Diff of the two buildlogs: -- --- b1/build.log 2024-04-22 22:42:23.640312124 +0000 +++ b2/build.log 2024-04-22 22:52:10.783337839 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Apr 22 10:39:01 -12 2024 -I: pbuilder-time-stamp: 1713825541 +I: Current time: Tue Apr 23 12:42:44 +14 2024 +I: pbuilder-time-stamp: 1713825764 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying hardening.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/14075/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/24682/tmp/hooks/D01_modify_environment starting +debug: Running on cbxi4pro0. +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 Apr 22 22:43 /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/24682/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/24682/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='trixie' - 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]="21" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='735dbef5a6974a93a74fb9a347c9a376' - 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='14075' - PS1='# ' - PS2='> ' + INVOCATION_ID=dacc8312f5d34e74a65ca0252c1263d5 + 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=24682 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.11bBA7Nw/pbuilderrc_qoNo --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.11bBA7Nw/b1 --logfile b1/build.log stringtie_2.2.1+ds-3.dsc' - SUDO_GID='114' - SUDO_UID='108' - 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.11bBA7Nw/pbuilderrc_KrCn --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.11bBA7Nw/b2 --logfile b2/build.log stringtie_2.2.1+ds-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 virt64a 6.1.0-20-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-armmp #1 SMP Debian 6.1.85-1 (2024-04-11) armv7l GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 21 07:13 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/14075/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 21 07:19 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/24682/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -171,7 +203,7 @@ Get: 49 http://deb.debian.org/debian trixie/main armhf libhts3 armhf 1.19+ds-1 [394 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf liblzma-dev armhf 5.6.1+really5.4.5-1 [281 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf libhts-dev armhf 1.19+ds-1 [1598 kB] -Fetched 23.8 MB in 1s (41.6 MB/s) +Fetched 23.8 MB in 2s (15.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 19635 files and directories currently installed.) @@ -390,7 +422,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/stringtie-2.2.1+ds/ && 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 > ../stringtie_2.2.1+ds-3_source.changes +I: user script /srv/workspace/pbuilder/24682/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/24682/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/stringtie-2.2.1+ds/ && 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 > ../stringtie_2.2.1+ds-3_source.changes dpkg-buildpackage: info: source package stringtie dpkg-buildpackage: info: source version 2.2.1+ds-3 dpkg-buildpackage: info: source distribution unstable @@ -402,7 +438,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/stringtie-2.2.1+ds' dh_auto_clean - make -j3 clean + make -j4 clean make[2]: Entering directory '/build/reproducible-path/stringtie-2.2.1+ds' rm -f stringtie stringtie.o* ./gclib/GBase.o ./gclib/GArgs.o ./gclib/GStr.o ./gclib/GSam.o ./gclib/gdna.o ./gclib/codons.o ./gclib/GFastaIndex.o ./gclib/GFaSeqGet.o ./gclib/gff.o ./gclib/GThreads.o rlink.o tablemaker.o tmerge.o rm -f core.* @@ -431,11 +467,16 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/stringtie-2.2.1+ds' dh_auto_build -- 'LINKER=$(CXX)' - make -j3 "INSTALL=install --strip-program=true" LINKER=\$\(CXX\) + make -j4 "INSTALL=install --strip-program=true" LINKER=\$\(CXX\) make[2]: Entering directory '/build/reproducible-path/stringtie-2.2.1+ds' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GBase.cpp -o gclib/GBase.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GArgs.cpp -o gclib/GArgs.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GStr.cpp -o gclib/GStr.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GSam.cpp -o gclib/GSam.o +In file included from gclib/GSam.cpp:1: +gclib/GSam.h:32:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] + 32 | struct { + | ^ In file included from gclib/GStr.h:5, from gclib/GStr.cpp:2: gclib/GStr.cpp: In static member function 'static GStr::Data* GStr::new_data(uint, uint)': @@ -507,7 +548,8 @@ gclib/GStr.cpp:38:15: note: 'data' was declared here 38 | Data* data; | ^~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GSam.cpp -o gclib/GSam.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/gdna.cpp -o gclib/gdna.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/codons.cpp -o gclib/codons.o In static member function 'static GStr::Data* GStr::new_data(uint, uint)', inlined from 'GStr& GStr::trim(char)' at gclib/GStr.cpp:463:23: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] @@ -580,10 +622,6 @@ gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ -In file included from gclib/GSam.cpp:1: -gclib/GSam.h:32:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] - 32 | struct { - | ^ In static member function 'static GStr::Data* GStr::new_data(uint, uint)', inlined from 'GStr& GStr::padC(uint, char)' at gclib/GStr.cpp:626:23: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] @@ -596,6 +634,7 @@ gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GFastaIndex.cpp -o gclib/GFastaIndex.o In static member function 'static GStr::Data* GStr::new_data(uint, uint)', inlined from 'GStr& GStr::tr(const char*, const char*)' at gclib/GStr.cpp:786:25: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] @@ -608,6 +647,7 @@ gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GFaSeqGet.cpp -o gclib/GFaSeqGet.o In static member function 'static GStr::Data* GStr::new_data(uint, uint)', inlined from 'GStr& GStr::paste(const GStr&, int, int)' at gclib/GStr.cpp:917:30: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] @@ -656,8 +696,7 @@ gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/gdna.cpp -o gclib/gdna.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/codons.cpp -o gclib/codons.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/gff.cpp -o gclib/gff.o In static member function 'static GStr::Data* GStr::new_data(uint, uint)', inlined from 'size_t GStr::read(FILE*, const char*, size_t)' at gclib/GStr.cpp:1380:22: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] @@ -670,9 +709,7 @@ gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GFastaIndex.cpp -o gclib/GFastaIndex.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GFaSeqGet.cpp -o gclib/GFaSeqGet.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/gff.cpp -o gclib/gff.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GThreads.cpp -o gclib/GThreads.o In file included from gclib/gff.cpp:1: gclib/gff.h:242:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 242 | struct { @@ -693,9 +730,9 @@ gclib/gff.cpp:426:19: warning: unknown escape sequence: '\%' 426 | GMessage("Warning: unexpected tab character in last column, line truncated:\n\%s\n",l); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GThreads.cpp -o gclib/GThreads.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c rlink.cpp -o rlink.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c tablemaker.cpp -o tablemaker.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c tmerge.cpp -o tmerge.o In file included from rlink.h:5, from rlink.cpp:1: ./gclib/gff.h:242:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] @@ -734,6 +771,28 @@ ./gclib/gff.h:1165:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 1165 | struct { | ^ +In file included from rlink.h:5, + from tmerge.h:5, + from tmerge.cpp:1: +./gclib/gff.h:242:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] + 242 | struct { + | ^ +./gclib/gff.h:245:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] + 245 | struct { + | ^ +In file included from rlink.h:6: +./gclib/GSam.h:32:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] + 32 | struct { + | ^ +./gclib/gff.h:343:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] + 343 | struct { + | ^ +./gclib/gff.h:706:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] + 706 | struct { + | ^ +./gclib/gff.h:1165:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] + 1165 | struct { + | ^ In file included from rlink.h:6: ./gclib/GSam.h:32:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 32 | struct { @@ -796,29 +855,6 @@ /usr/include/c++/13/bits/stl_algobase.h:437:30: warning: 'void* __builtin_memcpy(void*, const void*, unsigned int)' forming offset 4 is out of the bounds [0, 4] [-Warray-bounds=] 437 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c tmerge.cpp -o tmerge.o -In file included from rlink.h:5, - from tmerge.h:5, - from tmerge.cpp:1: -./gclib/gff.h:242:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] - 242 | struct { - | ^ -./gclib/gff.h:245:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] - 245 | struct { - | ^ -./gclib/gff.h:343:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] - 343 | struct { - | ^ -./gclib/gff.h:706:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] - 706 | struct { - | ^ -./gclib/gff.h:1165:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] - 1165 | struct { - | ^ -In file included from rlink.h:6: -./gclib/GSam.h:32:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] - 32 | struct { - | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c stringtie.cpp -o stringtie.o In file included from rlink.h:5, from stringtie.cpp:2: @@ -1019,12 +1055,14 @@ 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/24682/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/24682/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/14075 and its subdirectories -I: Current time: Mon Apr 22 10:42:19 -12 2024 -I: pbuilder-time-stamp: 1713825739 +I: removing directory /srv/workspace/pbuilder/24682 and its subdirectories +I: Current time: Tue Apr 23 12:52:06 +14 2024 +I: pbuilder-time-stamp: 1713826326