Thu Feb 27 07:11:24 UTC 2025 I: starting to build libpsortb/trixie/arm64 on jenkins on '2025-02-27 07:11' Thu Feb 27 07:11:24 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_4/59065/console.log Thu Feb 27 07:11:24 UTC 2025 I: Downloading source for trixie/libpsortb=1.0+dfsg-7 --2025-02-27 07:11:24-- 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% 403M=0s 2025-02-27 07:11:24 (403 MB/s) - ‘libpsortb_1.0+dfsg-7.dsc’ saved [2350/2350] Thu Feb 27 07:11:24 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----- Thu Feb 27 07:11:24 UTC 2025 I: Checking whether the package is not for us Thu Feb 27 07:11:24 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net. Thu Feb 27 07:11:24 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Thu Feb 27 07:13:09 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Apr 1 01:34:27 -12 2026 I: pbuilder-time-stamp: 1775050467 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [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/102153/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='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='92ccd3e1171c44a1a68691eed75e937c' 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='102153' 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.yf0aVT7F/pbuilderrc_q3pm --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.yf0aVT7F/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 codethink03-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/102153/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 ... 19915 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} libicu72{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, 39 newly installed, 0 to remove and 0 not upgraded. Need to get 20.6 MB of archives. After unpacking 82.0 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-4 [92.1 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-3 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 d-shlibs all 0.109 [11.1 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-3 [539 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.1 [920 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libhmmer2-dev arm64 2.3.2+dfsg-12+b2 [92.3 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libsquid1t64 arm64 1.9g+cvs20050121-15.1+b2 [71.4 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libsquid-dev arm64 1.9g+cvs20050121-15.1+b2 [141 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libsvm3 arm64 3.24+ds-6+b1 [38.3 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libsvm-dev arm64 3.24+ds-6+b1 [59.4 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Fetched 20.6 MB in 0s (45.6 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 ... 19915 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... 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_2.40.4-4_arm64.deb ... Unpacking bsdextrautils (2.40.4-4) ... 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_1.4.19-5_arm64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-3_all.deb ... Unpacking automake (1:1.17-3) ... 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_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.5.4-3_all.deb ... Unpacking libtool (2.5.4-3) ... 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_1.3-1_arm64.deb ... Unpacking libunistring5:arm64 (1.3-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../25-libicu72_72.1-6_arm64.deb ... Unpacking libicu72:arm64 (72.1-6) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../26-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.23.1-1_arm64.deb ... Unpacking gettext (0.23.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-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 .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.24.1_all.deb ... Unpacking debhelper (13.24.1) ... Selecting previously unselected package libhmmer2-dev:arm64. Preparing to unpack .../31-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 .../32-libpkgconf3_1.8.1-4_arm64.deb ... Unpacking libpkgconf3:arm64 (1.8.1-4) ... 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Unpacking pkgconf:arm64 (1.8.1-4) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libicu72:arm64 (72.1-6) ... Setting up bsdextrautils (2.40.4-4) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libunistring5:arm64 (1.3-1) ... 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) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... 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+really2.9.14-0.2+b1) ... 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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 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 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 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../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 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 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 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 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 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 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 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_calculation_funcs.c -fPIC -DPIC -o .libs/std_calculation_funcs.o readseqs_multialpha.c: In function 'get_sequence_std_multi': 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 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') { | ^~~~ 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); | ^~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readseqs_multialpha.c: In function 'get_sequences_msa_std_multi': 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); | ^~~~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 * 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); | ^~~~~~~~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~ 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: 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; | ^ 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; | ^ 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; | ^ 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: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_calculation_funcs.c: In function 'update_labelings': 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_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': 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); | ^ 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) { | ^ 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 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 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 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 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 '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-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 'libmodhmm-dev' in '../libmodhmm-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/102153 and its subdirectories I: Current time: Wed Apr 1 01:36:08 -12 2026 I: pbuilder-time-stamp: 1775050568 Thu Feb 27 07:13:10 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Thu Feb 27 07:13:10 UTC 2025 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Thu Feb 27 07:14:03 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Thu Feb 27 07:14:04 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: 107977e156fd4eae1feac7cc691aef95441fdba7 70264 libmodhmm-dev_1.0+dfsg-7_arm64.deb 4e691fd73db5c90260ab38cacc8023cdce1c146c 211192 libmodhmm0-dbgsym_1.0+dfsg-7_arm64.deb 2e6a8f7f2a32de97a070fe1c7c338c4cd2cae7ed 68072 libmodhmm0_1.0+dfsg-7_arm64.deb 683127f32c4679440b37e73f73610bac9f868241 6675 libpsortb_1.0+dfsg-7_arm64.buildinfo ad6c8349cc0bf8006c2e2e21e04495021f75f49c 12028 libsvmloc-dev_1.0+dfsg-7_arm64.deb 4631cb93f4fc920a4f9ac5d0f51a86be885c5988 98628 libsvmloc0-dbgsym_1.0+dfsg-7_arm64.deb 52953d91a1ed97211aca1811e9707deccf63d314 12832 libsvmloc0_1.0+dfsg-7_arm64.deb Checksums-Sha256: 2df35c3dae20f5fa1c8605c4918c0ed299798162a48a07d3db048ec823b85d80 70264 libmodhmm-dev_1.0+dfsg-7_arm64.deb 1cf1cd321d1daf5f54d958ba1f309412e7368c088d6b87d71de07c65f9a681d0 211192 libmodhmm0-dbgsym_1.0+dfsg-7_arm64.deb 8b56f61ba9f2ad9430eaa73531d47e7a438e72950c82de2bab552d3bb3a8baab 68072 libmodhmm0_1.0+dfsg-7_arm64.deb 4228cb75e0783d9764a164741589b939f327f3d36d658da110fd7bc382cf04dd 6675 libpsortb_1.0+dfsg-7_arm64.buildinfo 5bd5c45f3ef9cfc0b540fa356db1edefbe047138c82e66fcfcde8e786b111c9a 12028 libsvmloc-dev_1.0+dfsg-7_arm64.deb 0dcd3adea201665fc93f47180ab76121226d294dc3747d93ddda7c23c2773988 98628 libsvmloc0-dbgsym_1.0+dfsg-7_arm64.deb ad818618dccfd98be7405eef3f8ce83b29b196647efc7e4dc10b5cdbfc6853a1 12832 libsvmloc0_1.0+dfsg-7_arm64.deb Files: 53993f7e517ddae048e86d112991af12 70264 libdevel optional libmodhmm-dev_1.0+dfsg-7_arm64.deb fd30fa76c977be807cee5679eebc1660 211192 debug optional libmodhmm0-dbgsym_1.0+dfsg-7_arm64.deb 765714e0f0f8e5d7401541efea436083 68072 libs optional libmodhmm0_1.0+dfsg-7_arm64.deb cb513ab0973fb1e911551a06015b74c2 6675 science optional libpsortb_1.0+dfsg-7_arm64.buildinfo 1994aca84367f0378473fa5bd7379d1f 12028 libdevel optional libsvmloc-dev_1.0+dfsg-7_arm64.deb fe836955be01f654c2fbe24913eed594 98628 debug optional libsvmloc0-dbgsym_1.0+dfsg-7_arm64.deb 78c262e532efce3d20dec607cae8d0fe 12832 libs optional libsvmloc0_1.0+dfsg-7_arm64.deb Thu Feb 27 07:14:05 UTC 2025 I: diffoscope 289 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_4-59065.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.yf0aVT7F/libpsortb_1.0+dfsg-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.yf0aVT7F/libpsortb_1.0+dfsg-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.yf0aVT7F/libpsortb_1.0+dfsg-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.yf0aVT7F/b1/libpsortb_1.0+dfsg-7_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.yf0aVT7F/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: 225ms CPU time consumed: 224ms Thu Feb 27 07:14:05 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists. Thu Feb 27 07:14:05 UTC 2025 I: libpsortb from trixie built successfully and reproducibly on arm64. Thu Feb 27 07:14:06 UTC 2025 I: Submitting .buildinfo files to external archives: Thu Feb 27 07:14:06 UTC 2025 I: Submitting 8.0K b1/libpsortb_1.0+dfsg-7_arm64.buildinfo.asc Thu Feb 27 07:14:07 UTC 2025 I: Submitting 8.0K b2/libpsortb_1.0+dfsg-7_arm64.buildinfo.asc Thu Feb 27 07:14:08 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Feb 27 07:14:08 UTC 2025 I: Done submitting .buildinfo files. Thu Feb 27 07:14:08 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'