Sun Feb 2 04:53:40 UTC 2025 I: starting to build codonw/trixie/armhf on jenkins on '2025-02-02 04:53' Sun Feb 2 04:53:40 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_24/11655/console.log Sun Feb 2 04:53:40 UTC 2025 I: Downloading source for trixie/codonw=1.4.4-8 --2025-02-02 04:53:40-- http://deb.debian.org/debian/pool/main/c/codonw/codonw_1.4.4-8.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2055 (2.0K) [text/prs.lines.tag] Saving to: ‘codonw_1.4.4-8.dsc’ 0K .. 100% 372M=0s 2025-02-02 04:53:40 (372 MB/s) - ‘codonw_1.4.4-8.dsc’ saved [2055/2055] Sun Feb 2 04:53:40 UTC 2025 I: codonw_1.4.4-8.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: codonw Binary: codonw Architecture: any Version: 1.4.4-8 Maintainer: Debian Med Packaging Team Uploaders: Sascha Steinbiss Homepage: https://codonw.sourceforge.net Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/codonw Vcs-Git: https://salsa.debian.org/med-team/codonw.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: codonw deb science optional arch=any Checksums-Sha1: 5f5c5deb84b291692c9b00657357d4a2881badae 155815 codonw_1.4.4.orig.tar.gz 48761b3ee4ccd7dab829308ade9ddce42cbb609c 14732 codonw_1.4.4-8.debian.tar.xz Checksums-Sha256: 942d52c16e85d6f5f2543482a97a094d245180c0e6ba0845941f18d7cbe15aa1 155815 codonw_1.4.4.orig.tar.gz 12d0bda5cb945d9142cb5537f6d4cd7d75a8748e342e6d66fff50c801b4130bd 14732 codonw_1.4.4-8.debian.tar.xz Files: e8178e830b52e44b43f2c709cf838abb 155815 codonw_1.4.4.orig.tar.gz f7b346b3960073aa1c8e6b4e5dac3b13 14732 codonw_1.4.4-8.debian.tar.xz Dgit: be8700862b6e2e81b710521198c2f852234cc761 debian archive/debian/1.4.4-8 https://git.dgit.debian.org/codonw -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmX3K+oUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdrGEA//dkzBDZDulicYbY7nN0mFH3UAbqoa 4Sy0l+o+wLX7eJYkN0zIWzd67kIsfa16eKzpgVP0W9NqyPOfHcvGVosTrHUwfWz9 hymQPtcYnS2zATfItNWXxJ0XZPNCZqgu/ytm2DVtnfwhzQOeVzGGpTjZhVX4feW0 xHoJRsZRSwTMnQKcmXregzB5FRTsDVNuGXNjhUb7rDAOO3yeLv2k3Nd1fDpjZTJK l/3ZHgeYNeNHq4pM3dnyZf6VyDFkrfhTUeAk8uwUwojSJRXlNNZoCSZEupZNsv7L 0cvRfS2odJossK3EH4ZYkq46+cfPm2K/v4K0rooLsTTmb9X1o+mfVgteYoqddJCW aKqrO8CMyhHTqYjKMIe2MRu353MjH8vZYRV9Ap3N7KaE2y3EK2DPxu+3nkQqLlaN /m9cVBKg2PvVULdrbWZ/Vc0ESdKMyYwNSeOjw3Sf65P6KbNFSUa5ZgT4ei3Kv5lK a4xbE3bUPPbetKF8djSpPEsQMt+U64TlJ8LlLisYwoLffV9ya3rUMqpOfn1d1lxT /rUbfTr2qJ0RVoRZDZyv93iVO3SiBpHQUvbeXCkGzY+8ldEmLFPEtIYxiLhCpZll T386UYTIEfVcehEIdvqhdFtIw/zUinkHrUKCfKGtw7U0seyKUNZPU8Gp3JlgyFiC Uf3JXC/vXD8ZVyw= =ekk9 -----END PGP SIGNATURE----- Sun Feb 2 04:53:40 UTC 2025 I: Checking whether the package is not for us Sun Feb 2 04:53:40 UTC 2025 I: Starting 1st build on remote node ff4a-armhf-rb.debian.net. Sun Feb 2 04:53:40 UTC 2025 I: Preparing to do remote build '1' on ff4a-armhf-rb.debian.net. Sun Feb 2 04:55:31 UTC 2025 I: Deleting $TMPDIR on ff4a-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Feb 1 16:53:51 -12 2025 I: pbuilder-time-stamp: 1738472031 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 [codonw_1.4.4-8.dsc] I: copying [./codonw_1.4.4.orig.tar.gz] I: copying [./codonw_1.4.4-8.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./codonw_1.4.4-8.dsc: unsupported subcommand dpkg-source: info: extracting codonw in codonw-1.4.4 dpkg-source: info: unpacking codonw_1.4.4.orig.tar.gz dpkg-source: info: unpacking codonw_1.4.4-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening dpkg-source: info: applying enable_clean dpkg-source: info: applying remove_pause dpkg-source: info: applying define_linux dpkg-source: info: applying spelling dpkg-source: info: applying helpfile_location dpkg-source: info: applying fix_link_name_clashes dpkg-source: info: applying remove_nondeterminism dpkg-source: info: applying remove-gets.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/19906/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='4fd2ef31361e42378f32688755502d93' 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='19906' 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.DM5L1nsu/pbuilderrc_zDIJ --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.DM5L1nsu/b1 --logfile b1/build.log codonw_1.4.4-8.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux ff4a 6.1.0-30-armmp-lpae #1 SMP Debian 6.1.124-1 (2025-01-12) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/19906/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: armhf 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) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19573 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. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-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} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{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, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 19.7 MB of archives. After unpacking 74.3 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.23.1-1 [238 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-7 [1095 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40.4-1 [84.6 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-5 [272 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf libtool all 2.5.4-2 [539 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.14.1-1 [8584 B] Get: 22 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf libunistring5 armhf 1.3-1 [444 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-6 [9086 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.23.1-1 [1560 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf debhelper all 13.24.1 [920 kB] Fetched 19.7 MB in 1s (13.6 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 ... 19573 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_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_armhf.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_armhf.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_armhf.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.4-1_armhf.deb ... Unpacking bsdextrautils (2.40.4-1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../08-libpipeline1_1.5.8-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_armhf.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-5_armhf.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%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-2_all.deb ... Unpacking libtool (2.5.4-2) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-1) ... Selecting previously unselected package libelf1t64:armhf. Preparing to unpack .../21-libelf1t64_0.192-4_armhf.deb ... Unpacking libelf1t64:armhf (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b2_armhf.deb ... Unpacking dwz (0.15-1+b2) ... Selecting previously unselected package libunistring5:armhf. Preparing to unpack .../23-libunistring5_1.3-1_armhf.deb ... Unpacking libunistring5:armhf (1.3-1) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../24-libicu72_72.1-6_armhf.deb ... Unpacking libicu72:armhf (72.1-6) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_armhf.deb ... Unpacking libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-1_armhf.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_13.24.1_all.deb ... Unpacking debhelper (13.24.1) ... Setting up libpipeline1:armhf (1.5.8-1) ... Setting up libicu72:armhf (72.1-6) ... Setting up bsdextrautils (2.40.4-1) ... 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:armhf (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:armhf (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up libunistring5:armhf (1.3-1) ... Setting up autopoint (0.23.1-1) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:armhf (0.0.8-1+b2) ... Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-1) ... Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-1) ... 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 (13.24.1) ... Processing triggers for libc-bin (2.40-6) ... 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/codonw-1.4.4/ && 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 > ../codonw_1.4.4-8_source.changes dpkg-buildpackage: info: source package codonw dpkg-buildpackage: info: source version 1.4.4-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/codonw-1.4.4' rm -rf *.o *.coa *.blk *.out *raw codonw codonW.log make[1]: Leaving directory '/build/reproducible-path/codonw-1.4.4' debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/codonw-1.4.4' rm -rf debian/man dh_clean --exclude=Makefile.orig make[1]: Leaving directory '/build/reproducible-path/codonw-1.4.4' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j3 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/codonw-1.4.4' cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/codonw-1.4.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 codon_us.c cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/codonw-1.4.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 codons.c cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/codonw-1.4.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 open_fil.c codons.c: In function 'main': codons.c:190:55: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 190 | fprintf(pm->my_err,"\n\n\t\tNumber of sequences: %i\n", | ~^ | | | int | %li 191 | num_sequence); | ~~~~~~~~~~~~ | | | long int codons.c:196:32: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 196 | fprintf(pm->my_err, "\tWARNING\t At least one sequence in your" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 197 | " input file has\ninternal stop codons (found %i" 198 | " internal stops) \tWARNING\n",num_seq_int_stop); | ~~~~~~~~~~~~~~~~ | | | long int codons.c:197:68: note: format string is defined here 197 | " input file has\ninternal stop codons (found %i" | ~^ | | | int | %li codons.c:200:46: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 200 | fprintf(pm->my_err, "\tWARNING\t %i sequences had internal " | ~^ | | | int | %li 201 | "stop codons \tWARNING\n",num_seq_int_stop); | ~~~~~~~~~~~~~~~~ | | | long int open_fil.c: In function 'open_file': open_fil.c:88:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 88 | fgets(infile_name, BUFSIZ, stdin); /* get filename */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ open_fil.c:133:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 133 | fgets(answer, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ open_fil.c:166:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 166 | fgets(temp, 3, stdin); | ^~~~~~~~~~~~~~~~~~~~~ open_fil.c:186:21: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 186 | fgets(answer, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ open_fil.c:88:13: warning: 'fgets' writing 8192 bytes into a region of size 90 overflows the destination [-Wstringop-overflow=] 88 | fgets(infile_name, BUFSIZ, stdin); /* get filename */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ open_fil.c:71:12: note: destination object 'infile_name' of size 90 71 | char infile_name[MAX_FILENAME_LEN]=""; | ^~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from open_fil.c:47: /usr/include/arm-linux-gnueabihf/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, | ^~~~~ codons.c: In function 'toutput': codons.c:640:25: warning: unknown conversion type character '=' in format [-Wformat=] 640 | fprintf(pm->my_err, "%3li>\t%6li %-40.40s\tDNA\tGC%" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codons.c:641:11: note: format string is defined here 641 | " =%5.3f\n" /* with G+C content and length of gene */ | ^ codons.c:647:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 647 | fprintf(pm->my_err, "\t\t WARNING %d non IUBC standard characters " | ~^ | | | int | %ld 648 | "in sequence %i\n" 649 | ,non_std_char - IUBC_TOT | ~~~~~~~~~~~~~~~~~~~~~~~ | | | long int codons.c:647:27: warning: format '%i' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 647 | fprintf(pm->my_err, "\t\t WARNING %d non IUBC standard characters " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 650 | ,num_sequence); | ~~~~~~~~~~~~ | | | long int codons.c:648:25: note: format string is defined here 648 | "in sequence %i\n" | ~^ | | | int | %li codons.c:652:30: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 652 | fprintf(pm->my_err, "\t%3i>\t%6li %-40.40s\tPROTEIN\n" | ~~^ | | | int | %3li 653 | ,num_sequence | ~~~~~~~~~~~~ | | | long int codons.c:657:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 657 | fprintf(pm->my_err, "\t\t WARNING %d non " | ~^ | | | int | %ld ...... 660 | ,non_std_char | ~~~~~~~~~~~~ | | | long int codons.c:657:27: warning: format '%i' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 657 | fprintf(pm->my_err, "\t\t WARNING %d non " | ^~~~~~~~~~~~~~~~~~~~~~ ...... 661 | ,num_sequence); | ~~~~~~~~~~~~ | | | long int codons.c:659:25: note: format string is defined here 659 | "in sequence %i\n" | ~^ | | | int | %li codons.c: In function 'output': codon_us.c: In function 'codon_usage_out': codon_us.c:373:24: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 373 | fprintf(fblkout, "%i%c",nncod[x],sp); | ~^ ~~~~~~~~ | | | | int long int | %li codons.c:800:34: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'int' [-Wformat=] 800 | fprintf(stderr, "ERROR-23 %s bulk undefined\n", pm->prog); | ~^ ~~~~~~~~ | | | | char * int | %d codon_us.c: In function 'raau_usage_out': codon_us.c:479:21: warning: too many arguments for format [-Wformat-extra-args] 479 | fprintf(fblkout, "\n",sp); | ^~~~ codons.c:805:32: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'int' [-Wformat=] 805 | fprintf(stderr, "ERROR-24 %s -prog undefined\n", pm->prog); | ~^ ~~~~~~~~ | | | | char * int | %d codon_us.c: In function 'cbi_out': codon_us.c:831:32: warning: format '%f' expects argument of type 'double', but argument 3 has type 'int' [-Wformat=] 831 | sprintf(pm->messages, " Serious error in CBI information found" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 836 | pcbi->fop_cod[x], x); | ~~~~~~~~~~~~~~~~ | | | int codon_us.c:832:38: note: format string is defined here 832 | " an illegal CBI value of %f for codon %i" | ~^ | | | double | %d In file included from codons.c:90: codons.c: In function 'main': codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codons.c:204:35: note: in expansion of macro 'pause' 204 | if ( pm->codonW && pm->menu ) pause; | ^~~~~ codon_us.c: In function 'fop_out': codon_us.c:988:28: warning: format '%f' expects argument of type 'double', but argument 3 has type 'int' [-Wformat=] 988 | sprintf(pm->messages, " Serious error in fop information found" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 993 | pfop->fop_cod[x], x); | ~~~~~~~~~~~~~~~~ | | | int codon_us.c:989:37: note: format string is defined here 989 | " an illegal fop value of %f for codon %l" | ~^ | | | double | %d codon_us.c:988:28: warning: unknown conversion type character ' ' in format [-Wformat=] 988 | sprintf(pm->messages, " Serious error in fop information found" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c:990:11: note: format string is defined here 990 | " permissible values are \n 1 for non-optimal" | ^ codon_us.c:988:28: warning: too many arguments for format [-Wformat-extra-args] 988 | sprintf(pm->messages, " Serious error in fop information found" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c:994:25: warning: unknown conversion type character ',' in format [-Wformat=] 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); | ^ codon_us.c:994:33: warning: unknown conversion type character ',' in format [-Wformat=] 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); | ^ codon_us.c:994:44: warning: unknown conversion type character '\x0a' in format [-Wformat=] 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); | ^~ codon_us.c:994:18: warning: too many arguments for format [-Wformat-extra-args] 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c: In function 'gc_out': codons.c: In function 'chelp': codon_us.c:1181:10: warning: too many arguments for format [-Wformat-extra-args] 1181 | "Gene_description%cLen_aa%cLen_sym%cGC%cGC3s%cGCn3s%cGC1%cGC2" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codons.c:1078:20: note: in expansion of macro 'pause' 1078 | pause; /* make sure they Ack. the error mesg */ | ^~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codons.c:1097:35: note: in expansion of macro 'pause' 1097 | if ( line_counter )pause; | ^~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codons.c:1115:5: note: in expansion of macro 'pause' 1115 | pause; | ^~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codons.c:1124:4: note: in expansion of macro 'pause' 1124 | pause; | ^~~~~ codon_us.c: In function 'dinuc_out': codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codons.c:1128:5: note: in expansion of macro 'pause' 1128 | pause; | ^~~~~ codon_us.c:1476:39: warning: precision used with '%c' gnu_printf format [-Wformat=] 1476 | fprintf(fblkout,"%c%c%4.4c",bases[x],bases[i],sp); | ^ codon_us.c: In function 'hydro_out': codon_us.c:2115:27: warning: too many arguments for format [-Wformat-extra-args] 2115 | fprintf(pm->my_err, "No output was written to file \n", title); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c: In function 'aromo_out': codon_us.c:2148:27: warning: too many arguments for format [-Wformat-extra-args] 2148 | fprintf(pm->my_err, "No output was written to file \n", title); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from codon_us.c:77: codon_us.c: In function 'codon_error': codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c:347:6: note: in expansion of macro 'pause' 347 | pause; | ^~~~~ codon_us.c: In function 'cai_out': codon_us.c:652:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 652 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c: In function 'cbi_out': codon_us.c:759:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 759 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c: In function 'fop_out': In function 'fgets', inlined from 'open_file' at open_fil.c:88:13: /usr/include/arm-linux-gnueabihf/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c:899:10: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 899 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c:957:14: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 957 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c: In function 'gen_cusort_fop': codon_us.c:1699:8: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1699 | fgets(pm->junk, BUFSIZ,fnam);/* by scanning for lines of CU in */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c:1700:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 1700 | fscanf(fnam, "%s", pm->junk); /* now we know the name of seq i */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c:1703:8: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 1703 | fscanf(fnam, "%f", &v2); /* assign it initially to v2 */ | ^~~~~~~~~~~~~~~~~~~~~~~ codon_us.c:1711:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 1711 | fscanf(fnam, "%f\n", &v2); /* now read the last codon in */ | ^~~~~~~~~~~~~~~~~~~~~~~~~ cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/codonw-1.4.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 commline.c In file included from commline.c:28: commline.c: In function 'proc_comm_line': codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ commline.c:103:9: note: in expansion of macro 'pause' 103 | pause; | ^~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ commline.c:127:9: note: in expansion of macro 'pause' 127 | pause; | ^~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ commline.c:142:9: note: in expansion of macro 'pause' 142 | pause; | ^~~~~ commline.c:620:48: warning: '%s' directive argument is null [-Wformat-overflow=] 620 | printf("Could not open input file - %s\n", p ); | ^~ cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/codonw-1.4.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 menu.c In file included from menu.c:31: menu.c: In function 'main_menu': codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:69:9: note: in expansion of macro 'pause' 69 | pause; | ^~~~~ menu.c: In function 'menu_initial': menu.c:106:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 106 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:122:29: note: in expansion of macro 'pause' 122 | pause; | ^~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:132:17: note: in expansion of macro 'pause' 132 | pause; | ^~~~~ menu.c: In function 'menu_2': menu.c:233:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 233 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:250:17: note: in expansion of macro 'pause' 250 | pause; | ^~~~~ menu.c: In function 'menu_3': menu.c:305:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 305 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:322:17: note: in expansion of macro 'pause' 322 | pause; | ^~~~~ menu.c:345:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 345 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:382:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 382 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:401:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 401 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:425:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 425 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:450:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 450 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c: In function 'menu_4': menu.c:580:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 580 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:620:17: note: in expansion of macro 'pause' 620 | pause; | ^~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:640:17: note: in expansion of macro 'pause' 640 | pause; | ^~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:660:17: note: in expansion of macro 'pause' 660 | pause; | ^~~~~ menu.c: In function 'menu_5': menu.c:764:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 764 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:814:10: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 814 | fgets( pm->junk , BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c: In function 'menu_6': menu.c:844:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 844 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:861:17: note: in expansion of macro 'pause' 861 | pause; | ^~~~~ menu.c: In function 'menu_7': menu.c:893:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 893 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:912:17: note: in expansion of macro 'pause' 912 | pause; | ^~~~~ menu.c: In function 'menu_8': menu.c:975:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 975 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:1007:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1007 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:1024:11: note: in expansion of macro 'pause' 1024 | pause; | ^~~~~ menu.c: In function 'menu_coa': menu.c:1067:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1067 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:1085:9: note: in expansion of macro 'pause' 1085 | pause; | ^~~~~ menu.c:1097:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1097 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:1117:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1117 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:1130:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1130 | fgets ( pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c: In function 'select_coa': menu.c:1224:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1224 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/codonw-1.4.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 tester.c tester.c: In function 'tester': tester.c:88:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 88 | fgets( pm->junk , BUFSIZ, stdin) ; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tester.c:125:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 125 | fgets( pm->junk , BUFSIZ, stdin) ; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tester.c:170:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 170 | fgets( pm->junk , BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from tester.c:48: tester.c: In function 'asummary': codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tester.c:235:5: note: in expansion of macro 'pause' 235 | pause; | ^~~~~ cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/codonw-1.4.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 coresp.c coresp.c: In function 'textbin': coresp.c:98:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 98 | fscanf(pm->fcoa_in,"%s",pm->junk); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c:104:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 104 | fscanf(pm->fcoa_in,"%i",&v2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c:108:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 108 | fscanf(pm->fcoa_in,"%i\n",&v2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c:115:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 115 | fscanf(pm->fcoa_in,"%i",&v2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c:119:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 119 | fscanf(pm->fcoa_in,"%i\n",&v2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c:127:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 127 | fscanf(pm->fcoa_in,"%i",&v2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c:131:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 131 | fscanf(pm->fcoa_in,"%i\n",&v2); /* read last codon */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c: In function 'rowout': coresp.c:277:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 277 | fgets(pm->junk,BUFSIZ,fnam); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c: In function 'inertialig': coresp.c:1271:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1271 | fgets(pm->junk,BUFSIZ,fnam); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c:1315:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1315 | fgets(pm->junk,BUFSIZ,fnam); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c: In function 'suprow': coresp.c:1619:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1619 | fgets(pm->junk,BUFSIZ,fnam); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/codonw-1.4.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DLINUX -Wl,-z,relro -Wl,-z,now codon_us.o codons.o open_fil.o commline.o menu.o tester.o coresp.o -o codonw -lm make[1]: Leaving directory '/build/reproducible-path/codonw-1.4.4' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/codonw-1.4.4' mkdir -p debian/codonw/usr/bin cp codonw debian/codonw/usr/bin mkdir -p debian/codonw/usr/share/codonw cp codonW.hlp debian/codonw/usr/share/codonw chmod -x debian/codonw/usr/share/codonw/codonW.hlp make[1]: Leaving directory '/build/reproducible-path/codonw-1.4.4' dh_install debian/rules override_dh_installdocs make[1]: Entering directory '/build/reproducible-path/codonw-1.4.4' mkdir -p debian/codonw/usr/share/doc/codonw cp *.txt debian/codonw/usr/share/doc/codonw dh_installdocs -- make[1]: Leaving directory '/build/reproducible-path/codonw-1.4.4' dh_installchangelogs dh_installexamples debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/codonw-1.4.4' mkdir -p /build/reproducible-path/codonw-1.4.4/debian/man /build/reproducible-path/codonw-1.4.4/debian/make_man.pl /build/reproducible-path/codonw-1.4.4/debian/template.man \ /build/reproducible-path/codonw-1.4.4/debian/man silent base G+C+A+T calculating program calculate Effective Number of Codons (ENc) calculate Relative Synonymous Codon Usage (RSCU) detailed report of base composition G+C content of gene (all 3 codon positions) calculate Codon Adaptation Index (CAI) calculate codon usage calculate Amino Acid Usage (AAU) clean up sequence in FASTA format calculate Frequency of OPtimal codons index (FOP) calculate Codon Bias Index (CBI) tabulation of codon usage dinucleotide usage of the three codon positions conceptual translation of DNA to amino acid calculate Relative Amino Acid Usage (RAAU) GC of synonymous codons 3rd positions tabulation of datasets codon usage output sequence in reader format dh_installman -- make[1]: Leaving directory '/build/reproducible-path/codonw-1.4.4' dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/codonw-1.4.4' dh_fixperms chmod -x debian/codonw/usr/share/doc/codonw/examples/input.dat make[1]: Leaving directory '/build/reproducible-path/codonw-1.4.4' 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-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'codonw' in '../codonw_1.4.4-8_armhf.deb'. dpkg-deb: building package 'codonw-dbgsym' in '../codonw-dbgsym_1.4.4-8_armhf.deb'. dpkg-genbuildinfo --build=binary -O../codonw_1.4.4-8_armhf.buildinfo dpkg-genchanges --build=binary -O../codonw_1.4.4-8_armhf.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/19906 and its subdirectories I: Current time: Sat Feb 1 16:55:25 -12 2025 I: pbuilder-time-stamp: 1738472125 Sun Feb 2 04:55:34 UTC 2025 I: 1st build successful. Starting 2nd build on remote node virt64b-armhf-rb.debian.net. Sun Feb 2 04:55:34 UTC 2025 I: Preparing to do remote build '2' on virt64b-armhf-rb.debian.net. Sun Feb 2 04:56:35 UTC 2025 I: Deleting $TMPDIR on virt64b-armhf-rb.debian.net. Sun Feb 2 04:56:38 UTC 2025 I: codonw_1.4.4-8_armhf.changes: Format: 1.8 Date: Sun, 17 Mar 2024 18:32:09 +0100 Source: codonw Binary: codonw codonw-dbgsym Architecture: armhf Version: 1.4.4-8 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: codonw - Correspondence Analysis of Codon Usage Closes: 1066326 Changes: codonw (1.4.4-8) unstable; urgency=medium . * Team upload. * remove-gets.patch: new: replace gets by fgets. (Closes: #1066326) Checksums-Sha1: 8cefeb5183427c2e676e4a1c090e6b8a9184b13c 139696 codonw-dbgsym_1.4.4-8_armhf.deb 314b48e9c2dd0f2eadcb8075b2976f794752a1b2 4923 codonw_1.4.4-8_armhf.buildinfo 0aab5b43d4ffed3fe4817b423a2125ffc2f49ef8 137380 codonw_1.4.4-8_armhf.deb Checksums-Sha256: 996bf00a27d2e8eb59f208ae4d7d8dfa696727a525749e38612e9b331568b6ca 139696 codonw-dbgsym_1.4.4-8_armhf.deb cff603a0d918881e4f79311e9ba833bf79542aab9787b43eb91dfca2989c1812 4923 codonw_1.4.4-8_armhf.buildinfo daa8bcd3b37976204f500f2871b4c5371c2e6f061414a00926ae0ef988b33771 137380 codonw_1.4.4-8_armhf.deb Files: d8ee835673aa446129f9c8020239835c 139696 debug optional codonw-dbgsym_1.4.4-8_armhf.deb 320db03c7658e4a8d2225749eadade50 4923 science optional codonw_1.4.4-8_armhf.buildinfo 7d46d66d74905c12217eb59f8ab80b8f 137380 science optional codonw_1.4.4-8_armhf.deb Sun Feb 2 04:56:39 UTC 2025 I: diffoscope 287 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_24-11655.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.DM5L1nsu/codonw_1.4.4-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.DM5L1nsu/codonw_1.4.4-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.DM5L1nsu/codonw_1.4.4-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.DM5L1nsu/b1/codonw_1.4.4-8_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.DM5L1nsu/b2/codonw_1.4.4-8_armhf.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: 217ms CPU time consumed: 218ms Sun Feb 2 04:56:39 UTC 2025 I: diffoscope 287 found no differences in the changes files, and a .buildinfo file also exists. Sun Feb 2 04:56:39 UTC 2025 I: codonw from trixie built successfully and reproducibly on armhf. Sun Feb 2 04:56:40 UTC 2025 I: Submitting .buildinfo files to external archives: Sun Feb 2 04:56:40 UTC 2025 I: Submitting 8.0K b1/codonw_1.4.4-8_armhf.buildinfo.asc Sun Feb 2 04:56:41 UTC 2025 I: Submitting 8.0K b2/codonw_1.4.4-8_armhf.buildinfo.asc Sun Feb 2 04:56:42 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Feb 2 04:56:42 UTC 2025 I: Done submitting .buildinfo files. Sun Feb 2 04:56:42 UTC 2025 I: Removing signed codonw_1.4.4-8_armhf.buildinfo.asc files: removed './b1/codonw_1.4.4-8_armhf.buildinfo.asc' removed './b2/codonw_1.4.4-8_armhf.buildinfo.asc'