-7 dpkg-buildpackage: info: source distribution unstable @@ -517,13 +553,13 @@ make[2]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' Making all in svmloc make[3]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o binding.lo binding.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o svmloc.lo svmloc.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c svmloc.cpp -fPIC -DPIC -o .libs/svmloc.o +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o binding.lo binding.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o svmloc.lo svmloc.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c binding.cpp -fPIC -DPIC -o .libs/binding.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c svmloc.cpp -fPIC -DPIC -o .libs/svmloc.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c binding.cpp -o binding.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c svmloc.cpp -o svmloc.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -version-info 0:0:0 -lsvm -Wl,-z,relro -Wl,-z,now -o libsvmloc.la -rpath /usr/lib/aarch64-linux-gnu binding.lo svmloc.lo -lm +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -version-info 0:0:0 -lsvm -Wl,-z,relro -Wl,-z,now -o libsvmloc.la -rpath /usr/lib/aarch64-linux-gnu binding.lo svmloc.lo -lm libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o .libs/binding.o .libs/svmloc.o -lsvm -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -Werror=format-security -mbranch-protection=standard -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libsvmloc.so.0 -o .libs/libsvmloc.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libsvmloc.so.0" && ln -s "libsvmloc.so.0.0.0" "libsvmloc.so.0") libtool: link: (cd ".libs" && rm -f "libsvmloc.so" && ln -s "libsvmloc.so.0.0.0" "libsvmloc.so") @@ -533,79 +569,63 @@ make[3]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' Making all in modhmm0.92b make[3]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o core_algorithms_multialpha.lo core_algorithms_multialpha.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o debug_funcs.lo debug_funcs.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o hmmsearch.lo hmmsearch.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o readhmm.lo readhmm.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o readhmm_multialpha.lo readhmm_multialpha.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o readseqs_multialpha.lo readseqs_multialpha.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o std_calculation_funcs.lo std_calculation_funcs.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o std_funcs.lo std_funcs.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o training_algorithms_multialpha.lo training_algorithms_multialpha.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o core_algorithms_multialpha.lo core_algorithms_multialpha.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o debug_funcs.lo debug_funcs.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o hmmsearch.lo hmmsearch.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o readhmm.lo readhmm.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o readhmm_multialpha.lo readhmm_multialpha.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o readseqs_multialpha.lo readseqs_multialpha.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o std_calculation_funcs.lo std_calculation_funcs.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o std_funcs.lo std_funcs.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o training_algorithms_multialpha.lo training_algorithms_multialpha.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c debug_funcs.c -fPIC -DPIC -o .libs/debug_funcs.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readseqs_multialpha.c -fPIC -DPIC -o .libs/readseqs_multialpha.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c training_algorithms_multialpha.c -fPIC -DPIC -o .libs/training_algorithms_multialpha.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c core_algorithms_multialpha.c -fPIC -DPIC -o .libs/core_algorithms_multialpha.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readhmm_multialpha.c -fPIC -DPIC -o .libs/readhmm_multialpha.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readhmm.c -fPIC -DPIC -o .libs/readhmm.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c hmmsearch.c -fPIC -DPIC -o .libs/hmmsearch.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c std_calculation_funcs.c -fPIC -DPIC -o .libs/std_calculation_funcs.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readseqs_multialpha.c -fPIC -DPIC -o .libs/readseqs_multialpha.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readhmm.c -fPIC -DPIC -o .libs/readhmm.o debug_funcs.c:7:76: warning: 'struct hmm_multi_s' declared inside parameter list will not be visible outside of this definition or declaration 7 | int read_multi_prior_file_multi(struct emission_dirichlet_s *em_di, struct hmm_multi_s *hmmp, FILE *priorfile, int alphabet); | ^~~~~~~~~~~ debug_funcs.c:7:40: warning: 'struct emission_dirichlet_s' declared inside parameter list will not be visible outside of this definition or declaration 7 | int read_multi_prior_file_multi(struct emission_dirichlet_s *em_di, struct hmm_multi_s *hmmp, FILE *priorfile, int alphabet); | ^~~~~~~~~~~~~~~~~~~~ +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c std_calculation_funcs.c -fPIC -DPIC -o .libs/std_calculation_funcs.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c training_algorithms_multialpha.c -fPIC -DPIC -o .libs/training_algorithms_multialpha.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c std_funcs.c -fPIC -DPIC -o .libs/std_funcs.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c core_algorithms_multialpha.c -fPIC -DPIC -o .libs/core_algorithms_multialpha.o +hmmsearch.c: In function 'get_nullmodel_score_multi': +hmmsearch.c:656:42: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] + 656 | printf("Could not find letter %s when scoring null model\n", &seq[l]); + | ~^ ~~~~~~~ + | | | + | char * struct letter_s * +hmmsearch.c:674:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] + 674 | printf("Could not find letter %s when scoring null model\n", &seq_2[l]); + | ~^ ~~~~~~~~~ + | | | + | char * struct letter_s * +hmmsearch.c:693:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] + 693 | printf("Could not find letter %s when scoring null model\n", &seq_3[l]); + | ~^ ~~~~~~~~~ + | | | + | char * struct letter_s * +hmmsearch.c:712:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] + 712 | printf("Could not find letter %s when scoring null model\n", &seq[l]); + | ~^ ~~~~~~~ + | | | + | char * struct letter_s * readseqs_multialpha.c: In function 'get_sequence_std_multi': +readhmm_multialpha.c: In function 'readhmm_multialpha': readseqs_multialpha.c:121:55: warning: unknown escape sequence: '\s' 121 | if(line[0] == '<' || line[0] == '#' || line[0] == '\s' || line[0] == '\n' || line[0] == '/') { | ^~~~ +readhmm_multialpha.c:326:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 326 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ readseqs_multialpha.c: In function 'get_sequences_msa_std_multi': readseqs_multialpha.c:372:18: warning: unknown escape sequence: '\s' 372 | else if(i == '\s' && i == '\n') { | ^~~~ -readseqs_multialpha.c: In function 'get_sequence_std_multi': -readseqs_multialpha.c:286:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 286 | fgets(line, MAX_LINE, seqfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -training_algorithms_multialpha.c: In function 'msa_baum_welch_dirichlet_multi': -training_algorithms_multialpha.c:701:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 701 | alphabet = (int)hmmp->alphabet; - | ^ -training_algorithms_multialpha.c:710:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 710 | alphabet = (int)hmmp->alphabet_2; - | ^ -training_algorithms_multialpha.c:719:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 719 | alphabet = (int)hmmp->alphabet_3; - | ^ -training_algorithms_multialpha.c:728:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 728 | alphabet = (int)hmmp->alphabet_4; - | ^ -readseqs_multialpha.c: In function 'get_sequences_msa_std_multi': -readseqs_multialpha.c:625:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 625 | fgets(line, MAX_LINE, seqfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -readseqs_multialpha.c:754:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 754 | fgets(line, MAX_LINE, seqfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -readseqs_multialpha.c:874:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 874 | fgets(line, MAX_LINE, seqfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -readseqs_multialpha.c:995:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 995 | fgets(line, MAX_LINE, seqfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -readhmm_multialpha.c: In function 'readhmm_multialpha': -readhmm_multialpha.c:326:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 326 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -training_algorithms_multialpha.c: In function 'extended_msa_baum_welch_dirichlet_multi': -training_algorithms_multialpha.c:1639:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1639 | alphabet = (int)hmmp->alphabet; - | ^ -training_algorithms_multialpha.c:1646:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1646 | alphabet = (int)hmmp->alphabet_2; - | ^ readhmm_multialpha.c: In function 'read_module_multi': readhmm_multialpha.c:1039:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1039 | fgets(s, MAX_LINE, file); @@ -640,33 +660,36 @@ readhmm_multialpha.c:1233:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1233 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ -training_algorithms_multialpha.c:1653:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1653 | alphabet = (int)hmmp->alphabet_3; - | ^ -training_algorithms_multialpha.c:1660:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1660 | alphabet = (int)hmmp->alphabet_4; - | ^ -training_algorithms_multialpha.c:1784:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1784 | alphabet = (int)hmmp->alphabet; - | ^ -training_algorithms_multialpha.c:1791:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1791 | alphabet = (int)hmmp->alphabet_2; - | ^ -training_algorithms_multialpha.c:1798:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1798 | alphabet = (int)hmmp->alphabet_3; - | ^ -training_algorithms_multialpha.c:1805:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1805 | alphabet = (int)hmmp->alphabet_4; - | ^ +std_funcs.c: In function 'get_replacement_letter_index_single': readhmm.c: In function 'readhmm': readhmm.c:69:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm.c: In function 'readanhmm': +std_calculation_funcs.c: In function 'update_labelings': +readseqs_multialpha.c: In function 'get_sequence_std_multi': +readseqs_multialpha.c:286:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 286 | fgets(line, MAX_LINE, seqfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +std_calculation_funcs.c:1295:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1295 | cur_address = (int)((cur_rowp+v)->labeling); + | ^ +std_calculation_funcs.c:1309:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1309 | if((int)((cur_rowp+w)->labeling) == cur_address && (cur_rowp + w)->is_updated == NO) { + | ^ +std_calculation_funcs.c: In function 'deallocate_row_labelings': +std_calculation_funcs.c:1425:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1425 | cur_address = (int)((prev_rowp+v)->labeling); + | ^ +std_calculation_funcs.c:1430:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1430 | if((int)((prev_rowp+w)->labeling) == cur_address) { + | ^ readhmm.c:342:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 342 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ -training_algorithms_multialpha.c: In function 'add_to_E_multi': +std_funcs.c:680:62: warning: comparison between pointer and integer + 680 | if(((replacement_letters->letters + a_index)->letter)[0] == c) { + | ^~ readhmm.c: In function 'read_module': readhmm.c:745:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 745 | fgets(s, MAX_LINE, file); @@ -683,61 +706,74 @@ readhmm.c:848:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 848 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ +training_algorithms_multialpha.c: In function 'msa_baum_welch_dirichlet_multi': +training_algorithms_multialpha.c:701:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 701 | alphabet = (int)hmmp->alphabet; + | ^ +readhmm.c: In function 'read_prior_files': +readseqs_multialpha.c: In function 'get_sequences_msa_std_multi': +readseqs_multialpha.c:625:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 625 | fgets(line, MAX_LINE, seqfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +readseqs_multialpha.c:754:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 754 | fgets(line, MAX_LINE, seqfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +readseqs_multialpha.c:874:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 874 | fgets(line, MAX_LINE, seqfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +readseqs_multialpha.c:995:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 995 | fgets(line, MAX_LINE, seqfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +readhmm.c:1225:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1225 | fgets(ps, 2048, priorfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +training_algorithms_multialpha.c:710:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 710 | alphabet = (int)hmmp->alphabet_2; + | ^ +training_algorithms_multialpha.c:719:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 719 | alphabet = (int)hmmp->alphabet_3; + | ^ +training_algorithms_multialpha.c:728:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 728 | alphabet = (int)hmmp->alphabet_4; + | ^ +training_algorithms_multialpha.c: In function 'extended_msa_baum_welch_dirichlet_multi': +training_algorithms_multialpha.c:1639:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1639 | alphabet = (int)hmmp->alphabet; + | ^ +training_algorithms_multialpha.c:1646:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1646 | alphabet = (int)hmmp->alphabet_2; + | ^ +training_algorithms_multialpha.c:1653:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1653 | alphabet = (int)hmmp->alphabet_3; + | ^ +training_algorithms_multialpha.c:1660:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1660 | alphabet = (int)hmmp->alphabet_4; + | ^ +training_algorithms_multialpha.c:1784:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1784 | alphabet = (int)hmmp->alphabet; + | ^ +training_algorithms_multialpha.c:1791:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1791 | alphabet = (int)hmmp->alphabet_2; + | ^ +training_algorithms_multialpha.c:1798:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1798 | alphabet = (int)hmmp->alphabet_3; + | ^ +training_algorithms_multialpha.c:1805:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1805 | alphabet = (int)hmmp->alphabet_4; + | ^ +training_algorithms_multialpha.c: In function 'add_to_E_multi': training_algorithms_multialpha.c:3589:43: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 3589 | (char*)alphabet); | ^ training_algorithms_multialpha.c:3593:49: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 3593 | (char*)alphabet); | ^ -readhmm.c: In function 'read_prior_files': -readhmm.c:1225:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1225 | fgets(ps, 2048, priorfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c:3618:36: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 3618 | (char*)alphabet); | ^ training_algorithms_multialpha.c:3622:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 3622 | (char*)alphabet); | ^ -hmmsearch.c: In function 'get_nullmodel_score_multi': -hmmsearch.c:656:42: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] - 656 | printf("Could not find letter %s when scoring null model\n", &seq[l]); - | ~^ ~~~~~~~ - | | | - | char * struct letter_s * -hmmsearch.c:674:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] - 674 | printf("Could not find letter %s when scoring null model\n", &seq_2[l]); - | ~^ ~~~~~~~~~ - | | | - | char * struct letter_s * -hmmsearch.c:693:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] - 693 | printf("Could not find letter %s when scoring null model\n", &seq_3[l]); - | ~^ ~~~~~~~~~ - | | | - | char * struct letter_s * -hmmsearch.c:712:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] - 712 | printf("Could not find letter %s when scoring null model\n", &seq[l]); - | ~^ ~~~~~~~ - | | | - | char * struct letter_s * -std_calculation_funcs.c: In function 'update_labelings': -std_calculation_funcs.c:1295:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1295 | cur_address = (int)((cur_rowp+v)->labeling); - | ^ -std_calculation_funcs.c:1309:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1309 | if((int)((cur_rowp+w)->labeling) == cur_address && (cur_rowp + w)->is_updated == NO) { - | ^ -std_calculation_funcs.c: In function 'deallocate_row_labelings': -std_calculation_funcs.c:1425:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1425 | cur_address = (int)((prev_rowp+v)->labeling); - | ^ -std_calculation_funcs.c:1430:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1430 | if((int)((prev_rowp+w)->labeling) == cur_address) { - | ^ -std_funcs.c: In function 'get_replacement_letter_index_single': -std_funcs.c:680:62: warning: comparison between pointer and integer - 680 | if(((replacement_letters->letters + a_index)->letter)[0] == c) { - | ^~ std_funcs.c: In function 'get_nr_alphabets': std_funcs.c:2726:10: warning: 'fgets' writing 4000 bytes into a region of size 1000 overflows the destination [-Wstringop-overflow=] 2726 | if(fgets(s, MAX_LINE, hmmfile) != NULL) { @@ -761,10 +797,10 @@ | ^~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c hmmsearch.c -o hmmsearch.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c debug_funcs.c -o debug_funcs.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readhmm_multialpha.c -o readhmm_multialpha.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readseqs_multialpha.c -o readseqs_multialpha.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readhmm.c -o readhmm.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c std_calculation_funcs.c -o std_calculation_funcs.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readhmm_multialpha.c -o readhmm_multialpha.o >/dev/null 2>&1 In function 'fgets', inlined from 'get_nr_alphabets' at std_funcs.c:2726:10: /usr/include/aarch64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] @@ -775,10 +811,10 @@ /usr/include/aarch64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c std_funcs.c -o std_funcs.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c core_algorithms_multialpha.c -o core_algorithms_multialpha.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c std_funcs.c -o std_funcs.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c training_algorithms_multialpha.c -o training_algorithms_multialpha.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -version-info 0:0:0 -Wl,-z,relro -Wl,-z,now -o libmodhmm.la -rpath /usr/lib/aarch64-linux-gnu core_algorithms_multialpha.lo debug_funcs.lo hmmsearch.lo readhmm.lo readhmm_multialpha.lo readseqs_multialpha.lo std_calculation_funcs.lo std_funcs.lo training_algorithms_multialpha.lo -lm +/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -version-info 0:0:0 -Wl,-z,relro -Wl,-z,now -o libmodhmm.la -rpath /usr/lib/aarch64-linux-gnu core_algorithms_multialpha.lo debug_funcs.lo hmmsearch.lo readhmm.lo readhmm_multialpha.lo readseqs_multialpha.lo std_calculation_funcs.lo std_funcs.lo training_algorithms_multialpha.lo -lm libtool: link: gcc -shared -fPIC -DPIC .libs/core_algorithms_multialpha.o .libs/debug_funcs.o .libs/hmmsearch.o .libs/readhmm.o .libs/readhmm_multialpha.o .libs/readseqs_multialpha.o .libs/std_calculation_funcs.o .libs/std_funcs.o .libs/training_algorithms_multialpha.o -lm -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -Werror=format-security -mbranch-protection=standard -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libmodhmm.so.0 -o .libs/libmodhmm.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libmodhmm.so.0" && ln -s "libmodhmm.so.0.0.0" "libmodhmm.so.0") libtool: link: (cd ".libs" && rm -f "libmodhmm.so" && ln -s "libmodhmm.so.0.0.0" "libmodhmm.so") @@ -815,7 +851,7 @@ make[3]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' make[4]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' /usr/bin/mkdir -p '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libsvmloc.la '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libsvmloc.la '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libsvmloc.so.0.0.0 /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.so.0.0.0 libtool: install: (cd /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libsvmloc.so.0.0.0 libsvmloc.so.0 || { rm -f libsvmloc.so.0 && ln -s libsvmloc.so.0.0.0 libsvmloc.so.0; }; }) libtool: install: (cd /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libsvmloc.so.0.0.0 libsvmloc.so || { rm -f libsvmloc.so && ln -s libsvmloc.so.0.0.0 libsvmloc.so; }; }) @@ -831,7 +867,7 @@ make[3]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' make[4]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' /usr/bin/mkdir -p '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libmodhmm.la '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libmodhmm.la '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libmodhmm.so.0.0.0 /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.so.0.0.0 libtool: install: (cd /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libmodhmm.so.0.0.0 libmodhmm.so.0 || { rm -f libmodhmm.so.0 && ln -s libmodhmm.so.0.0.0 libmodhmm.so.0; }; }) libtool: install: (cd /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libmodhmm.so.0.0.0 libmodhmm.so || { rm -f libmodhmm.so && ln -s libmodhmm.so.0.0.0 libmodhmm.so; }; }) @@ -907,12 +943,12 @@ dh_gencontrol dh_md5sums dh_builddeb +dpkg-deb: building package 'libmodhmm-dev' in '../libmodhmm-dev_1.0+dfsg-7_arm64.deb'. dpkg-deb: building package 'libmodhmm0' in '../libmodhmm0_1.0+dfsg-7_arm64.deb'. +dpkg-deb: building package 'libsvmloc-dev' in '../libsvmloc-dev_1.0+dfsg-7_arm64.deb'. dpkg-deb: building package 'libmodhmm0-dbgsym' in '../libmodhmm0-dbgsym_1.0+dfsg-7_arm64.deb'. -dpkg-deb: building package 'libmodhmm-dev' in '../libmodhmm-dev_1.0+dfsg-7_arm64.deb'. dpkg-deb: building package 'libsvmloc0' in '../libsvmloc0_1.0+dfsg-7_arm64.deb'. dpkg-deb: building package 'libsvmloc0-dbgsym' in '../libsvmloc0-dbgsym_1.0+dfsg-7_arm64.deb'. -dpkg-deb: building package 'libsvmloc-dev' in '../libsvmloc-dev_1.0+dfsg-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libpsortb_1.0+dfsg-7_arm64.buildinfo dpkg-genchanges --build=binary -O../libpsortb_1.0+dfsg-7_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -920,12 +956,14 @@ 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/311063/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/311063/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/2862450 and its subdirectories -I: Current time: Tue Apr 22 18:13:17 -12 2025 -I: pbuilder-time-stamp: 1745388797 +I: removing directory /srv/workspace/pbuilder/311063 and its subdirectories +I: Current time: Wed May 27 02:38:13 +14 2026 +I: pbuilder-time-stamp: 1779799093 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/libpsortb_1.0+dfsg-7.diff: 87.1% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/libpsortb_1.0+dfsg-7.diff.gz b2/build.log: 83.1% -- replaced with stdout Compressing the 1st log... b1/build.log: 83.7% -- replaced with stdout Wed Apr 23 06:15:17 UTC 2025 I: diffoscope 294 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_libpsortb_unstable_arm64_1745388917 + touch /var/log/reproducible-builds/diffoscope_stamp_libpsortb_unstable_arm64_1745388917 + RESULT=0 + systemd-run '--description=diffoscope on libpsortb/1.0+dfsg-7 in unstable/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_7-68107 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.REw1aXKj --run-session -c jenkins-reproducible-unstable-diffoscope-4fc0f929-4ec0-4cda-b3f1-a70c5a12aa01 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.REw1aXKj/dbd-tmp-dCw5aR5 ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.REw1aXKj/libpsortb_1.0+dfsg-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.REw1aXKj/libpsortb_1.0+dfsg-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.REw1aXKj/libpsortb_1.0+dfsg-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.REw1aXKj/b1/libpsortb_1.0+dfsg-7_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.REw1aXKj/b2/libpsortb_1.0+dfsg-7_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_7-68107.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.REw1aXKj/libpsortb_1.0+dfsg-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.REw1aXKj/libpsortb_1.0+dfsg-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.REw1aXKj/libpsortb_1.0+dfsg-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.REw1aXKj/b1/libpsortb_1.0+dfsg-7_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.REw1aXKj/b2/libpsortb_1.0+dfsg-7_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: 224ms CPU time consumed: 224ms _ _ _ _ _ | (_) |__ _ __ ___ ___ _ __| |_| |__ | | | '_ \| '_ \/ __|/ _ \| '__| __| '_ \ | | | |_) | |_) \__ \ (_) | | | |_| |_) | |_|_|_.__/| .__/|___/\___/|_| \__|_.__/ |_| Wed Apr 23 06:15:18 UTC 2025 I: diffoscope 294 found no differences in the changes files, and a .buildinfo file also exists. Wed Apr 23 06:15:18 UTC 2025 I: libpsortb from unstable built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-04-23 06:15:19] INFO: Starting at 2025-04-23 06:15:19.041110 [2025-04-23 06:15:19] INFO: Generating the pages of 1 package(s) [2025-04-23 06:15:19] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/arm64/libpsortb didn't produce a buildlog, even though it has been built. [2025-04-23 06:15:19] INFO: Finished at 2025-04-23 06:15:19.469793, took: 0:00:00.428688 Wed Apr 23 06:15:19 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/libpsortb.html Wed Apr 23 06:15:19 UTC 2025 I: Submitting .buildinfo files to external archives: Wed Apr 23 06:15:19 UTC 2025 I: Submitting 8.0K b1/libpsortb_1.0+dfsg-7_arm64.buildinfo.asc https://buildinfo.debian.net/711ec596061689e433d251b68207998b87f71381/libpsortb_1.0+dfsg-7_arm64 Wed Apr 23 06:15:27 UTC 2025 I: Submitting 8.0K b2/libpsortb_1.0+dfsg-7_arm64.buildinfo.asc https://buildinfo.debian.net/9b8df9bfb876632f3e45cc5fe4941c2281054faa/libpsortb_1.0+dfsg-7_arm64 Wed Apr 23 06:15:34 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Apr 23 06:15:34 UTC 2025 I: Done submitting .buildinfo files. Wed Apr 23 06:15:34 UTC 2025 I: Removing signed libpsortb_1.0+dfsg-7_arm64.buildinfo.asc files: removed './b1/libpsortb_1.0+dfsg-7_arm64.buildinfo.asc' removed './b2/libpsortb_1.0+dfsg-7_arm64.buildinfo.asc' 1745388934 arm64 unstable libpsortb Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/libpsortb_1.0+dfsg-7.rbuild.log: 80.9% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/libpsortb_1.0+dfsg-7.rbuild.log.gz [2025-04-23 06:15:34] INFO: Starting at 2025-04-23 06:15:34.596814 [2025-04-23 06:15:34] INFO: Generating the pages of 1 package(s) [2025-04-23 06:15:35] INFO: Finished at 2025-04-23 06:15:35.032752, took: 0:00:00.435944 All cleanup done. Wed Apr 23 06:15:35 UTC 2025 - total duration: 0h 3m 11s. Wed Apr 23 06:15:35 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-z0jgsj0J, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 3min 27.611s CPU time consumed: 6.920s