Diff of the two buildlogs: -- --- b1/build.log 2024-09-09 12:50:56.873646314 +0000 +++ b2/build.log 2024-09-09 12:52:18.206188219 +0000 @@ -1,7 +1,6 @@ -W: cgroups are not available on the host, not using them. I: pbuilder: network access will be disabled during build -I: Current time: Sun Oct 12 07:12:18 -12 2025 -I: pbuilder-time-stamp: 1760296338 +I: Current time: Tue Sep 10 02:51:00 +14 2024 +I: pbuilder-time-stamp: 1725886260 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -35,51 +34,84 @@ dpkg-source: info: applying tempfile.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2848977/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1601931/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-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 Sep 9 12:51 /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/1601931/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1601931/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' + 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]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.32(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 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='2848977' - PS1='# ' - PS2='> ' + INVOCATION_ID=46d695162b0f4549ab348e9b844e7428 + 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=1601931 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.EmZPaPye/pbuilderrc_oVi8 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.EmZPaPye/b1 --logfile b1/build.log crac_2.5.2+dfsg-6.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/sbin/chroot' - 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.EmZPaPye/pbuilderrc_nE2D --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.EmZPaPye/b2 --logfile b2/build.log crac_2.5.2+dfsg-6.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' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2848977/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1601931/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -219,7 +251,7 @@ Get: 86 http://deb.debian.org/debian trixie/main arm64 libhts-dev arm64 1.20+ds-1 [1613 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libjellyfish-2.0-2 arm64 2.3.1-3+b5 [62.1 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libjellyfish-2.0-dev arm64 2.3.1-3+b5 [136 kB] -Fetched 36.8 MB in 1s (63.3 MB/s) +Fetched 36.8 MB in 0s (111 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19883 files and directories currently installed.) @@ -588,7 +620,11 @@ Building tag database... -> Finished parsing the build-deps 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-6_source.changes +I: user script /srv/workspace/pbuilder/1601931/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1601931/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-6_source.changes dpkg-buildpackage: info: source package crac dpkg-buildpackage: info: source version 2.5.2+dfsg-6 dpkg-buildpackage: info: source distribution unstable @@ -830,16 +866,6 @@ samHeader.cpp:160:15: warning: ignoring return value of 'int sam_hdr_write(samFile*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 160 | sam_hdr_write(out,h); | ~~~~~~~~~~~~~^~~~~~~ -samLine.cpp: In constructor 'OptionalField::OptionalField(const char*, char)': -samLine.cpp:60:10: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation] - 60 | strncpy(tag,tag_name,2); - | ^ -samLine.cpp: In constructor 'CharOptionalField::CharOptionalField(const char*, char)': -samLine.cpp:60:10: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation] -samLine.cpp: In constructor 'IntOptionalField::IntOptionalField(const char*, int)': -samLine.cpp:60:10: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation] -samLine.cpp: In constructor 'IntOptionalField::IntOptionalField(const char*, uint)': -samLine.cpp:60:10: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation] In file included from ../libReadsReader/readsReader.h:57, from ../Read.h:55, from ../ReadIndex.h:52, @@ -855,6 +881,16 @@ ../libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ +samLine.cpp: In constructor 'OptionalField::OptionalField(const char*, char)': +samLine.cpp:60:10: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation] + 60 | strncpy(tag,tag_name,2); + | ^ +samLine.cpp: In constructor 'CharOptionalField::CharOptionalField(const char*, char)': +samLine.cpp:60:10: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation] +samLine.cpp: In constructor 'IntOptionalField::IntOptionalField(const char*, int)': +samLine.cpp:60:10: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation] +samLine.cpp: In constructor 'IntOptionalField::IntOptionalField(const char*, uint)': +samLine.cpp:60:10: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation] samLine.cpp: In constructor 'StringOptionalField::StringOptionalField(const char*, std::string)': samLine.cpp:60:10: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation] samLine.cpp: In constructor 'StringOptionalField::StringOptionalField(const char*, char*)': @@ -890,18 +926,6 @@ 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, @@ -918,6 +942,18 @@ ./seqan/basic/basic_holder.h:1051:66: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] 1051 | typedef typename Value >::Type THostValue; | ^~~~~~~~~~ +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:38: ./seqan/sequence/lexical.h: In function 'void seqan::compare_(Lexical&, TLeft&, TRight&)': ./seqan/sequence/lexical.h:239:45: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] @@ -1192,7 +1228,7 @@ /usr/include/c++/14/new:131:26: note: in a call to allocation function 'void* operator new(std::size_t)' declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ -/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 @@ -1229,20 +1265,6 @@ 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, - 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 /usr/include/libGkArrays/bitvector.hxx:104, from /usr/include/libGkArrays/solArray.h:106, from /usr/include/libGkArrays/gkArrays.h:112, @@ -1375,8 +1397,7 @@ In file included from libReadsReader/readsReader.h:57, from Read.h:55, from ReadIndex.h:52, - from Support.h:59, - from SupportBreak.cpp:55: + from GkReadIndex.h:59: 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) \ | ^~~~~~~~~ @@ -1390,21 +1411,8 @@ 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 libReadsReader/readsReader.h:57, - from Read.h:55, - from ReadIndex.h:52, - from GkReadIndex.h:59: + 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) \ | ^~~~~~~~~ @@ -1414,6 +1422,17 @@ libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ +locateServer.cpp: In function 'void* launchSubServer(void*)': +locateServer.cpp:464:8: warning: unused variable 'threshold' [-Wunused-variable] + 464 | uint threshold = indexTags->getFactorLength(); + | ^~~~~~~~~ +locateServer.cpp:466:9: warning: variable 'dontCare' set but not used [-Wunused-but-set-variable] + 466 | char *dontCare, *variable, *tag_length, *factor; + | ^~~~~~~~ +locateServer.cpp: In function 'void locateServer(ClassifyTags*, const char*, const char*)': +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, @@ -1428,23 +1447,11 @@ ./libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ -locateServer.cpp: In function 'void* launchSubServer(void*)': -locateServer.cpp:464:8: warning: unused variable 'threshold' [-Wunused-variable] - 464 | uint threshold = indexTags->getFactorLength(); - | ^~~~~~~~~ -locateServer.cpp:466:9: warning: variable 'dontCare' set but not used [-Wunused-but-set-variable] - 466 | char *dontCare, *variable, *tag_length, *factor; - | ^~~~~~~~ -locateServer.cpp: In function 'void locateServer(ClassifyTags*, const char*, const char*)': -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 classifyTags.h:53, - from locateServer.cpp:59: -libReadsReader/readsReader.h: At global scope: + 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) \ | ^~~~~~~~~ @@ -1576,16 +1583,41 @@ /usr/include/libGkArrays/largebinvect.cxx:757:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 757 | LargeBinVect LargeBinVect::Split(const CountWordSize i) throw (std::out_of_range, std::bad_alloc) { | ^~~~~ +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/solArray.h:160:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | SolArray(void *ptr, array_type t, uintSA nbElements) throw (invalid_argument); | ^~~~~ /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: 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) { - | ^ +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 libReadsReader/readsReader.h:57, from Read.h:55, from ReadIndex.h:52, @@ -1600,6 +1632,10 @@ 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) { + | ^ In file included from libReadsReader/readsReader.h:57, from Read.h:55, from ReadIndex.h:52, @@ -1615,6 +1651,19 @@ libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ +Classifier.cpp: In member function 'virtual void SingleReadClassifier::classify()': +Classifier.cpp:203:40: warning: 'bioundetermined_type' may be used uninitialized [-Wmaybe-uninitialized] + 203 | taginfo->addBioUndetermined(suppoBreak->getLocationStartBreak(), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 204 | suppoBreak->getPositionStartBreak(), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 205 | bioundetermined_type, + | ~~~~~~~~~~~~~~~~~~~~~ + 206 | message.c_str()); + | ~~~~~~~~~~~~~~~~ +Classifier.cpp:187:33: note: 'bioundetermined_type' was declared here + 187 | BioUndeterminedInfo::Type bioundetermined_type; + | ^~~~~~~~~~~~~~~~~~~~ In member function 'ChrPosition* Support::getLocation(uint)', inlined from 'void Support::checkPairedConnection()' at Support.cpp:1085:38: Support.cpp:470:20: warning: 'best_candidate1' may be used uninitialized [-Wmaybe-uninitialized] @@ -1633,20 +1682,7 @@ Support.cpp:1030:25: note: 'best_candidate2' was declared here 1030 | uint best_candidate1, best_candidate2; | ^~~~~~~~~~~~~~~ -Classifier.cpp: In member function 'virtual void SingleReadClassifier::classify()': -Classifier.cpp:203:40: warning: 'bioundetermined_type' may be used uninitialized [-Wmaybe-uninitialized] - 203 | taginfo->addBioUndetermined(suppoBreak->getLocationStartBreak(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 204 | suppoBreak->getPositionStartBreak(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 205 | bioundetermined_type, - | ~~~~~~~~~~~~~~~~~~~~~ - 206 | message.c_str()); - | ~~~~~~~~~~~~~~~~ -Classifier.cpp:187:33: note: 'bioundetermined_type' was declared here - 187 | BioUndeterminedInfo::Type bioundetermined_type; - | ^~~~~~~~~~~~~~~~~~~~ -/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' @@ -1786,7 +1822,7 @@ 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' @@ -1811,7 +1847,7 @@ 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' @@ -1915,12 +1951,14 @@ 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/1601931/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1601931/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/2848977 and its subdirectories -I: Current time: Sun Oct 12 07:13:55 -12 2025 -I: pbuilder-time-stamp: 1760296435 +I: removing directory /srv/workspace/pbuilder/1601931 and its subdirectories +I: Current time: Tue Sep 10 02:52:17 +14 2024 +I: pbuilder-time-stamp: 1725886337