Diff of the two buildlogs: -- --- b1/build.log 2024-05-21 22:49:34.143775758 +0000 +++ b2/build.log 2024-05-21 22:51:10.839662222 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jun 23 17:09:42 -12 2025 -I: pbuilder-time-stamp: 1750741782 +I: Current time: Wed May 22 12:49:36 +14 2024 +I: pbuilder-time-stamp: 1716331776 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -26,51 +26,83 @@ dpkg-source: info: unpacking proalign_0.603-5.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2630357/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2803038/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 21 22:49 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2803038/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2803038/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + 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=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='9f8c0a1f5f914e41b1483e7d9eb3faea' - 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='2630357' - PS1='# ' - PS2='> ' + INVOCATION_ID=5302fe5407d34615a176326f9d3b8cc2 + 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=2803038 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Fd5YXj0m/pbuilderrc_6IMf --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Fd5YXj0m/b1 --logfile b1/build.log proalign_0.603-5.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Fd5YXj0m/pbuilderrc_83Ft --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Fd5YXj0m/b2 --logfile b2/build.log proalign_0.603-5.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom02-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 22 14:05 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2630357/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 20 07:42 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2803038/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -336,7 +368,7 @@ Get: 224 http://deb.debian.org/debian unstable/main amd64 fastjar amd64 2:0.98-7 [80.1 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 jarwrapper all 0.79 [10.1 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 javahelper all 0.79 [84.6 kB] -Fetched 213 MB in 3s (69.4 MB/s) +Fetched 213 MB in 2s (102 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1: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 ... 19718 files and directories currently installed.) @@ -1081,8 +1113,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Jun 24 05:12:04 UTC 2025. -Universal Time is now: Tue Jun 24 05:12:04 UTC 2025. +Local time is now: Tue May 21 22:50:37 UTC 2024. +Universal Time is now: Tue May 21 22:50:37 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libasound2-data (1.2.11-1) ... @@ -1461,7 +1493,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/proalign-0.603/ && 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 > ../proalign_0.603-5_source.changes +I: user script /srv/workspace/pbuilder/2803038/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2803038/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/proalign-0.603/ && 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 > ../proalign_0.603-5_source.changes dpkg-buildpackage: info: source package proalign dpkg-buildpackage: info: source version 0.603-5 dpkg-buildpackage: info: source distribution unstable @@ -1482,15 +1518,6 @@ warning: [options] source value 7 is obsolete and will be removed in a future release warning: [options] target value 7 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. -./SequenceReader.java:242: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal - int numTaxa = new Integer(row.substring(0,row.indexOf(" ")).trim()).intValue(); - ^ -./SequenceReader.java:243: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal - int seqLength = new Integer(row.substring(row.indexOf(" ")+1).trim()).intValue(); - ^ -./SequenceReader.java:307: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal - names.put(row,new Integer(s)); - ^ ./ResultWindow.java:1341: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rwFontSize = new Integer(target.getText()).intValue(); ^ @@ -1500,15 +1527,6 @@ ./ResultWindow.java:1345: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal verticalCharSpace = new Integer(target.getText()).intValue(); ^ -./NeighborJoining.java:151: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal - int no = new Integer(row.trim()).intValue(); - ^ -./NeighborJoining.java:162: warning: [removal] Double(String) in Double has been deprecated and marked for removal - distance[i][j] = new Double(value).doubleValue(); - ^ -./NeighborJoining.java:165: warning: [removal] Double(String) in Double has been deprecated and marked for removal - distance[i][no-1] = new Double(row.trim()).doubleValue(); - ^ ./SetParameters.java:557: warning: [removal] Double(String) in Double has been deprecated and marked for removal setFreqs[i] = new Double(textFreq[i].getText()).doubleValue(); ^ @@ -1545,9 +1563,18 @@ ./SetParameters.java:774: warning: [removal] Double(String) in Double has been deprecated and marked for removal double scale = new Double(textScale.getText()).doubleValue(); ^ -./SampleAlignments.java:340: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal - int maxRun = new Integer(textNumber.getText()).intValue(); - ^ +./TreeReader.java:68: warning: [removal] Float(String) in Float has been deprecated and marked for removal + distance[0] = new Float(tmp.substring(tmp.indexOf(":")+1)).floatValue(); + ^ +./TreeReader.java:92: warning: [removal] Float(String) in Float has been deprecated and marked for removal + distance[1] = new Float(tmp).floatValue(); + ^ +./TreeReader.java:111: warning: [removal] Float(String) in Float has been deprecated and marked for removal + distance[0] = new Float(tmp).floatValue(); + ^ +./TreeReader.java:140: warning: [removal] Float(String) in Float has been deprecated and marked for removal + distance[1] = new Float(tmp).floatValue(); + ^ ./ReadArguments.java:53: warning: [removal] Double(String) in Double has been deprecated and marked for removal double tmp = new Double( ^ @@ -1569,24 +1596,33 @@ ./ReadArguments.java:188: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal int tmp = new Integer( ^ -./TreeReader.java:68: warning: [removal] Float(String) in Float has been deprecated and marked for removal - distance[0] = new Float(tmp.substring(tmp.indexOf(":")+1)).floatValue(); - ^ -./TreeReader.java:92: warning: [removal] Float(String) in Float has been deprecated and marked for removal - distance[1] = new Float(tmp).floatValue(); - ^ -./TreeReader.java:111: warning: [removal] Float(String) in Float has been deprecated and marked for removal - distance[0] = new Float(tmp).floatValue(); - ^ -./TreeReader.java:140: warning: [removal] Float(String) in Float has been deprecated and marked for removal - distance[1] = new Float(tmp).floatValue(); - ^ -./NicePrint.java:34: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal - full = begin+"."+zeros+(new Integer(end.substring(0,prec)).intValue()+1); - ^ +./NeighborJoining.java:151: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal + int no = new Integer(row.trim()).intValue(); + ^ +./NeighborJoining.java:162: warning: [removal] Double(String) in Double has been deprecated and marked for removal + distance[i][j] = new Double(value).doubleValue(); + ^ +./NeighborJoining.java:165: warning: [removal] Double(String) in Double has been deprecated and marked for removal + distance[i][no-1] = new Double(row.trim()).doubleValue(); + ^ +./SampleAlignments.java:340: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal + int maxRun = new Integer(textNumber.getText()).intValue(); + ^ ./SaveData.java:827: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal begin = ""+(new Integer(begin).intValue()+add); ^ +./NicePrint.java:34: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal + full = begin+"."+zeros+(new Integer(end.substring(0,prec)).intValue()+1); + ^ +./SequenceReader.java:242: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal + int numTaxa = new Integer(row.substring(0,row.indexOf(" ")).trim()).intValue(); + ^ +./SequenceReader.java:243: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal + int seqLength = new Integer(row.substring(row.indexOf(" ")+1).trim()).intValue(); + ^ +./SequenceReader.java:307: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal + names.put(row,new Integer(s)); + ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. @@ -1623,12 +1659,14 @@ 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/2803038/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2803038/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/2630357 and its subdirectories -I: Current time: Mon Jun 23 17:12:33 -12 2025 -I: pbuilder-time-stamp: 1750741953 +I: removing directory /srv/workspace/pbuilder/2803038 and its subdirectories +I: Current time: Wed May 22 12:51:09 +14 2024 +I: pbuilder-time-stamp: 1716331869