Diff of the two buildlogs: -- --- b1/build.log 2024-12-11 02:10:15.338710636 +0000 +++ b2/build.log 2024-12-11 02:12:56.223406203 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Dec 10 14:05:31 -12 2024 -I: pbuilder-time-stamp: 1733882731 +I: Current time: Wed Dec 11 16:10:45 +14 2024 +I: pbuilder-time-stamp: 1733883045 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying cross.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/10222/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/22766/tmp/hooks/D01_modify_environment starting +debug: Running on virt64b. +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 Dec 11 02:10 /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/22766/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/22766/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='armhf' + 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]="37" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='37fed329725c452391e57a61d883d029' - 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='10222' - PS1='# ' - PS2='> ' + INVOCATION_ID=c73c64f2218448ffa5ffe41b1eab7737 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=22766 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.yw9fzkKf/pbuilderrc_8w5X --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.yw9fzkKf/b1 --logfile b1/build.log prank_0.0.170427+dfsg-3.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.yw9fzkKf/pbuilderrc_uixo --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.yw9fzkKf/b2 --logfile b2/build.log prank_0.0.170427+dfsg-3.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux ff4a 6.1.0-28-armmp-lpae #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/10222/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/22766/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -140,7 +172,7 @@ Get: 27 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main armhf debhelper all 13.20 [915 kB] -Fetched 19.1 MB in 1s (13.3 MB/s) +Fetched 19.1 MB in 0s (38.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19680 files and directories currently installed.) @@ -271,7 +303,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/prank-0.0.170427+dfsg/ && 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 > ../prank_0.0.170427+dfsg-3_source.changes +I: user script /srv/workspace/pbuilder/22766/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/22766/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/prank-0.0.170427+dfsg/ && 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 > ../prank_0.0.170427+dfsg-3_source.changes dpkg-buildpackage: info: source package prank dpkg-buildpackage: info: source version 0.0.170427+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -300,22 +336,24 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/prank-0.0.170427+dfsg' dh_auto_build --verbose - cd src && make -j3 "INSTALL=install --strip-program=true" + cd src && make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/prank-0.0.170427+dfsg/src' g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o writefile.o writefile.cpp g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o treenode.o treenode.cpp g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o translatesequences.o translatesequences.cpp +g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o terminalsequence.o terminalsequence.cpp In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, - from treenode.cpp:25: + from terminalsequence.cpp:24: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:353:63: warning: no return statement in function returning non-void [-Wreturn-type] 353 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ In file included from ancestralnode.h:24, - from writefile.h:25, - from writefile.cpp:27: + from hmmodel.h:36, + from config.h:31, + from translatesequences.cpp:22: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:353:63: warning: no return statement in function returning non-void [-Wreturn-type] 353 | virtual bool updateInsertionSite(int i, bool has_parent) {} @@ -323,28 +361,26 @@ In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, - from translatesequences.cpp:22: + from treenode.cpp:25: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:353:63: warning: no return statement in function returning non-void [-Wreturn-type] 353 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ -g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o terminalsequence.o terminalsequence.cpp In file included from ancestralnode.h:24, - from hmmodel.h:36, - from config.h:31, - from terminalsequence.cpp:24: + from writefile.h:25, + from writefile.cpp:27: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:353:63: warning: no return statement in function returning non-void [-Wreturn-type] 353 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o terminalnode.o terminalnode.cpp -g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o site.o site.cpp In file included from terminalnode.h:23, from terminalnode.cpp:22: ./treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': ./treenode.h:353:63: warning: no return statement in function returning non-void [-Wreturn-type] 353 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ +g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o site.o site.cpp In file included from ancestralnode.h:24, from hmmodel.h:36, from site.cpp:22: @@ -355,13 +391,13 @@ g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o sequence.o sequence.cpp g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o readnewick.o readnewick.cpp g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o readfile.o readfile.cpp -g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o readalignment.o readalignment.cpp In file included from readnewick.h:29, from readnewick.cpp:26: treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': treenode.h:353:63: warning: no return statement in function returning non-void [-Wreturn-type] 353 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ +g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o readalignment.o readalignment.cpp In file included from readalignment.h:28, from readalignment.cpp:23: treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': @@ -370,6 +406,7 @@ | ^ g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o pwsite.o pwsite.cpp g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o pwhirschberg.o pwhirschberg.cpp +g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o progressivealignment.o progressivealignment.cpp In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, @@ -378,7 +415,6 @@ ./treenode.h:353:63: warning: no return statement in function returning non-void [-Wreturn-type] 353 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ -g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o progressivealignment.o progressivealignment.cpp In file included from readnewick.h:29, from progressivealignment.cpp:28: treenode.h: In member function 'virtual bool TreeNode::updateInsertionSite(int, bool)': @@ -396,6 +432,7 @@ 353 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o postprobability.o postprobability.cpp +g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o phylomatchscore.o phylomatchscore.cpp In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, @@ -404,8 +441,6 @@ ./treenode.h:353:63: warning: no return statement in function returning non-void [-Wreturn-type] 353 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ -g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o phylomatchscore.o phylomatchscore.cpp -g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o node.o node.cpp In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, @@ -414,9 +449,9 @@ ./treenode.h:353:63: warning: no return statement in function returning non-void [-Wreturn-type] 353 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ +g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o node.o node.cpp g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o intmatrix.o intmatrix.cpp g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o hmmodel.o hmmodel.cpp -g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o hirschberg.o hirschberg.cpp In file included from ancestralnode.h:24, from hmmodel.h:36, from hmmodel.cpp:26: @@ -424,6 +459,7 @@ ./treenode.h:353:63: warning: no return statement in function returning non-void [-Wreturn-type] 353 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ +g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o hirschberg.o hirschberg.cpp In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, @@ -433,6 +469,7 @@ 353 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o guidetree.o guidetree.cpp +g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o fullprobability.o fullprobability.cpp In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, @@ -441,26 +478,6 @@ ./treenode.h:353:63: warning: no return statement in function returning non-void [-Wreturn-type] 353 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ -guidetree.cpp: In member function 'void GuideTree::computeTree(std::vector >*, std::vector >*, IntMatrix*)': -guidetree.cpp:162:37: warning: '%i' directive writing between 1 and 10 bytes into a region of size between 6 and 15 [-Wformat-overflow=] - 162 | sprintf(prop,"%i to %i",i,j); - | ^~ -guidetree.cpp:162:30: note: directive argument in the range [1, 2147483647] - 162 | sprintf(prop,"%i to %i",i,j); - | ^~~~~~~~~~ -In file included from /usr/include/stdio.h:970, - from /usr/include/c++/14/cstdio:42, - from guidetree.cpp:21: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'void GuideTree::computeTree(std::vector >*, std::vector >*, IntMatrix*)' at guidetree.cpp:162:24: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 25 bytes into a destination of size 20 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o fullprobability.o fullprobability.cpp In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, @@ -489,10 +506,31 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +guidetree.cpp: In member function 'void GuideTree::computeTree(std::vector >*, std::vector >*, IntMatrix*)': +guidetree.cpp:162:37: warning: '%i' directive writing between 1 and 10 bytes into a region of size between 6 and 15 [-Wformat-overflow=] + 162 | sprintf(prop,"%i to %i",i,j); + | ^~ +guidetree.cpp:162:30: note: directive argument in the range [1, 2147483647] + 162 | sprintf(prop,"%i to %i",i,j); + | ^~~~~~~~~~ +In file included from /usr/include/stdio.h:970, + from /usr/include/c++/14/cstdio:42, + from guidetree.cpp:21: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'void GuideTree::computeTree(std::vector >*, std::vector >*, IntMatrix*)' at guidetree.cpp:162:24: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 25 bytes into a destination of size 20 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o flmatrix.o flmatrix.cpp g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o eigen.o eigen.cpp g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o dbmatrix.o dbmatrix.cpp g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o characterprobability.o characterprobability.cpp +g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o boolmatrix.o boolmatrix.cpp +g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o ancestralsequence.o ancestralsequence.cpp In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, @@ -501,8 +539,6 @@ ./treenode.h:353:63: warning: no return statement in function returning non-void [-Wreturn-type] 353 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ -g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o boolmatrix.o boolmatrix.cpp -g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o ancestralsequence.o ancestralsequence.cpp In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, @@ -526,7 +562,6 @@ | ^ g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o check_version.o check_version.cpp g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o exonerate_reads.o exonerate_reads.cpp -g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o mafft_alignment.o mafft_alignment.cpp In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, @@ -535,6 +570,7 @@ ./treenode.h:353:63: warning: no return statement in function returning non-void [-Wreturn-type] 353 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ +g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o mafft_alignment.o mafft_alignment.cpp In file included from ancestralnode.h:24, from hmmodel.h:36, from config.h:31, @@ -544,6 +580,7 @@ 353 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ g++ -c -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/prank-0.0.170427+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=gnu++98 -pipe -O3 -I. -I/usr/include -o bppancestors.o bppancestors.cpp +pod2man --utf8 --center "The Probabilistic Alignment Kit" -release="v.121211" --section=1 --name="PRANK" prank.1.pod >prank.1 In file included from ancestralnode.h:24, from bppancestors.h:24, from bppancestors.cpp:29: @@ -551,7 +588,6 @@ ./treenode.h:353:63: warning: no return statement in function returning non-void [-Wreturn-type] 353 | virtual bool updateInsertionSite(int i, bool has_parent) {} | ^ -pod2man --utf8 --center "The Probabilistic Alignment Kit" -release="v.121211" --section=1 --name="PRANK" prank.1.pod >prank.1 g++ -o prank writefile.o treenode.o translatesequences.o terminalsequence.o terminalnode.o site.o sequence.o readnewick.o readfile.o readalignment.o pwsite.o pwhirschberg.o progressivealignment.o prank.o postprobability.o phylomatchscore.o node.o intmatrix.o hmmodel.o hirschberg.o guidetree.o fullprobability.o flmatrix.o eigen.o dbmatrix.o characterprobability.o boolmatrix.o ancestralsequence.o ancestralnode.o check_version.o exonerate_reads.o mafft_alignment.o bppancestors.o -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/prank-0.0.170427+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/prank-0.0.170427+dfsg' @@ -601,12 +637,14 @@ 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/22766/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/22766/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/10222 and its subdirectories -I: Current time: Tue Dec 10 14:10:08 -12 2024 -I: pbuilder-time-stamp: 1733883008 +I: removing directory /srv/workspace/pbuilder/22766 and its subdirectories +I: Current time: Wed Dec 11 16:12:48 +14 2024 +I: pbuilder-time-stamp: 1733883168