Diff of the two buildlogs: -- --- b1/build.log 2021-07-18 13:34:27.642050347 +0000 +++ b2/build.log 2021-07-18 13:35:11.344413446 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Aug 20 07:56:45 -12 2022 -I: pbuilder-time-stamp: 1661025405 +I: Current time: Mon Jul 19 03:34:29 +14 2021 +I: pbuilder-time-stamp: 1626615269 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Sun Sep 23 09:08:04 2018 -12 +gpgv: Signature made Mon Sep 24 11:08:04 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -30,136 +30,170 @@ dpkg-source: info: applying fix-gcc6.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/7175/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/57843/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-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 +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/57843/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/57843/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 parallel=16' - DISTRIBUTION='' - 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]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.0.3(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 parallel=15' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='d4c5672c64874e0b8e2781250ab8dcd4' - 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='7175' - PS1='# ' - PS2='> ' + INVOCATION_ID=f33650c5fd8841e0906325c7e2d33c20 + 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=57843 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/tmp.uZRq6gW4z8/pbuilderrc_bBOV --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.uZRq6gW4z8/b1 --logfile b1/build.log parsinsert_1.04-4.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://85.184.249.68:3128' + 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/tmp.uZRq6gW4z8/pbuilderrc_xqQt --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.uZRq6gW4z8/b2 --logfile b2/build.log parsinsert_1.04-4.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://78.137.99.97:3128 I: uname -a - Linux ionos15-amd64 5.10.0-0.bpo.7-amd64 #1 SMP Debian 5.10.40-1~bpo10+1 (2021-06-04) x86_64 GNU/Linux + Linux i-capture-the-hostname 4.19.0-17-amd64 #1 SMP Debian 4.19.194-2 (2021-06-21) x86_64 GNU/Linux I: ls -l /bin total 5116 - -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat - -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown - -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp - -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash - -rwxr-xr-x 1 root root 109408 Feb 28 2019 date - -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93744 Feb 28 2019 df - -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir - -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 35424 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln - -rwxr-xr-x 1 root root 56760 Jul 26 2018 login - -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 43008 Jan 9 2019 more - -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm - -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 9 02:47 sh -> dash - -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty - -rwsr-xr-x 1 root root 63568 Jan 9 2019 su - -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync - -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar - -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch - -rwxr-xr-x 1 root root 35424 Feb 28 2019 true - -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount - -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/7175/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat + -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown + -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp + -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash + -rwxr-xr-x 1 root root 109408 Mar 1 2019 date + -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93744 Mar 1 2019 df + -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir + -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 35424 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln + -rwxr-xr-x 1 root root 56760 Jul 27 2018 login + -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 43008 Jan 10 2019 more + -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm + -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 19 03:34 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 7 22:24 sh.distrib -> dash + -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty + -rwsr-xr-x 1 root root 63568 Jan 10 2019 su + -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync + -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar + -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch + -rwxr-xr-x 1 root root 35424 Mar 1 2019 true + -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount + -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/57843/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -228,7 +262,7 @@ Get: 31 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] -Fetched 19.0 MB in 0s (68.3 MB/s) +Fetched 19.0 MB in 0s (73.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (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 ... 19195 files and directories currently installed.) @@ -383,7 +417,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/parsinsert-1.04/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/parsinsert-1.04/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package parsinsert dpkg-buildpackage: info: source version 1.04-4 dpkg-buildpackage: info: source distribution unstable @@ -397,7 +431,7 @@ mv parsinsert ParsInsert || true mv: cannot stat 'parsinsert': No such file or directory dh_auto_clean - make -j16 clean + make -j15 clean make[2]: Entering directory '/build/parsinsert-1.04' rm -f ParsInsert AttrList.o Knox_Stddef.o PNode.o SeqList.o Taxonomy.o ParsInsert.o *.fasta *.log *.results *.tree make[2]: Leaving directory '/build/parsinsert-1.04' @@ -411,7 +445,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/parsinsert-1.04' dh_auto_build - make -j16 "INSTALL=install --strip-program=true" + make -j15 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/parsinsert-1.04' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/parsinsert-1.04=. -fstack-protector-strong -Wformat -Werror=format-security -c -o AttrList.o AttrList.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/parsinsert-1.04=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Knox_Stddef.o Knox_Stddef.cpp @@ -445,8 +479,8 @@ AttrList.cpp:173:15: warning: format '%X' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] sprintf(buf, "0x%08X", value); ^~~~~~~~ ~~~~~ -In file included from ParsInsert.h:29, - from ParsInsert.cpp:34: +In file included from PNode.h:31, + from PNode.cpp:27: ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': ParsimonySet.h:429:35: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("%s [", label); @@ -458,7 +492,7 @@ DisplayL("]\n"); ^ In file included from PNode.h:31, - from PNode.cpp:27: + from SeqList.cpp:27: ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': ParsimonySet.h:429:35: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("%s [", label); @@ -469,8 +503,15 @@ ParsimonySet.h:432:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("]\n"); ^ -In file included from PNode.h:31, - from SeqList.cpp:27: +PNode.cpp: In member function 'void CPTree::Parse(const char*)': +PNode.cpp:299:64: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + DisplayL("Could not process all the chars in NEWICK file\n"); + ^ +PNode.cpp:304:63: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + DisplayL("Processed %d chars of %d\n", nProcess, totalProcess); + ^ +In file included from ParsInsert.h:29, + from ParsInsert.cpp:34: ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': ParsimonySet.h:429:35: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("%s [", label); @@ -481,6 +522,33 @@ ParsimonySet.h:432:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("]\n"); ^ +SeqList.cpp: In member function 'int CSequenceFile::ReadSequenceIndexFile(const char*)': +SeqList.cpp:490:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + DisplayT("Loading sequence %d [%s]\n", count, name); + ^ +SeqList.cpp:492:44: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + DisplayT("Loading sequence %d\n", count); + ^ +SeqList.cpp:496:61: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + DisplayT("Loaded %d sequences from [%s]\n", count, filename); + ^ +SeqList.cpp: In member function 'int CSequenceFile::ReadTaxonomyFile()': +SeqList.cpp:529:71: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + DisplayT("Loading sequence %d [%s]\n", seqCount, seq->name.c_str()); + ^ +SeqList.cpp:531:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + DisplayT("Loading sequence %d\n", seqCount); + ^ +SeqList.cpp: In member function 'int CSequenceFile::ReadSequenceFile(int)': +SeqList.cpp:565:72: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + DisplayT("Loading sequence %d [%s]\n", seqCount, seq->name.c_str()); + ^ +SeqList.cpp:580:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + DisplayL("Duplicate sequence found [%s]\n", seq->name.c_str()); + ^ +SeqList.cpp:605:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + DisplayT("Loading sequence %d [%s]\n", seqCount, seq->name.c_str()); + ^ ParsInsert.cpp: At global scope: ParsInsert.cpp:92:39: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] char *statsName = "PI_Results.log"; @@ -494,40 +562,16 @@ ParsInsert.cpp:95:39: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] char *seqFilename = "PI_Tree.fasta"; ^~~~~~~~~~~~~~~ -PNode.cpp: In member function 'void CPTree::Parse(const char*)': -PNode.cpp:299:64: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - DisplayL("Could not process all the chars in NEWICK file\n"); - ^ -PNode.cpp:304:63: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - DisplayL("Processed %d chars of %d\n", nProcess, totalProcess); - ^ ParsInsert.cpp: In function 'int main(int, char**)': ParsInsert.cpp:247:28: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("%s\n", COPYRIGHT); ^ -SeqList.cpp: In member function 'int CSequenceFile::ReadSequenceIndexFile(const char*)': -SeqList.cpp:490:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - DisplayT("Loading sequence %d [%s]\n", count, name); - ^ ParsInsert.cpp:288:81: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Setting Tree Floating Point Precision to %d\n", v); ^ -SeqList.cpp:492:44: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - DisplayT("Loading sequence %d\n", count); - ^ -SeqList.cpp:496:61: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - DisplayT("Loaded %d sequences from [%s]\n", count, filename); - ^ ParsInsert.cpp:388:73: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("invalid command option '%c'\n", argv[i][1]); ^ -SeqList.cpp: In member function 'int CSequenceFile::ReadTaxonomyFile()': -SeqList.cpp:529:71: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - DisplayT("Loading sequence %d [%s]\n", seqCount, seq->name.c_str()); - ^ -SeqList.cpp:531:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - DisplayT("Loading sequence %d\n", seqCount); - ^ ParsInsert.cpp:411:58: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("%s\nCommand Line:[%s]\n", VERSION, cmd.c_str()); ^ @@ -546,10 +590,6 @@ ParsInsert.cpp:434:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL(" mask file: %s\n", maskName); ^ -SeqList.cpp: In member function 'int CSequenceFile::ReadSequenceFile(int)': -SeqList.cpp:565:72: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - DisplayT("Loading sequence %d [%s]\n", seqCount, seq->name.c_str()); - ^ ParsInsert.cpp:438:51: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayT("Cannot open mask file [%s]", maskName); ^ @@ -565,12 +605,6 @@ ParsInsert.cpp:484:58: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Process Completed: %d sec\n", time(NULL)-start); ^ -SeqList.cpp:580:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - DisplayL("Duplicate sequence found [%s]\n", seq->name.c_str()); - ^ -SeqList.cpp:605:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - DisplayT("Loading sequence %d [%s]\n", seqCount, seq->name.c_str()); - ^ ParsInsert.cpp: In function 'int ParsimonyInsertion()': ParsInsert.cpp:532:57: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Reading Newick Tree: [%s]\n", treeFilename); @@ -698,10 +732,18 @@ ParsInsert.cpp:1224:84: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Insertion of %d sequences in [%d sec]\n", inserts.size(), finish-start+1); ^ +SeqList.cpp: In member function 'const char* CSequenceItem::ReadSeqHeader(FILE*)': +SeqList.cpp:202:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(buffer, sizeof(buffer)-1, f); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ParsInsert.cpp: In function 'void FindInsertLocations(CSequenceFile*, CPNode*, CSequenceItem*, CInsertPos*)': ParsInsert.cpp:1244:60: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("**** Error: could not generate Parsimony Set\n"); ^ +SeqList.cpp: In member function 'const char* CSequenceItem::ReadSeqData(FILE*)': +SeqList.cpp:229:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(buffer, sizeof(buffer)-1, f); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ParsInsert.cpp: In function 'void FindInsertLocations(CSequenceFile*, CPTree*, CSequenceFile*, CInsertPosArray&)': ParsInsert.cpp:1324:77: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("**** Sequence is already in core tree: %s\n", seq->name.c_str()); @@ -903,14 +945,6 @@ ParsInsert.cpp:3077:86: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Newick Tree Read Completed: %d taxa\n", (fullTree->nodeList.size()+1)/2); ^ -SeqList.cpp: In member function 'const char* CSequenceItem::ReadSeqHeader(FILE*)': -SeqList.cpp:202:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(buffer, sizeof(buffer)-1, f); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -SeqList.cpp: In member function 'const char* CSequenceItem::ReadSeqData(FILE*)': -SeqList.cpp:229:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(buffer, sizeof(buffer)-1, f); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/parsinsert-1.04=. -fstack-protector-strong -Wformat -Werror=format-security -o ParsInsert AttrList.o Knox_Stddef.o PNode.o SeqList.o Taxonomy.o ParsInsert.o -lm -lc -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/parsinsert-1.04' mv ParsInsert parsinsert @@ -952,12 +986,14 @@ dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/57843/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/57843/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/7175 and its subdirectories -I: Current time: Sat Aug 20 07:57:27 -12 2022 -I: pbuilder-time-stamp: 1661025447 +I: removing directory /srv/workspace/pbuilder/57843 and its subdirectories +I: Current time: Mon Jul 19 03:35:10 +14 2021 +I: pbuilder-time-stamp: 1626615310