Diff of the two buildlogs: -- --- b1/build.log 2023-08-07 00:11:53.978130540 +0000 +++ b2/build.log 2023-08-07 00:12:22.185179003 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Aug 6 12:11:25 -12 2023 -I: pbuilder-time-stamp: 1691367085 +I: Current time: Sun Sep 8 20:35:01 +14 2024 +I: pbuilder-time-stamp: 1725777301 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ I: copying [./codonw_1.4.4-6.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.9qnnfGVt/trustedkeys.kbx': General error -gpgv: Signature made Fri Feb 19 21:55:37 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.aZJ8BF4O/trustedkeys.kbx': General error +gpgv: Signature made Sat Feb 20 23:55:37 2021 +14 gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./codonw_1.4.4-6.dsc @@ -36,135 +36,166 @@ dpkg-source: info: applying remove_nondeterminism I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/619225/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4055324/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Sep 8 20:35 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/4055324/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4055324/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - 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,-fixfilepath parallel=15 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16 ' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='9a03060ea96f4e298fedf603fabe64c3' - 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='619225' - PS1='# ' - PS2='> ' + INVOCATION_ID=60d80655de8842649a6e4892bf5c14e1 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=4055324 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.aF7J3PHE/pbuilderrc_8YTr --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.aF7J3PHE/b1 --logfile b1/build.log codonw_1.4.4-6.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://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.aF7J3PHE/pbuilderrc_oA72 --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.aF7J3PHE/b2 --logfile b2/build.log codonw_1.4.4-6.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos11-amd64 6.1.0-10-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.38-2 (2023-07-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-10-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.38-2 (2023-07-27) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Jan 20 2022 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 69032 Jan 20 2022 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98048 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Jan 20 2022 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Jan 20 2022 more - -rwsr-xr-x 1 root root 55528 Jan 20 2022 mount - -rwxr-xr-x 1 root root 18664 Jan 20 2022 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 6 21:25 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Jan 20 2022 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Jan 20 2022 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Jan 20 2022 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/619225/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Mar 28 2022 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Jan 21 2022 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 69032 Jan 21 2022 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98048 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Jan 21 2022 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Jan 21 2022 more + -rwsr-xr-x 1 root root 55528 Jan 21 2022 mount + -rwxr-xr-x 1 root root 18664 Jan 21 2022 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 9 Sep 8 20:35 sh -> /bin/bash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Jan 21 2022 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Jan 21 2022 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Jan 21 2022 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/4055324/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -231,7 +262,7 @@ Get: 29 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] -Fetched 18.3 MB in 0s (40.4 MB/s) +Fetched 18.3 MB in 0s (75.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19707 files and directories currently installed.) @@ -371,7 +402,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/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_1.4.4-6_source.changes +I: user script /srv/workspace/pbuilder/4055324/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/4055324/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/codonw-1.4.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../codonw_1.4.4-6_source.changes dpkg-buildpackage: info: source package codonw dpkg-buildpackage: info: source version 1.4.4-6 dpkg-buildpackage: info: source distribution unstable @@ -395,7 +430,7 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j15 "INSTALL=install --strip-program=true" + make -j16 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/codonw-1.4.4' cc -c -g -O2 -fdebug-prefix-map=/build/codonw-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 codon_us.c cc -c -g -O2 -fdebug-prefix-map=/build/codonw-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 codons.c @@ -404,6 +439,114 @@ cc -c -g -O2 -fdebug-prefix-map=/build/codonw-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 menu.c cc -c -g -O2 -fdebug-prefix-map=/build/codonw-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 tester.c cc -c -g -O2 -fdebug-prefix-map=/build/codonw-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 coresp.c +In file included from codon_us.c:77: +codon_us.c: In function 'codon_error': +open_fil.c: In function 'open_file': +open_fil.c:88:13: warning: implicit declaration of function 'gets'; did you mean 'fgets'? [-Wimplicit-function-declaration] + 88 | gets(infile_name); /* get filename */ + | ^~~~ + | fgets +codonW.h:38:74: warning: implicit declaration of function 'gets'; did you mean 'fgets'? [-Wimplicit-function-declaration] + 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");gets(pm->junk);} + | ^~~~ +codon_us.c:347:6: note: in expansion of macro 'pause' + 347 | pause; + | ^~~~~ +codon_us.c: In function 'codon_usage_out': +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} +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 +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} +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); + | ^~~~ +open_fil.c:166:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 166 | fgets(temp, 3, stdin); + | ^~~~~~~~~~~~~~~~~~~~~ +In file included from commline.c:28: +commline.c: In function 'proc_comm_line': +codonW.h:38:74: warning: implicit declaration of function 'gets'; did you mean 'fgets'? [-Wimplicit-function-declaration] + 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");gets(pm->junk);} + | ^~~~ +commline.c:103:2: note: in expansion of macro 'pause' + 103 | pause; + | ^~~~~ +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 +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:994:18: warning: unknown conversion type character ',' in format [-Wformat=] + 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); + | ^ +codon_us.c:994:26: warning: unknown conversion type character ',' in format [-Wformat=] + 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); + | ^ +codon_us.c:994:37: warning: unknown conversion type character '\x0a' in format [-Wformat=] + 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); + | ^~ +codon_us.c:994:11: warning: too many arguments for format [-Wformat-extra-args] + 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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", @@ -439,6 +582,7 @@ | ~~~~~~~~~~~~~~~~ | | | long int +codon_us.c: In function 'gc_out': In file included from codons.c:90: codonW.h:38:74: warning: implicit declaration of function 'gets'; did you mean 'fgets'? [-Wimplicit-function-declaration] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");gets(pm->junk);} @@ -446,6 +590,13 @@ codons.c:204:35: note: in expansion of macro 'pause' 204 | if ( pm->codonW && pm->menu ) pause; | ^~~~~ +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" + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codon_us.c: In function 'dinuc_out': +codon_us.c:1476:32: 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 '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%" @@ -513,14 +664,6 @@ | | | int | %li -In file included from commline.c:28: -commline.c: In function 'proc_comm_line': -codonW.h:38:74: warning: implicit declaration of function 'gets'; did you mean 'fgets'? [-Wimplicit-function-declaration] - 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");gets(pm->junk);} - | ^~~~ -commline.c:103:2: note: in expansion of macro 'pause' - 103 | pause; - | ^~~~~ codons.c: In function 'output': 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); @@ -534,52 +677,6 @@ | | | | char * int | %d -open_fil.c: In function 'open_file': -open_fil.c:88:13: warning: implicit declaration of function 'gets'; did you mean 'fgets'? [-Wimplicit-function-declaration] - 88 | gets(infile_name); /* get filename */ - | ^~~~ - | fgets -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} -In file included from codon_us.c:77: -codon_us.c: In function 'codon_error': -codonW.h:38:74: warning: implicit declaration of function 'gets'; did you mean 'fgets'? [-Wimplicit-function-declaration] - 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");gets(pm->junk);} - | ^~~~ -codon_us.c:347:6: note: in expansion of macro 'pause' - 347 | pause; - | ^~~~~ -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 -codon_us.c: In function 'raau_usage_out': -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} -codon_us.c:479:21: warning: too many arguments for format [-Wformat-extra-args] - 479 | fprintf(fblkout, "\n",sp); - | ^~~~ In file included from menu.c:31: menu.c: In function 'main_menu': codonW.h:38:74: warning: implicit declaration of function 'gets'; did you mean 'fgets'? [-Wimplicit-function-declaration] @@ -588,74 +685,6 @@ menu.c:69:9: note: in expansion of macro 'pause' 69 | pause; | ^~~~~ -open_fil.c:166:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 166 | fgets(temp, 3, stdin); - | ^~~~~~~~~~~~~~~~~~~~~ -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 -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:994:18: warning: unknown conversion type character ',' in format [-Wformat=] - 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); - | ^ -codon_us.c:994:26: warning: unknown conversion type character ',' in format [-Wformat=] - 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); - | ^ -codon_us.c:994:37: warning: unknown conversion type character '\x0a' in format [-Wformat=] - 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); - | ^~ -codon_us.c:994:11: 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': -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" - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codon_us.c: In function 'dinuc_out': -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} -codon_us.c:1476:32: warning: precision used with '%c' gnu_printf format [-Wformat=] - 1476 | fprintf(fblkout,"%c%c%4.4c",bases[x],bases[i],sp); - | ^ tester.c: In function 'tester': tester.c:88:17: warning: implicit declaration of function 'gets'; did you mean 'fgets'? [-Wimplicit-function-declaration] 88 | gets( pm->junk ) ; @@ -669,7 +698,13 @@ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +menu.c: In function 'printinfo': codon_us.c: In function 'gen_cusort_fop': +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} 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 */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -708,13 +743,6 @@ coresp.c:277:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 277 | fgets(pm->junk,BUFSIZ,fnam); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:867, - from commline.c:26: -In function 'printf', - inlined from 'proc_comm_line' at commline.c:620:5: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:107:10: warning: '%s' directive argument is null [-Wformat-overflow=] - 107 | return __printf_chk (__USE_FORTIFY_LEVEL - 1, __fmt, __va_arg_pack ()); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); @@ -726,6 +754,13 @@ coresp.c:1619:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1619 | fgets(pm->junk,BUFSIZ,fnam); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:867, + from commline.c:26: +In function 'printf', + inlined from 'proc_comm_line' at commline.c:620:5: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:107:10: warning: '%s' directive argument is null [-Wformat-overflow=] + 107 | return __printf_chk (__USE_FORTIFY_LEVEL - 1, __fmt, __va_arg_pack ()); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -fdebug-prefix-map=/build/codonw-1.4.4=. -fstack-protector-strong -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 /usr/bin/ld: codon_us.o: in function `cai_out': ./codon_us.c:652: warning: the `gets' function is dangerous and should not be used. @@ -757,24 +792,24 @@ mkdir -p /build/codonw-1.4.4/debian/man /build/codonw-1.4.4/debian/make_man.pl /build/codonw-1.4.4/debian/template.man \ /build/codonw-1.4.4/debian/man +output sequence in reader format +conceptual translation of DNA to amino acid +clean up sequence in FASTA format +dinucleotide usage of the three codon positions +tabulation of datasets codon usage +calculate Effective Number of Codons (ENc) +calculate Frequency of OPtimal codons index (FOP) calculate Relative Synonymous Codon Usage (RSCU) +calculate Relative Amino Acid Usage (RAAU) silent base G+C+A+T calculating program -GC of synonymous codons 3rd positions tabulation of codon usage -dinucleotide usage of the three codon positions calculate Codon Bias Index (CBI) -output sequence in reader format -detailed report of base composition -calculate Codon Adaptation Index (CAI) calculate Amino Acid Usage (AAU) -calculate Effective Number of Codons (ENc) -clean up sequence in FASTA format +detailed report of base composition calculate codon usage -calculate Relative Amino Acid Usage (RAAU) -conceptual translation of DNA to amino acid -tabulation of datasets codon usage +GC of synonymous codons 3rd positions G+C content of gene (all 3 codon positions) -calculate Frequency of OPtimal codons index (FOP) +calculate Codon Adaptation Index (CAI) dh_installman -- make[1]: Leaving directory '/build/codonw-1.4.4' dh_perl @@ -804,12 +839,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/4055324/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4055324/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/619225 and its subdirectories -I: Current time: Sun Aug 6 12:11:53 -12 2023 -I: pbuilder-time-stamp: 1691367113 +I: removing directory /srv/workspace/pbuilder/4055324 and its subdirectories +I: Current time: Sun Sep 8 20:35:26 +14 2024 +I: pbuilder-time-stamp: 1725777326