Diff of the two buildlogs: -- --- b1/build.log 2021-12-11 12:23:15.721954709 +0000 +++ b2/build.log 2021-12-11 12:27:51.753350946 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Dec 11 00:16:58 -12 2021 -I: pbuilder-time-stamp: 1639225018 +I: Current time: Sat Jan 14 08:46:21 +14 2023 +I: pbuilder-time-stamp: 1673635581 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 Fri Dec 14 05:20:41 2018 -12 +gpgv: Signature made Sat Dec 15 07:20:41 2018 +14 gpgv: using RSA key B1A51EB2779DD01743CC19BA1CF792111B5228B0 gpgv: issuer "mestia@debian.org" gpgv: Can't check signature: No public key @@ -30,136 +30,170 @@ dpkg-source: info: applying py3_boost.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/653651/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3400253/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 +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/3400253/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3400253/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=15' - 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=16' + 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='0399e361b29b4985bd0ef1e8c21ab433' - 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='653651' - PS1='# ' - PS2='> ' + INVOCATION_ID=959d349518fc4dd9a4e8f29e92a291ee + 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=3400253 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.xMo2mnj8mY/pbuilderrc_y0LC --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.xMo2mnj8mY/b1 --logfile b1/build.log python-freecontact_1.1-4.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://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/tmp.xMo2mnj8mY/pbuilderrc_JsRQ --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.xMo2mnj8mY/b2 --logfile b2/build.log python-freecontact_1.1-4.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://85.184.249.68:3128 I: uname -a - Linux ionos11-amd64 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) 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 Nov 7 09:58 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/653651/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 Jan 14 08:46 sh -> bash + lrwxrwxrwx 1 root root 4 Dec 11 18:21 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/3400253/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -292,7 +326,7 @@ Get: 85 http://deb.debian.org/debian buster/main amd64 python-all-dev amd64 2.7.16-1 [1068 B] Get: 86 http://deb.debian.org/debian buster/main amd64 python3-all amd64 3.7.3-1 [1068 B] Get: 87 http://deb.debian.org/debian buster/main amd64 python3-all-dev amd64 3.7.3-1 [1064 B] -Fetched 126 MB in 3s (38.7 MB/s) +Fetched 126 MB in 4s (30.2 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.) @@ -669,7 +703,8 @@ 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/python-freecontact-1.1/ && 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 > ../python-freecontact_1.1-4_source.changes +hostname: Name or service not known +I: Running cd /build/python-freecontact-1.1/ && 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 > ../python-freecontact_1.1-4_source.changes dpkg-buildpackage: info: source package python-freecontact dpkg-buildpackage: info: source version 1.1-4 dpkg-buildpackage: info: source distribution unstable @@ -755,27 +790,27 @@ SSE2 veczweight, wchunk = 128 total weight (variation) of alignment = 620.777515304633 -seq weight loop for 1000 seqs took 0.050629 secs +seq weight loop for 1000 seqs took 0.006487 secs will use 1 OMP threads calculated column aa frequencies, gap cols = 4 -calculated pair frequency table in 0.207421 secs +calculated pair frequency table in 0.082391 secs collected apc_mean[MI] = 0.174031486973761 aa freq sum (cell) = 0.999997158936352, pairfreq sum (cell) = 0.999994420985606 formed covariance matrix (122/126,4) -LU factorization took 11.6843 secs, inverted matrix (incl LUf) in 33.9542 secs +LU factorization took 5.66558 secs, inverted matrix (incl LUf) in 30.5889 secs density of inverse covariance matrix = 1 (cksum 346842.2) went back to gapped (126) wwi matrix collected apc_mean[l1norm] = 117.987054769839 collected apc_mean[fro] = 3.35437751555787 -all done in 34.7416 secs +all done in 30.9522 secs will use 1 OMP threads SSE2 veczweight, wchunk = 128 total weight (variation) of alignment = 561.595172234625 -seq weight loop for 1000 seqs took 0.005806 secs +seq weight loop for 1000 seqs took 0.004541 secs will use 1 OMP threads calculated column aa frequencies, gap cols = 4 -calculated pair frequency table in 0.305707 secs +calculated pair frequency table in 0.134892 secs collected apc_mean[MI] = 0.165528914074767 aa freq sum (cell) = 0.999993945475299, pairfreq sum (cell) = 0.999988196197513 formed covariance matrix (126/126,4) @@ -793,25 +828,25 @@ cov matrix Cholesky... not positive definite, dmean dev: 0.0143657 cov matrix Cholesky... not positive definite, dmean dev: 0.0129291 cov matrix Cholesky... -shrank covariance matrix in 24.3687 secs +shrank covariance matrix in 18.1254 secs will try rho 0.00178064, exact solution - iteration = 1will use 1 OMP threads + iteration = 1 iteration = 2will use 1 OMP threads SSE2 veczweight, wchunk = 128 total weight (variation) of alignment = 620.777515304633 will use 1 OMP threads calculated column aa frequencies, gap cols = 4 -calculated pair frequency table in 0.351533 secs +calculated pair frequency table in 0.151701 secs collected apc_mean[MI] = 0.174031486973761 aa freq sum (cell) = 0.999997158936352, pairfreq sum (cell) = 0.999994420985606 formed covariance matrix (122/126,4) -LU factorization took 10.2218 secs, inverted matrix (incl LUf) in 36.0101 secs +LU factorization took 6.40034 secs, inverted matrix (incl LUf) in 28.2648 secs density of inverse covariance matrix = 1 (cksum 346842.2) went back to gapped (126) wwi matrix collected apc_mean[l1norm] = 117.987054769839 collected apc_mean[fro] = 3.35437751555787 . ---------------------------------------------------------------------- -Ran 3 tests in 101.185s +Ran 3 tests in 80.737s OK pybuild --test -i python{version} -p 3.7 @@ -820,22 +855,22 @@ SSE2 veczweight, wchunk = 128 total weight (variation) of alignment = 620.777515304633 -seq weight loop for 1000 seqs took 0.014053 secs +seq weight loop for 1000 seqs took 0.009747 secs will use 1 OMP threads calculated column aa frequencies, gap cols = 4 -calculated pair frequency table in 0.362986 secs +calculated pair frequency table in 0.149128 secs collected apc_mean[MI] = 0.174031486973761 aa freq sum (cell) = 0.999997158936352, pairfreq sum (cell) = 0.999994420985606 formed covariance matrix (122/126,4) -LU factorization took 7.93744 secs, inverted matrix (incl LUf) in 33.1989 secs +LU factorization took 5.48977 secs, inverted matrix (incl LUf) in 31.5339 secs density of inverse covariance matrix = 1 (cksum 346842.2) went back to gapped (126) wwi matrix collected apc_mean[l1norm] = 117.987054769839 collected apc_mean[fro] = 3.35437751555787 -all done in 34.204 secs +all done in 32.0772 secs . ---------------------------------------------------------------------- -Ran 3 tests in 34.225s +Ran 3 tests in 32.103s OK  @@ -907,7 +942,7 @@ I: dh_python2 fs:343: renaming freecontact.so to freecontact.x86_64-linux-gnu.so D: dh_python2 fs:260: package python-freecontact details = {'requires.txt': set(), 'egg-info': {'debian/python-freecontact/usr/lib/python2.7/dist-packages/python_freecontact-1.1.egg-info'}, 'nsp.txt': set(), 'shebangs': set(), 'public_vers': {Version('2.7')}, 'private_dirs': {}, 'compile': False, 'ext_vers': {Version('2.7')}, 'ext_no_version': set()} D: dh_python2 depends:114: generating dependencies for package python-freecontact -D: dh_python2 depends:272: D={'python:any (<< 2.8)', 'python (<< 2.8)', 'python (>= 2.7~)', 'python:any (>= 2.7~)'}; R=[]; S=[]; E=[], B=[]; RT=[] +D: dh_python2 depends:272: D={'python:any (>= 2.7~)', 'python (<< 2.8)', 'python (>= 2.7~)', 'python:any (<< 2.8)'}; R=[]; S=[]; E=[], B=[]; RT=[] dh_python3 -O--buildsystem=pybuild -O--builddirectory=/build/python-freecontact-1.1/builddir D: dh_python3 dh_python3:161: version: 3.20190308 D: dh_python3 dh_python3:162: argv: ['/usr/bin/dh_python3', '-O--buildsystem=pybuild', '-O--builddirectory=/build/python-freecontact-1.1/builddir'] @@ -921,7 +956,7 @@ D: dh_python3 tools:232: invoking: /usr/bin/python3.7 -c 'import sysconfig as s;print("__SEP__".join(i or "" for i in s.get_config_vars("SOABI", "MULTIARCH", "INCLUDEPY", "LIBPL", "LDLIBRARY")))' D: dh_python3 fs:260: package python3-freecontact details = {'requires.txt': set(), 'egg-info': {'debian/python3-freecontact/usr/lib/python3/dist-packages/python_freecontact-1.1.egg-info'}, 'nsp.txt': set(), 'shebangs': set(), 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': False, 'ext_vers': {Version('3.7')}, 'ext_no_version': set()} D: dh_python3 depends:114: generating dependencies for package python3-freecontact -D: dh_python3 depends:272: D={'python3 (<< 3.8)', 'python3 (>= 3.7~)'}; R=[]; S=[]; E=[], B=[]; RT=[] +D: dh_python3 depends:272: D={'python3 (>= 3.7~)', 'python3 (<< 3.8)'}; R=[]; S=[]; E=[], B=[]; RT=[] dh_installinit -O--buildsystem=pybuild -O--builddirectory=/build/python-freecontact-1.1/builddir dh_perl -O--buildsystem=pybuild -O--builddirectory=/build/python-freecontact-1.1/builddir dh_link -O--buildsystem=pybuild -O--builddirectory=/build/python-freecontact-1.1/builddir @@ -979,19 +1014,14 @@ debian/rules override_dh_gencontrol make[1]: Entering directory '/build/python-freecontact-1.1' dh_gencontrol -- '-VDescription=FreeContact is a protein residue contact predictor optimized for speed.${Newline}Its input is a multiple sequence alignment. FreeContact can function as an${Newline}accelerated drop-in for the published contact predictors${Newline}EVfold-mfDCA of DS. Marks (2011) and${Newline}PSICOV of D. Jones (2011).${Newline}${Newline}FreeContact is accelerated by a combination of vector instructions, multiple${Newline}threads, and faster implementation of key parts.${Newline}Depending on the alignment, 8-fold or higher speedups are possible.${Newline}${Newline}A sufficiently large alignment is required for meaningful results.${Newline}As a minimum, an alignment with an effective (after-weighting) sequence count${Newline}bigger than the length of the query sequence should be used. Alignments with${Newline}tens of thousands of (effective) sequences are considered good input.${Newline}${Newline}jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite${Newline}can be used to generate the alignments, for example.' - echo misc:Depends= >> debian/python-freecontact.substvars - echo misc:Pre-Depends= >> debian/python-freecontact.substvars - install -d debian/.debhelper/python-freecontact/dbgsym-root/DEBIAN - dpkg-gencontrol -ppython-freecontact -ldebian/changelog -Tdebian/python-freecontact.substvars -Pdebian/.debhelper/python-freecontact/dbgsym-root "-VDescription=FreeContact is a protein residue contact predictor optimized for speed.\${Newline}Its input is a multiple sequence alignment. FreeContact can function as an\${Newline}accelerated drop-in for the published contact predictors\${Newline}EVfold-mfDCA of DS. Marks (2011) and\${Newline}PSICOV of D. Jones (2011).\${Newline}\${Newline}FreeContact is accelerated by a combination of vector instructions, multiple\${Newline}threads, and faster implementation of key parts.\${Newline}Depending on the alignment, 8-fold or higher speedups are possible.\${Newline}\${Newline}A sufficiently large alignment is required for meaningful results.\${Newline}As a minimum, an alignment with an effective (after-weighting) sequence count\${Newline}bigger than the length of the query sequence should be used. Alignments with\${Newline}tens of thousands of (effective) sequences are considered good input.\${Newline}\${Newline}jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite\${Newline}can be used to generate the alignments, for example." -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -DPackage=python-freecontact-dbgsym "-DDepends=python-freecontact (= \${binary:Version})" "-DDescription=debug symbols for python-freecontact" -DBuild-Ids=29c1dd7750772507edcaa7ff052b7ea3e73ba4d9 -DSection=debug -UMulti-Arch -UReplaces -UBreaks echo misc:Depends= >> debian/python3-freecontact.substvars echo misc:Pre-Depends= >> debian/python3-freecontact.substvars install -d debian/.debhelper/python3-freecontact/dbgsym-root/DEBIAN dpkg-gencontrol -ppython3-freecontact -ldebian/changelog -Tdebian/python3-freecontact.substvars -Pdebian/.debhelper/python3-freecontact/dbgsym-root "-VDescription=FreeContact is a protein residue contact predictor optimized for speed.\${Newline}Its input is a multiple sequence alignment. FreeContact can function as an\${Newline}accelerated drop-in for the published contact predictors\${Newline}EVfold-mfDCA of DS. Marks (2011) and\${Newline}PSICOV of D. Jones (2011).\${Newline}\${Newline}FreeContact is accelerated by a combination of vector instructions, multiple\${Newline}threads, and faster implementation of key parts.\${Newline}Depending on the alignment, 8-fold or higher speedups are possible.\${Newline}\${Newline}A sufficiently large alignment is required for meaningful results.\${Newline}As a minimum, an alignment with an effective (after-weighting) sequence count\${Newline}bigger than the length of the query sequence should be used. Alignments with\${Newline}tens of thousands of (effective) sequences are considered good input.\${Newline}\${Newline}jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite\${Newline}can be used to generate the alignments, for example." -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -DPackage=python3-freecontact-dbgsym "-DDepends=python3-freecontact (= \${binary:Version})" "-DDescription=debug symbols for python3-freecontact" -DBuild-Ids=35982f6a0ffc90f951cf0005c4a2905be4ac8642 -DSection=debug -UMulti-Arch -UReplaces -UBreaks -dpkg-gencontrol: warning: package python-freecontact: substitution variable ${python:Provides} unused, but is defined -dpkg-gencontrol: warning: package python-freecontact: substitution variable ${python:Versions} unused, but is defined - chmod 0644 -- debian/.debhelper/python-freecontact/dbgsym-root/DEBIAN/control - chown 0:0 -- debian/.debhelper/python-freecontact/dbgsym-root/DEBIAN/control - dpkg-gencontrol -ppython-freecontact -ldebian/changelog -Tdebian/python-freecontact.substvars -Pdebian/python-freecontact -UMulti-Arch "-VDescription=FreeContact is a protein residue contact predictor optimized for speed.\${Newline}Its input is a multiple sequence alignment. FreeContact can function as an\${Newline}accelerated drop-in for the published contact predictors\${Newline}EVfold-mfDCA of DS. Marks (2011) and\${Newline}PSICOV of D. Jones (2011).\${Newline}\${Newline}FreeContact is accelerated by a combination of vector instructions, multiple\${Newline}threads, and faster implementation of key parts.\${Newline}Depending on the alignment, 8-fold or higher speedups are possible.\${Newline}\${Newline}A sufficiently large alignment is required for meaningful results.\${Newline}As a minimum, an alignment with an effective (after-weighting) sequence count\${Newline}bigger than the length of the query sequence should be used. Alignments with\${Newline}tens of thousands of (effective) sequences are considered good input.\${Newline}\${Newline}jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite\${Newline}can be used to generate the alignments, for example." + echo misc:Depends= >> debian/python-freecontact.substvars + echo misc:Pre-Depends= >> debian/python-freecontact.substvars + install -d debian/.debhelper/python-freecontact/dbgsym-root/DEBIAN + dpkg-gencontrol -ppython-freecontact -ldebian/changelog -Tdebian/python-freecontact.substvars -Pdebian/.debhelper/python-freecontact/dbgsym-root "-VDescription=FreeContact is a protein residue contact predictor optimized for speed.\${Newline}Its input is a multiple sequence alignment. FreeContact can function as an\${Newline}accelerated drop-in for the published contact predictors\${Newline}EVfold-mfDCA of DS. Marks (2011) and\${Newline}PSICOV of D. Jones (2011).\${Newline}\${Newline}FreeContact is accelerated by a combination of vector instructions, multiple\${Newline}threads, and faster implementation of key parts.\${Newline}Depending on the alignment, 8-fold or higher speedups are possible.\${Newline}\${Newline}A sufficiently large alignment is required for meaningful results.\${Newline}As a minimum, an alignment with an effective (after-weighting) sequence count\${Newline}bigger than the length of the query sequence should be used. Alignments with\${Newline}tens of thousands of (effective) sequences are considered good input.\${Newline}\${Newline}jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite\${Newline}can be used to generate the alignments, for example." -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -DPackage=python-freecontact-dbgsym "-DDepends=python-freecontact (= \${binary:Version})" "-DDescription=debug symbols for python-freecontact" -DBuild-Ids=29c1dd7750772507edcaa7ff052b7ea3e73ba4d9 -DSection=debug -UMulti-Arch -UReplaces -UBreaks dpkg-gencontrol: warning: package python3-freecontact: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-freecontact: substitution variable ${python3:Versions} unused, but is defined chmod 0644 -- debian/.debhelper/python3-freecontact/dbgsym-root/DEBIAN/control @@ -999,12 +1029,17 @@ dpkg-gencontrol -ppython3-freecontact -ldebian/changelog -Tdebian/python3-freecontact.substvars -Pdebian/python3-freecontact -UMulti-Arch "-VDescription=FreeContact is a protein residue contact predictor optimized for speed.\${Newline}Its input is a multiple sequence alignment. FreeContact can function as an\${Newline}accelerated drop-in for the published contact predictors\${Newline}EVfold-mfDCA of DS. Marks (2011) and\${Newline}PSICOV of D. Jones (2011).\${Newline}\${Newline}FreeContact is accelerated by a combination of vector instructions, multiple\${Newline}threads, and faster implementation of key parts.\${Newline}Depending on the alignment, 8-fold or higher speedups are possible.\${Newline}\${Newline}A sufficiently large alignment is required for meaningful results.\${Newline}As a minimum, an alignment with an effective (after-weighting) sequence count\${Newline}bigger than the length of the query sequence should be used. Alignments with\${Newline}tens of thousands of (effective) sequences are considered good input.\${Newline}\${Newline}jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite\${Newline}can be used to generate the alignments, for example." dpkg-gencontrol: warning: package python-freecontact: substitution variable ${python:Provides} unused, but is defined dpkg-gencontrol: warning: package python-freecontact: substitution variable ${python:Versions} unused, but is defined - chmod 0644 -- debian/python-freecontact/DEBIAN/control - chown 0:0 -- debian/python-freecontact/DEBIAN/control + chmod 0644 -- debian/.debhelper/python-freecontact/dbgsym-root/DEBIAN/control + chown 0:0 -- debian/.debhelper/python-freecontact/dbgsym-root/DEBIAN/control + dpkg-gencontrol -ppython-freecontact -ldebian/changelog -Tdebian/python-freecontact.substvars -Pdebian/python-freecontact -UMulti-Arch "-VDescription=FreeContact is a protein residue contact predictor optimized for speed.\${Newline}Its input is a multiple sequence alignment. FreeContact can function as an\${Newline}accelerated drop-in for the published contact predictors\${Newline}EVfold-mfDCA of DS. Marks (2011) and\${Newline}PSICOV of D. Jones (2011).\${Newline}\${Newline}FreeContact is accelerated by a combination of vector instructions, multiple\${Newline}threads, and faster implementation of key parts.\${Newline}Depending on the alignment, 8-fold or higher speedups are possible.\${Newline}\${Newline}A sufficiently large alignment is required for meaningful results.\${Newline}As a minimum, an alignment with an effective (after-weighting) sequence count\${Newline}bigger than the length of the query sequence should be used. Alignments with\${Newline}tens of thousands of (effective) sequences are considered good input.\${Newline}\${Newline}jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite\${Newline}can be used to generate the alignments, for example." dpkg-gencontrol: warning: package python3-freecontact: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-freecontact: substitution variable ${python3:Versions} unused, but is defined chmod 0644 -- debian/python3-freecontact/DEBIAN/control chown 0:0 -- debian/python3-freecontact/DEBIAN/control +dpkg-gencontrol: warning: package python-freecontact: substitution variable ${python:Provides} unused, but is defined +dpkg-gencontrol: warning: package python-freecontact: substitution variable ${python:Versions} unused, but is defined + chmod 0644 -- debian/python-freecontact/DEBIAN/control + chown 0:0 -- debian/python-freecontact/DEBIAN/control make[1]: Leaving directory '/build/python-freecontact-1.1' dh_md5sums -O--buildsystem=pybuild -O--builddirectory=/build/python-freecontact-1.1/builddir cd debian/python3-freecontact >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums @@ -1015,19 +1050,19 @@ chown 0:0 -- debian/python-freecontact/DEBIAN/md5sums cd debian/.debhelper/python3-freecontact/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/.debhelper/python-freecontact/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums - chmod 0644 -- debian/.debhelper/python-freecontact/dbgsym-root/DEBIAN/md5sums - chown 0:0 -- debian/.debhelper/python-freecontact/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/python3-freecontact/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/python3-freecontact/dbgsym-root/DEBIAN/md5sums + chmod 0644 -- debian/.debhelper/python-freecontact/dbgsym-root/DEBIAN/md5sums + chown 0:0 -- debian/.debhelper/python-freecontact/dbgsym-root/DEBIAN/md5sums dh_builddeb -O--buildsystem=pybuild -O--builddirectory=/build/python-freecontact-1.1/builddir dpkg-deb --build debian/python-freecontact .. - dpkg-deb --build debian/.debhelper/python3-freecontact/dbgsym-root .. dpkg-deb --build debian/python3-freecontact .. + dpkg-deb --build debian/.debhelper/python3-freecontact/dbgsym-root .. dpkg-deb --build debian/.debhelper/python-freecontact/dbgsym-root .. dpkg-deb: building package 'python-freecontact' in '../python-freecontact_1.1-4_amd64.deb'. dpkg-deb: building package 'python3-freecontact' in '../python3-freecontact_1.1-4_amd64.deb'. -dpkg-deb: building package 'python3-freecontact-dbgsym' in '../python3-freecontact-dbgsym_1.1-4_amd64.deb'. dpkg-deb: building package 'python-freecontact-dbgsym' in '../python-freecontact-dbgsym_1.1-4_amd64.deb'. +dpkg-deb: building package 'python3-freecontact-dbgsym' in '../python3-freecontact-dbgsym_1.1-4_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../python-freecontact_1.1-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1036,12 +1071,14 @@ 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/3400253/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3400253/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/653651 and its subdirectories -I: Current time: Sat Dec 11 00:23:15 -12 2021 -I: pbuilder-time-stamp: 1639225395 +I: removing directory /srv/workspace/pbuilder/3400253 and its subdirectories +I: Current time: Sat Jan 14 08:50:55 +14 2023 +I: pbuilder-time-stamp: 1673635855