Mon May 13 07:16:35 UTC 2024 I: starting to build codonw/trixie/amd64 on jenkins on '2024-05-13 07:16' Mon May 13 07:16:35 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_27/20469/console.log Mon May 13 07:16:35 UTC 2024 I: Downloading source for trixie/codonw=1.4.4-8 --2024-05-13 07:16:35-- 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% 259M=0s 2024-05-13 07:16:35 (259 MB/s) - ‘codonw_1.4.4-8.dsc’ saved [2055/2055] Mon May 13 07:16:35 UTC 2024 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----- Mon May 13 07:16:35 UTC 2024 I: Checking whether the package is not for us Mon May 13 07:16:35 UTC 2024 I: Starting 1st build on remote node ionos11-amd64.debian.net. Mon May 13 07:16:35 UTC 2024 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Mon May 13 07:17:25 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun May 12 19:16:37 -12 2024 I: pbuilder-time-stamp: 1715584597 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 gpgv: Signature made Sun Mar 17 17:44:10 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./codonw_1.4.4-8.dsc: no acceptable signature found 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/675035/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='3efc48e1ceaa4902b53d88cc70a9c8a6' 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='675035' 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.4DKhYrAW/pbuilderrc_UnOG --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.4DKhYrAW/b1 --logfile b1/build.log codonw_1.4.4-8.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 10 11:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/675035/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19699 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} libsub-override-perl{a} libtool{a} libuchardet0{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 19.0 MB of archives. After unpacking 73.6 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Fetched 19.0 MB in 0s (71.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19699 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40-8_amd64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.1-1_amd64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../22-libelf1t64_0.191-1+b1_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../24-libicu72_72.1-4+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-4+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_amd64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.38-10) ... 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 amd64 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 -j20 "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 -fcf-protection -DLINUX -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 -fcf-protection -DLINUX -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 -fcf-protection -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 open_fil.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 -fcf-protection -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 commline.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 -fcf-protection -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 menu.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 -fcf-protection -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 tester.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 -fcf-protection -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 coresp.c open_fil.c: In function 'open_file': open_fil.c:128:28: warning: field precision specifier '.*' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 128 | fprintf(stderr,"\nThese are the files in the current directory " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 129 | "I cannot find %.*s \n\n",strlen(infile_name),infile_name); | ~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} open_fil.c:129:34: note: format string is defined here 129 | "I cannot find %.*s \n\n",strlen(infile_name),infile_name); | ~~^~ | | | int open_fil.c:162:52: warning: field precision specifier '.*' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 162 | fprintf(stderr, "\nWarning :File %.*s " | ~~^~ | | | int ...... 165 | strlen(infile_name), infile_name); | ~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} 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:964, from open_fil.c:47: /usr/include/x86_64-linux-gnu/bits/stdio2.h:195:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' 195 | fgets (char *__restrict __s, int __n, FILE *__restrict __stream) | ^~~~~ 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': 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);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tester.c:235:5: note: in expansion of macro 'pause' 235 | 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: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; | ^~~~~ 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 menu.c: In function 'printinfo': menu.c:1285:26: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1285 | printf("\tVersion : %.*s\n", strlen(Revision) , Revision ); | ~~^~ ~~~~~~~~~~~~~~~~ | | | | int size_t {aka long unsigned int} coresp.c: In function 'textbin': codon_us.c: In function 'codon_usage_out': 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 */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from menu.c:31: menu.c: In function 'main_menu': codons.c: In function 'toutput': 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; | ^~~~~ 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: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 */ | ^ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c: In function 'menu_initial': codon_us.c: In function 'raau_usage_out': 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; | ^~~~~ codon_us.c:479:21: warning: too many arguments for format [-Wformat-extra-args] 479 | fprintf(fblkout, "\n",sp); | ^~~~ 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; | ^~~~~ 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 menu.c: In function 'menu_2': codons.c:648:25: note: format string is defined here 648 | "in sequence %i\n" | ~^ | | | int | %li 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; | ^~~~~ 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 In function 'fgets', inlined from 'open_file' at open_fil.c:88:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:201:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 201 | return __fgets_chk_warn (__s, sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 codon_us.c: In function 'cbi_out': 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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 codon_us.c:832:38: note: format string is defined here 832 | " an illegal CBI value of %f for codon %i" | ~^ | | | double | %d 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 'fop_out': 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; | ^~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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:989:37: note: format string is defined here 989 | " an illegal fop value of %f for codon %l" | ~^ | | | double | %d 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:988:28: warning: unknown conversion type character ' ' in format [-Wformat=] 988 | sprintf(pm->messages, " Serious error in fop information found" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:814:10: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 814 | fgets( pm->junk , BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c:990:11: note: format string is defined here 990 | " permissible values are \n 1 for non-optimal" | ^ 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; | ^~~~~ codon_us.c:988:28: warning: too many arguments for format [-Wformat-extra-args] 988 | sprintf(pm->messages, " Serious error in fop information found" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c: In function 'menu_7': 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); | ^ 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; | ^~~~~ 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); | ^ menu.c: In function 'menu_8': 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); | ^~ 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; | ^~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c: In function 'gc_out': 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 'dinuc_out': 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); | ^ codons.c: In function 'chelp': 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; | ^~~~~ codon_us.c: In function 'hydro_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:1124:4: note: in expansion of macro 'pause' 1124 | pause; | ^~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: 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': 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 */ | ^~~~~~~~~~~~~~~~~~~~~~~~~ commline.c:620:48: warning: '%s' directive argument is null [-Wformat-overflow=] 620 | printf("Could not open input file - %s\n", p ); | ^~ 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 -fcf-protection -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 calculate Effective Number of Codons (ENc) calculate Codon Bias Index (CBI) calculate codon usage clean up sequence in FASTA format calculate Relative Synonymous Codon Usage (RSCU) calculate Amino Acid Usage (AAU) G+C content of gene (all 3 codon positions) tabulation of datasets codon usage dinucleotide usage of the three codon positions tabulation of codon usage output sequence in reader format conceptual translation of DNA to amino acid calculate Codon Adaptation Index (CAI) calculate Frequency of OPtimal codons index (FOP) GC of synonymous codons 3rd positions detailed report of base composition calculate Relative Amino Acid Usage (RAAU) silent base G+C+A+T calculating program 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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'codonw-dbgsym' in '../codonw-dbgsym_1.4.4-8_amd64.deb'. dpkg-deb: building package 'codonw' in '../codonw_1.4.4-8_amd64.deb'. dpkg-genbuildinfo --build=binary -O../codonw_1.4.4-8_amd64.buildinfo dpkg-genchanges --build=binary -O../codonw_1.4.4-8_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/675035 and its subdirectories I: Current time: Sun May 12 19:17:24 -12 2024 I: pbuilder-time-stamp: 1715584644 Mon May 13 07:17:26 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Mon May 13 07:17:26 UTC 2024 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Mon May 13 07:18:17 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Mon May 13 07:18:18 UTC 2024 I: codonw_1.4.4-8_amd64.changes: Format: 1.8 Date: Sun, 17 Mar 2024 18:32:09 +0100 Source: codonw Binary: codonw codonw-dbgsym Architecture: amd64 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: db7ac956e4305251895a2b78ddd3112bb75f30ac 140660 codonw-dbgsym_1.4.4-8_amd64.deb b629a2bc3a857f21022a29a9900ac79c46b06e70 5109 codonw_1.4.4-8_amd64.buildinfo a3fdfc0304a2620b846ac517b9104c69f2443adc 140872 codonw_1.4.4-8_amd64.deb Checksums-Sha256: b118a62f0b2d0a56cb1a796afbd3e017ed5201e07d96b6918303d5557b811a05 140660 codonw-dbgsym_1.4.4-8_amd64.deb 589baed4fdfe683d73e22d62cf8cf503fd8b8dbc6f3143f010f8651549ede3ce 5109 codonw_1.4.4-8_amd64.buildinfo e736c464abacaa954f23f7ba3989db8bd518f002930ff45f9fb937009c796676 140872 codonw_1.4.4-8_amd64.deb Files: 797779c43c8111e9d976eaf47a903ebf 140660 debug optional codonw-dbgsym_1.4.4-8_amd64.deb 8dc29008d060594f9d7794fc13f362cd 5109 science optional codonw_1.4.4-8_amd64.buildinfo 7a78a215485702e6c64c47a9da9f2fa3 140872 science optional codonw_1.4.4-8_amd64.deb Mon May 13 07:18:19 UTC 2024 I: diffoscope 266 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_27-20469.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.4DKhYrAW/codonw_1.4.4-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.4DKhYrAW/codonw_1.4.4-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.4DKhYrAW/codonw_1.4.4-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.4DKhYrAW/b1/codonw_1.4.4-8_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.4DKhYrAW/b2/codonw_1.4.4-8_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.367s) 0.367s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.017s) 0.017s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 703ms CPU time consumed: 704ms Mon May 13 07:18:20 UTC 2024 I: diffoscope 266 found no differences in the changes files, and a .buildinfo file also exists. Mon May 13 07:18:20 UTC 2024 I: codonw from trixie built successfully and reproducibly on amd64. Mon May 13 07:18:21 UTC 2024 I: Submitting .buildinfo files to external archives: Mon May 13 07:18:21 UTC 2024 I: Submitting 8.0K b1/codonw_1.4.4-8_amd64.buildinfo.asc Mon May 13 07:18:22 UTC 2024 I: Submitting 8.0K b2/codonw_1.4.4-8_amd64.buildinfo.asc Mon May 13 07:18:23 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon May 13 07:18:23 UTC 2024 I: Done submitting .buildinfo files. Mon May 13 07:18:23 UTC 2024 I: Removing signed codonw_1.4.4-8_amd64.buildinfo.asc files: removed './b1/codonw_1.4.4-8_amd64.buildinfo.asc' removed './b2/codonw_1.4.4-8_amd64.buildinfo.asc'