Diff of the two buildlogs: -- --- b1/build.log 2022-01-21 02:46:12.502973655 +0000 +++ b2/build.log 2022-01-21 02:53:54.288714822 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Feb 22 21:05:00 -12 2023 -I: pbuilder-time-stamp: 1677143100 +I: Current time: Fri Jan 21 16:46:14 +14 2022 +I: pbuilder-time-stamp: 1642733174 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./parsinsert_1.04-10.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.HGithtUd/trustedkeys.kbx': General error -gpgv: Signature made Tue Jan 19 07:51:44 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.AmfDw9oD/trustedkeys.kbx': General error +gpgv: Signature made Wed Jan 20 09:51:44 2021 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key @@ -30,135 +30,169 @@ dpkg-source: info: applying 020_hardening.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/623636/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/706552/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/706552/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/706552/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=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]="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=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='bb093e04daa24ce396a4e1b255537ff0' - 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='623636' - PS1='# ' - PS2='> ' + INVOCATION_ID=97e0aa6cef3d40b49a4949a62cfb73d3 + 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=706552 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.O9oiCMJwxj/pbuilderrc_891y --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.O9oiCMJwxj/b1 --logfile b1/build.log parsinsert_1.04-10.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.O9oiCMJwxj/pbuilderrc_uNQr --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.O9oiCMJwxj/b2 --logfile b2/build.log parsinsert_1.04-10.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 5.15.0-0.bpo.2-amd64 #1 SMP Debian 5.15.5-2~bpo11+1 (2022-01-02) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-11-amd64 #1 SMP Debian 5.10.92-1 (2022-01-18) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Aug 4 2021 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 Jul 28 2021 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 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 69032 Jul 28 2021 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 98048 Mar 2 2021 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 Jul 28 2021 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 Jul 28 2021 more - -rwsr-xr-x 1 root root 55528 Jul 28 2021 mount - -rwxr-xr-x 1 root root 18664 Jul 28 2021 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 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 2021 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 Feb 9 03:47 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 Jul 28 2021 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 Jul 28 2021 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Jul 28 2021 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/623636/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Aug 5 10:25 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 Jul 29 09:09 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 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 69032 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 98048 Mar 3 2021 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 Jul 29 09:09 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 Jul 29 09:09 more + -rwsr-xr-x 1 root root 55528 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 18664 Jul 29 09:09 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 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 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 4 Jan 21 16:46 sh -> bash + lrwxrwxrwx 1 root root 4 Jan 7 23:25 sh.distrib -> dash + -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 Jul 29 09:09 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 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Jul 29 09:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/706552/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -225,7 +259,7 @@ 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 (71.6 MB/s) +Fetched 18.3 MB in 0s (39.6 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 ... 19655 files and directories currently installed.) @@ -365,7 +399,8 @@ Building tag database... -> Finished parsing the build-deps 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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../parsinsert_1.04-10_source.changes +hostname: Name or service not known +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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../parsinsert_1.04-10_source.changes dpkg-buildpackage: info: source package parsinsert dpkg-buildpackage: info: source version 1.04-10 dpkg-buildpackage: info: source distribution unstable @@ -379,7 +414,7 @@ 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' @@ -393,7 +428,7 @@ 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 -fdebug-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 -fdebug-prefix-map=/build/parsinsert-1.04=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Knox_Stddef.o Knox_Stddef.cpp @@ -427,8 +462,12 @@ | | long unsigned int | unsigned int | %08lX +Taxonomy.cpp: In member function 'int CTaxEntry::Display(const char*, int)': +Taxonomy.cpp:96:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 96 | DisplayL("%s[%s] %d\n", leader, name.c_str(), count); + | ^~~~~~~~~~~~~ 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:429:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 429 | DisplayL("%s [", label); @@ -439,12 +478,8 @@ ParsimonySet.h:432:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 432 | DisplayL("]\n"); | ^~~~~ -Taxonomy.cpp: In member function 'int CTaxEntry::Display(const char*, int)': -Taxonomy.cpp:96:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | DisplayL("%s[%s] %d\n", leader, name.c_str(), count); - | ^~~~~~~~~~~~~ -In file included from PNode.h:31, - from SeqList.cpp:27: +In file included from ParsInsert.h:29, + from ParsInsert.cpp:34: ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': ParsimonySet.h:429:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 429 | DisplayL("%s [", label); @@ -455,8 +490,8 @@ ParsimonySet.h:432:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 432 | DisplayL("]\n"); | ^~~~~ -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:429:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 429 | DisplayL("%s [", label); @@ -467,13 +502,6 @@ ParsimonySet.h:432:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 432 | DisplayL("]\n"); | ^~~~~ -PNode.cpp: In member function 'void CPTree::Parse(const char*)': -PNode.cpp:299:14: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 299 | DisplayL("Could not process all the chars in NEWICK file\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -PNode.cpp:304:11: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 304 | DisplayL("Processed %d chars of %d\n", nProcess, totalProcess); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ SeqList.cpp: In member function 'int CSequenceFile::ReadSequenceIndexFile(const char*)': SeqList.cpp:490:14: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 490 | DisplayT("Loading sequence %d [%s]\n", count, name); @@ -514,6 +542,13 @@ ParsInsert.cpp:95:39: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 95 | char *seqFilename = "PI_Tree.fasta"; | ^~~~~~~~~~~~~~~ +PNode.cpp: In member function 'void CPTree::Parse(const char*)': +PNode.cpp:299:14: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 299 | DisplayL("Could not process all the chars in NEWICK file\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +PNode.cpp:304:11: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 304 | DisplayL("Processed %d chars of %d\n", nProcess, totalProcess); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ParsInsert.cpp: In function 'int main(int, char**)': ParsInsert.cpp:247:11: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 247 | DisplayL("%s\n", COPYRIGHT); @@ -881,6 +916,10 @@ ParsInsert.cpp:2407:11: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 2407 | DisplayL("Taxonomies List:\n"); | ^~~~~~~~~~~~~~~~~~~~ +ParsInsert.cpp: In function 'int BuildInsertTree(CTreeInserts*, CPTree*)': +ParsInsert.cpp:2647:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 2647 | DisplayL("[%s] at %d%% does not meet threshold (%d%%)\n", in->seq->name.c_str(), score, 100-scoreThresh); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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] 202 | fgets(buffer, sizeof(buffer)-1, f); @@ -889,10 +928,6 @@ SeqList.cpp:229:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 229 | fgets(buffer, sizeof(buffer)-1, f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -ParsInsert.cpp: In function 'int BuildInsertTree(CTreeInserts*, CPTree*)': -ParsInsert.cpp:2647:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 2647 | DisplayL("[%s] at %d%% does not meet threshold (%d%%)\n", in->seq->name.c_str(), score, 100-scoreThresh); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ParsInsert.cpp: In function 'int SetMyTaxonomy(CPNode*)': ParsInsert.cpp:2804:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 2804 | DisplayL("No Taxnomy for [%s][%s]\n", name.c_str(), child->title.c_str()); @@ -972,7 +1007,7 @@ Newick Tree Read Completed: 10143 taxa, 0 sec Tree Sequence Reading: [core_rdp.fasta] Loading sequence 10143 [51224] -Tree Sequence Read Completed: 10143 sequences, 0 sec +Tree Sequence Read Completed: 10143 sequences, 1 sec Reading sequences for insertion: [set1000.fasta] Duplicate sequence found [175015] Duplicate sequence found [290252] @@ -1059,15 +1094,15 @@ [Thermotogae] 24 [Verrucomicrobia] 87 [WS3] 7 -Internal Taxonomy Completed: 5 sec +Internal Taxonomy Completed: 6 sec Setting internal parsimony sequences ... Calculating internal parsimony sequences ... Calculating Parsimony ... CalcParsimony 20000 nodes remaining CalcParsimony 19000 nodes remaining CalcParsimony 18000 nodes remaining CalcParsimony 17000 nodes remaining CalcParsimony 16000 nodes remaining CalcParsimony 15000 nodes remaining CalcParsimony 14000 nodes remaining CalcParsimony 13000 nodes remaining CalcParsimony 12000 nodes remaining CalcParsimony 11000 nodes remaining CalcParsimony 10000 nodes remaining CalcParsimony 9000 nodes remaining CalcParsimony 8000 nodes remaining CalcParsimony 7000 nodes remaining CalcParsimony 6000 nodes remaining CalcParsimony 5000 nodes remaining CalcParsimony 4000 nodes remaining CalcParsimony 3000 nodes remaining CalcParsimony 2000 nodes remaining CalcParsimony 1000 nodes remaining CalcParsimony 0 nodes remaining Applying parsimonious selections back down the tree. 10147 nodes were modified -Processed 20285 nodes in 5 seconds, 4057 nodes per sec -Parsimony Calculation Completed: 4 sec -[10 sec elapsed] Searching for insertion points: +Processed 20285 nodes in 8 seconds, 2536 nodes per sec +Parsimony Calculation Completed: 7 sec +[15 sec elapsed] Searching for insertion points: **** Sequence is already in core tree: 100403 **** Sequence is already in core tree: 100628 Insert [ 100769](len=7683) [ 1235 sites] (147 - 6732) [Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Streptosporangineae;Nocardiopsaceae;Nocardiopsis] @@ -2067,28 +2102,28 @@ Insert [ 99538](len=7683) [ 1184 sites] (137 - 6427) [Bacteria;Bacteroidetes;Flavobacteria;Flavobacteriales;Flavobacteriaceae;Chryseobacterium] Insert [ 99764](len=7683) [ 1261 sites] (130 - 6790) [Bacteria;Proteobacteria;Alphaproteobacteria;Rhizobiales;Brucellaceae;Brucella] Searching for position to insert 957 sequences in tree of 20285 nodes. {Setup: 1 sec} -[ 1000/20285] {16 sec} [I_1000] -[ 2000/20285] {35 sec} [7996] -[ 3000/20285] {53 sec} [39961] -[ 4000/20285] {67 sec} [81358] -[ 5000/20285] {81 sec} [I_5000] -[ 6000/20285] {94 sec} [4546] -[ 7000/20285] {107 sec} [67802] -[ 8000/20285] {118 sec} [135894] -[ 9000/20285] {126 sec} [I_9000] -[ 10000/20285] {134 sec} [137100] -[ 11000/20285] {142 sec} [I_11000] -[ 12000/20285] {150 sec} [63458] -[ 13000/20285] {158 sec} [47043] -[ 14000/20285] {165 sec} [I_14000] -[ 15000/20285] {173 sec} [44776] -[ 16000/20285] {179 sec} [16125] -[ 17000/20285] {184 sec} [I_17000] -[ 18000/20285] {188 sec} [99851] -[ 19000/20285] {191 sec} [104182] -[ 20000/20285] {194 sec} [63281] -Insertion of 957 sequences in [195 sec] -[204 sec elapsed] Insert Locations Completed: 194 sec +[ 1000/20285] {23 sec} [I_1000] +[ 2000/20285] {46 sec} [7996] +[ 3000/20285] {69 sec} [39961] +[ 4000/20285] {95 sec} [81358] +[ 5000/20285] {119 sec} [I_5000] +[ 6000/20285] {143 sec} [4546] +[ 7000/20285] {158 sec} [67802] +[ 8000/20285] {181 sec} [135894] +[ 9000/20285] {196 sec} [I_9000] +[ 10000/20285] {207 sec} [137100] +[ 11000/20285] {222 sec} [I_11000] +[ 12000/20285] {247 sec} [63458] +[ 13000/20285] {278 sec} [47043] +[ 14000/20285] {291 sec} [I_14000] +[ 15000/20285] {312 sec} [44776] +[ 16000/20285] {325 sec} [16125] +[ 17000/20285] {336 sec} [I_17000] +[ 18000/20285] {343 sec} [99851] +[ 19000/20285] {347 sec} [104182] +[ 20000/20285] {351 sec} [63281] +Insertion of 957 sequences in [351 sec] +[365 sec elapsed] Insert Locations Completed: 350 sec ====================================================================== Insertion: [ 100769] [ 1235 sites] @@ -9294,8 +9329,8 @@ Family: 830 821 ( 98.92%) 821 876 ( 93.72%) Genus: 573 563 ( 98.25%) 563 706 ( 79.75%) Species: 49 49 (100.00%) 49 53 ( 92.45%) -Insert Time = 194, 17758 per hour -Process Completed: 204 sec +Insert Time = 350, 9843 per hour +Process Completed: 366 sec make[1]: Leaving directory '/build/parsinsert-1.04' create-stamp debian/debhelper-build-stamp dh_prep @@ -9321,9 +9356,9 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'parsinsert' in '../parsinsert_1.04-10_amd64.deb'. -dpkg-deb: building package 'parsinsert-testdata' in '../parsinsert-testdata_1.04-10_all.deb'. dpkg-deb: building package 'parsinsert-dbgsym' in '../parsinsert-dbgsym_1.04-10_amd64.deb'. +dpkg-deb: building package 'parsinsert-testdata' in '../parsinsert-testdata_1.04-10_all.deb'. +dpkg-deb: building package 'parsinsert' in '../parsinsert_1.04-10_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../parsinsert_1.04-10_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -9331,12 +9366,14 @@ 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/706552/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/706552/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/623636 and its subdirectories -I: Current time: Wed Feb 22 21:09:12 -12 2023 -I: pbuilder-time-stamp: 1677143352 +I: removing directory /srv/workspace/pbuilder/706552 and its subdirectories +I: Current time: Fri Jan 21 16:53:53 +14 2022 +I: pbuilder-time-stamp: 1642733633