Diff of the two buildlogs: -- --- b1/build.log 2025-11-03 05:23:00.326255980 +0000 +++ b2/build.log 2025-11-03 05:24:41.658385260 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Nov 2 17:21:59 -12 2025 -I: pbuilder-time-stamp: 1762147319 +I: Current time: Mon Dec 7 01:46:06 +14 2026 +I: pbuilder-time-stamp: 1796557566 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -32,53 +32,85 @@ dpkg-source: info: applying make-shuffle.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3229535/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4082812/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +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 6 11:46 /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/4082812/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4082812/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='arm64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='arm64' + 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]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 nocheck' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='814f82d32ac24ef38000a59b7d7b72e3' - 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='3229535' - PS1='# ' - PS2='> ' + INVOCATION_ID=c8a042670c81428392a54f0736b5d1ad + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=4082812 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.J5QITK2h/pbuilderrc_nBiO --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.J5QITK2h/b1 --logfile b1/build.log crac_2.5.2+dfsg-7.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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/r-b-build.J5QITK2h/pbuilderrc_jn0t --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.J5QITK2h/b2 --logfile b2/build.log crac_2.5.2+dfsg-7.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3229535/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/4082812/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -91,7 +123,7 @@ Depends: debhelper-compat (= 13), architecture-is-64-bit, zlib1g-dev, libhts-dev, libjellyfish-2.0-dev, libgzstream-dev, libgkarrays-dev, pkg-config, rsync dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. -(Reading database ... 19971 files and directories currently installed.) +(Reading database ... 19964 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: @@ -232,10 +264,10 @@ Get: 100 http://deb.debian.org/debian forky/main arm64 libhts-dev arm64 1.22.1+ds2-1 [1684 kB] Get: 101 http://deb.debian.org/debian forky/main arm64 libjellyfish-2.0-2 arm64 2.3.1-4+b1 [61.9 kB] Get: 102 http://deb.debian.org/debian forky/main arm64 libjellyfish-2.0-dev arm64 2.3.1-4+b1 [136 kB] -Fetched 31.6 MB in 0s (160 MB/s) +Fetched 31.6 MB in 0s (74.4 MB/s) Preconfiguring packages ... Selecting previously unselected package libpopt0:arm64. -(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 ... 19971 files and directories currently installed.) +(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 ... 19964 files and directories currently installed.) Preparing to unpack .../000-libpopt0_1.19+dfsg-2_arm64.deb ... Unpacking libpopt0:arm64 (1.19+dfsg-2) ... Selecting previously unselected package rsync. @@ -663,7 +695,11 @@ Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/crac-2.5.2+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 > ../crac_2.5.2+dfsg-7_source.changes +I: user script /srv/workspace/pbuilder/4082812/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/4082812/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/crac-2.5.2+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 > ../crac_2.5.2+dfsg-7_source.changes dpkg-buildpackage: info: source package crac dpkg-buildpackage: info: source version 2.5.2+dfsg-7 dpkg-buildpackage: info: source distribution unstable @@ -711,8 +747,8 @@ checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes -checking whether UID '1111' is supported by ustar format... yes -checking whether GID '1111' is supported by ustar format... yes +checking whether UID '2222' is supported by ustar format... yes +checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu @@ -970,18 +1006,6 @@ cracIndex.cpp:85:30: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 85 | cerr << "\tCompiled on " <<__DATE__ << endl << endl; | ^~~~~~~~ -In file included from /usr/include/libGkArrays/readsReader.h:109, - from locateTags.h:60, - from locateTags.cpp:53: -/usr/include/libGkArrays/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] - 169 | static int kseq_read(kseq_t *seq) \ - | ^~~~~~~~~ -/usr/include/libGkArrays/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' - 227 | __KSEQ_READ - | ^~~~~~~~~~~ -/usr/include/libGkArrays/readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' - 111 | KSEQ_INIT(gzFile, gzread) - | ^~~~~~~~~ In file included from ./seqan/basic.h:64, from ./seqan/sequence.h:27, from /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, @@ -1057,6 +1081,18 @@ ./seqan/sequence/string_alloc.h:456:70: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] 456 | typedef typename Size< String > >::Type TSize; | ^~~~~ +In file included from /usr/include/libGkArrays/readsReader.h:109, + from locateTags.h:60, + from locateTags.cpp:53: +/usr/include/libGkArrays/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] + 169 | static int kseq_read(kseq_t *seq) \ + | ^~~~~~~~~ +/usr/include/libGkArrays/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' + 227 | __KSEQ_READ + | ^~~~~~~~~~~ +/usr/include/libGkArrays/readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' + 111 | KSEQ_INIT(gzFile, gzread) + | ^~~~~~~~~ In file included from ./seqan/sequence.h:57: ./seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': ./seqan/sequence/string_packed.h:594:62: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] @@ -1272,7 +1308,7 @@ /usr/include/c++/15/new:137:26: note: in a call to allocation function 'void* operator new(std::size_t)' declared here 137 | _GLIBCXX_NODISCARD void* operator new(std::size_t) | ^~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -lm -lpthread -lSSA -L/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/ -Wl,-z,relro -Wl,-z,now -o crac-index cracIndex.o libSSA.a -lhts -lz -lpthread -lm +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -lm -lpthread -lSSA -L/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/ -Wl,-z,relro -Wl,-z,now -o crac-index cracIndex.o libSSA.a -lhts -lz -lpthread -lm libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z -Wl,relro -Wl,-z -Wl,now -o crac-index cracIndex.o -lSSA -L/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/ libSSA.a -lhts -lz -lpthread -lm make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA' Making all in libReadsReader @@ -1304,6 +1340,9 @@ classifyTags.cpp:421:38: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 421 | headerTemplate << "#Created on " <<__DATE__ << endl << "#" << endl; | ^~~~~~~~ +crac.cpp:213:34: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] + 213 | printf("\tCompiled on %s.\n\n",__DATE__); + | ^~~~~~~~ In file included from /usr/include/libGkArrays/bitvector.hxx:104, from /usr/include/libGkArrays/solArray.h:106, from /usr/include/libGkArrays/gkArrays.h:112, @@ -1433,9 +1472,6 @@ /usr/include/libGkArrays/solArray.h:202:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 202 | void realloc(uintSA nbElements) throw (logic_error); | ^~~~~ -crac.cpp:213:34: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] - 213 | printf("\tCompiled on %s.\n\n",__DATE__); - | ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Bitset.o Bitset.cpp In file included from libReadsReader/readsReader.h:57, from Read.h:55, @@ -1451,34 +1487,6 @@ 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ ln -s -f /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/crac-index crac-index -In file included from libReadsReader/readsReader.h:57, - from Read.h:55, - from ReadIndex.h:52, - from Support.h:59, - from SupportBreak.cpp:55: -libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] - 169 | static int kseq_read(kseq_t *seq) \ - | ^~~~~~~~~ -libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' - 227 | __KSEQ_READ - | ^~~~~~~~~~~ -libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' - 59 | KSEQ_INIT(gzFile, gzread) - | ^~~~~~~~~ -In file included from libReadsReader/readsReader.h:57, - from Read.h:55, - from ReadIndex.h:52, - from classifyTags.h:53, - from classifyTags.cpp:52: -libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] - 169 | static int kseq_read(kseq_t *seq) \ - | ^~~~~~~~~ -libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' - 227 | __KSEQ_READ - | ^~~~~~~~~~~ -libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' - 59 | KSEQ_INIT(gzFile, gzread) - | ^~~~~~~~~ In file included from ./libReadsReader/readsReader.h:57, from ./Read.h:55, from ./ReadIndex.h:52, @@ -1504,20 +1512,6 @@ locateServer.cpp:717:9: warning: variable 'dontCare' set but not used [-Wunused-but-set-variable] 717 | char *dontCare; | ^~~~~~~~ -In file included from libReadsReader/readsReader.h:57, - from Read.h:55, - from ReadIndex.h:52, - from Support.h:59, - from Support.cpp:57: -libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] - 169 | static int kseq_read(kseq_t *seq) \ - | ^~~~~~~~~ -libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' - 227 | __KSEQ_READ - | ^~~~~~~~~~~ -libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' - 59 | KSEQ_INIT(gzFile, gzread) - | ^~~~~~~~~ In file included from /usr/include/libGkArrays/bitvector.hxx:104, from /usr/include/libGkArrays/solArray.h:106, from /usr/include/libGkArrays/gkArrays.h:112, @@ -1537,21 +1531,6 @@ /usr/include/libGkArrays/largebinvect.hxx:155:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 155 | inline LargeBinVect operator()(const CountWordSize b = 0, const CountWordSize lg = ~((CountWordSize)0)) const throw (std::bad_alloc, std::out_of_range); | ^~~~~ -In file included from libReadsReader/readsReader.h:57, - from Read.h:55, - from ReadIndex.h:52, - from classifyTags.h:53, - from locateServer.cpp:59: -libReadsReader/readsReader.h: At global scope: -libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] - 169 | static int kseq_read(kseq_t *seq) \ - | ^~~~~~~~~ -libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' - 227 | __KSEQ_READ - | ^~~~~~~~~~~ -libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' - 59 | KSEQ_INIT(gzFile, gzread) - | ^~~~~~~~~ /usr/include/libGkArrays/largebinvect.hxx:158:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 158 | inline unsigned long int GetValue(const CountWordSize b = 0, const CountWordSize lg = ~((CountWordSize)0)) const throw (std::bad_alloc, std::out_of_range); | ^~~~~ @@ -1661,6 +1640,63 @@ /usr/include/libGkArrays/solArray.h:202:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 202 | void realloc(uintSA nbElements) throw (logic_error); | ^~~~~ +In file included from libReadsReader/readsReader.h:57, + from Read.h:55, + from ReadIndex.h:52, + from classifyTags.h:53, + from locateServer.cpp:59: +libReadsReader/readsReader.h: At global scope: +libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] + 169 | static int kseq_read(kseq_t *seq) \ + | ^~~~~~~~~ +libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' + 227 | __KSEQ_READ + | ^~~~~~~~~~~ +libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' + 59 | KSEQ_INIT(gzFile, gzread) + | ^~~~~~~~~ +In file included from libReadsReader/readsReader.h:57, + from Read.h:55, + from ReadIndex.h:52, + from Support.h:59, + from SupportBreak.cpp:55: +libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] + 169 | static int kseq_read(kseq_t *seq) \ + | ^~~~~~~~~ +libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' + 227 | __KSEQ_READ + | ^~~~~~~~~~~ +libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' + 59 | KSEQ_INIT(gzFile, gzread) + | ^~~~~~~~~ +In file included from libReadsReader/readsReader.h:57, + from Read.h:55, + from ReadIndex.h:52, + from JellyReadIndex.h:59, + from JellyReadIndex.cpp:55: +libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] + 169 | static int kseq_read(kseq_t *seq) \ + | ^~~~~~~~~ +libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' + 227 | __KSEQ_READ + | ^~~~~~~~~~~ +libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' + 59 | KSEQ_INIT(gzFile, gzread) + | ^~~~~~~~~ +In file included from libReadsReader/readsReader.h:57, + from Read.h:55, + from ReadIndex.h:52, + from classifyTags.h:53, + from classifyTags.cpp:52: +libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] + 169 | static int kseq_read(kseq_t *seq) \ + | ^~~~~~~~~ +libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' + 227 | __KSEQ_READ + | ^~~~~~~~~~~ +libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' + 59 | KSEQ_INIT(gzFile, gzread) + | ^~~~~~~~~ crac.cpp: In function 'int main(int, char**)': crac.cpp:1009:26: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 1009 | } catch (bad_alloc e) { @@ -1668,8 +1704,8 @@ In file included from libReadsReader/readsReader.h:57, from Read.h:55, from ReadIndex.h:52, - from JellyReadIndex.h:59, - from JellyReadIndex.cpp:55: + from Support.h:59, + from Support.cpp:57: libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ @@ -1725,7 +1761,7 @@ Support.cpp:1030:25: note: 'best_candidate2' was declared here 1030 | uint best_candidate1, best_candidate2; | ^~~~~~~~~~~~~~~ -/bin/bash ../libtool --tag=CXX --mode=link g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -lGkArrays -ljellyfish-2.0 -lm -lpthread -lhts -lSSA -lReadsInfo -lReadsReader -lgzstream -L/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -L/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsInfo -L/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader -ljellyfish-2.0 -lGkArrays -lProgressBar -Wl,-z,relro -Wl,-z,now -o crac Classifier.o classifyTags.o GkReadIndex.o JellyReadIndex.o crac.o Parameters.o SupportBreak.o BreakList.o CandidatBreak.o Support.o locateServer.o utils.o Bitset.o /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/libSSA.a /build/reproducible-path/crac-2.5.2+dfsg/src/libReadsInfo/libReadsInfo.a /build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader/libReadsReader.a -lhts -lz -lpthread -lm +/bin/sh ../libtool --tag=CXX --mode=link g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -lGkArrays -ljellyfish-2.0 -lm -lpthread -lhts -lSSA -lReadsInfo -lReadsReader -lgzstream -L/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -L/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsInfo -L/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader -ljellyfish-2.0 -lGkArrays -lProgressBar -Wl,-z,relro -Wl,-z,now -o crac Classifier.o classifyTags.o GkReadIndex.o JellyReadIndex.o crac.o Parameters.o SupportBreak.o BreakList.o CandidatBreak.o Support.o locateServer.o utils.o Bitset.o /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/libSSA.a /build/reproducible-path/crac-2.5.2+dfsg/src/libReadsInfo/libReadsInfo.a /build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader/libReadsReader.a -lhts -lz -lpthread -lm libtool: link: g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z -Wl,relro -Wl,-z -Wl,now -o crac Classifier.o classifyTags.o GkReadIndex.o JellyReadIndex.o crac.o Parameters.o SupportBreak.o BreakList.o CandidatBreak.o Support.o locateServer.o utils.o Bitset.o -lSSA -lReadsInfo -lReadsReader -lgzstream -L/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -L/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsInfo -L/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader /usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so -lGkArrays -lProgressBar /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/libSSA.a /build/reproducible-path/crac-2.5.2+dfsg/src/libReadsInfo/libReadsInfo.a /build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader/libReadsReader.a -lhts -lz -lpthread -lm make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src' make[2]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src' @@ -1763,90 +1799,6 @@ make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg' make[1]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg' - debian/rules override_dh_auto_test -make[1]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg' -# Sequence of tests is important so parallel execution is no option -dh_auto_test --no-parallel - make -j1 check TESTSUITEFLAGS="-j1 --verbose" VERBOSE=1 -make[2]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg' -Making check in src -make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src' -Making check in libReadsInfo -make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsInfo' -make[4]: Nothing to be done for 'check'. -make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsInfo' -Making check in libSSA -make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA' -make[4]: Nothing to be done for 'check'. -make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA' -Making check in libReadsReader -make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader' -Making check in kseq -make[5]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader/kseq' -make[5]: Nothing to be done for 'check'. -make[5]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader/kseq' -make[5]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader' -make[5]: Nothing to be done for 'check-am'. -make[5]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader' -make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader' -make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src' -make[4]: Nothing to be done for 'check-am'. -make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src' -make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src' -Making check in man -make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/man' -make[3]: Nothing to be done for 'check'. -make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/man' -Making check in scripts -make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/scripts' -make[3]: Nothing to be done for 'check'. -make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/scripts' -Making check in test_f -make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f' -Making check in causes -make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/causes' -make[4]: Nothing to be done for 'check'. -make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/causes' -Making check in bug -make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/bug' -make[4]: Nothing to be done for 'check'. -make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/bug' -Making check in cigar -make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/cigar' -make[4]: Nothing to be done for 'check'. -make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/cigar' -Making check in splices_adjust -make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/splices_adjust' -make[4]: Nothing to be done for 'check'. -make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/splices_adjust' -make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f' -make check-TESTS -make[5]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f' -make[6]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f' -PASS: index_genomes.sh -PASS: launch_sg.sh -PASS: test_index.sh -============================================================================ -Testsuite summary for crac 2.5.2 -============================================================================ -# TOTAL: 3 -# PASS: 3 -# SKIP: 0 -# XFAIL: 0 -# FAIL: 0 -# XPASS: 0 -# ERROR: 0 -============================================================================ -make[6]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f' -make[5]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f' -make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f' -make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f' -make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg' -make[3]: Nothing to be done for 'check-am'. -make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg' -make[2]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg' -find test_f -type f \( -name '*~' -o -name '*.tap' -o -name '*.ssa' -o -name '*.conf' -o -name '*.sam' -o -name '*.valgrind' -o -name '*.log' \) -delete -make[1]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/crac/ @@ -1865,7 +1817,7 @@ make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA' make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA' /usr/bin/mkdir -p '/build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c crac-index '/build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c crac-index '/build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/bin' libtool: install: /usr/bin/install -c crac-index /build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/bin/crac-index make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA' @@ -1890,7 +1842,7 @@ make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src' make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src' /usr/bin/mkdir -p '/build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/bin' - /bin/bash ../libtool --mode=install /usr/bin/install -c crac '/build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/bin' + /bin/sh ../libtool --mode=install /usr/bin/install -c crac '/build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/bin' libtool: install: /usr/bin/install -c crac /build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/bin/crac make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src' @@ -1994,12 +1946,14 @@ 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/4082812/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4082812/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/3229535 and its subdirectories -I: Current time: Sun Nov 2 17:22:59 -12 2025 -I: pbuilder-time-stamp: 1762147379 +I: removing directory /srv/workspace/pbuilder/4082812 and its subdirectories +I: Current time: Mon Dec 7 01:47:40 +14 2026 +I: pbuilder-time-stamp: 1796557660