Diff of the two buildlogs: -- --- b1/build.log 2024-03-11 20:58:46.763518803 +0000 +++ b2/build.log 2024-03-11 21:02:21.531307431 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Apr 13 15:20:41 -12 2025 -I: pbuilder-time-stamp: 1744600841 +I: Current time: Tue Mar 12 10:58:50 +14 2024 +I: pbuilder-time-stamp: 1710190730 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -32,54 +32,86 @@ dpkg-source: info: applying hardening.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/78072/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2576/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-i386. +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 Mar 11 20:59 /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/2576/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2576/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='i386' + 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]="i686-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=7 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='f11e5c5e4b474f92b5456554d4532024' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='78072' - PS1='# ' - PS2='> ' + INVOCATION_ID=0b1cee4100c54f8cb816ec5b9c233cb8 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2576 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.i6aIHmJr/pbuilderrc_iaaH --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.i6aIHmJr/b1 --logfile b1/build.log stringtie_2.2.1+ds-3.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + 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.i6aIHmJr/pbuilderrc_De1D --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.i6aIHmJr/b2 --logfile b2/build.log stringtie_2.2.1+ds-3.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos6-i386 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 13 17:48 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/78072/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 10 11:24 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2576/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -174,7 +206,7 @@ Get: 49 http://deb.debian.org/debian trixie/main i386 libhts3 i386 1.19+ds-1 [490 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 liblzma-dev i386 5.6.0-0.2 [281 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 libhts-dev i386 1.19+ds-1 [1660 kB] -Fetched 25.2 MB in 1s (32.4 MB/s) +Fetched 25.2 MB in 2s (11.3 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 ... 19818 files and directories currently installed.) @@ -393,7 +425,11 @@ 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/2576/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2576/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 @@ -405,7 +441,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/stringtie-2.2.1+ds' dh_auto_clean - make -j16 clean + make -j7 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.* @@ -434,7 +470,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/stringtie-2.2.1+ds' dh_auto_build -- 'LINKER=$(CXX)' - make -j16 "INSTALL=install --strip-program=true" LINKER=\$\(CXX\) + make -j7 "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 -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 -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 @@ -444,50 +480,6 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -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 -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 -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 -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 -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 -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 -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 -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 -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -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 gclib/GSam.cpp:1: -gclib/GSam.h:32:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] - 32 | struct { - | ^ -In file included from rlink.h:5, - from stringtie.cpp:2: -./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 { - | ^ -In file included from rlink.h:5, - from tablemaker.cpp:2: -./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: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 { - | ^ -./gclib/gff.h:1165:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] - 1165 | 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)': @@ -510,21 +502,6 @@ gclib/GStr.cpp:38:15: note: 'data' was declared here 38 | Data* data; | ^~~~ -In file included from rlink.h:6: -./gclib/GSam.h:32:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] - 32 | struct { - | ^ -In file included from rlink.h:6: -./gclib/GSam.h:32:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] - 32 | struct { - | ^ -In file included from gclib/gff.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 static member function 'static GStr::Data* GStr::new_data(uint, uint)', inlined from 'void GStr::make_unique()' at gclib/GStr.cpp:91:30: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] @@ -537,24 +514,6 @@ gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ -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: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 static member function 'static GStr::Data* GStr::new_data(uint, uint)', inlined from 'GStr& GStr::cut(int, int)' at gclib/GStr.cpp:890:26: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] @@ -567,33 +526,11 @@ gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ -./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 { - | ^ -In file included from rlink.h:5, - from rlink.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 { +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -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 file included from gclib/GSam.cpp:1: +gclib/GSam.h:32:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] + 32 | struct { | ^ -gclib/gff.cpp: In constructor 'GffLine::GffLine(GffReader*, const char*)': -gclib/gff.cpp:426:19: warning: unknown escape sequence: '\%' - 426 | GMessage("Warning: unexpected tab character in last column, line truncated:\n\%s\n",l); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -./gclib/gff.h:343:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] - 343 | struct { - | ^ -./gclib/gff.h:1165:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] - 1165 | struct { - | ^ -./gclib/gff.h:706:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] - 706 | struct { - | ^ In static member function 'static GStr::Data* GStr::new_data(uint, uint)', inlined from 'void GStr::make_unique()' at gclib/GStr.cpp:91:30, inlined from 'char* GStr::detach()' at gclib/GStr.cpp:130:13: @@ -607,33 +544,6 @@ gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ -stringtie.cpp: In function 'int main(int, char**)': -stringtie.cpp:468:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - 468 | if (tstackSize std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = double]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 205 | bind2nd( minus(), avg)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_function.h:1438, - from /usr/include/c++/13/functional:49, - from ./gclib/khashl.hh:25, - from ./gclib/GHashMap.hh:8, - from ./gclib/GFastaIndex.h:11, - from ./gclib/GFaSeqGet.h:3, - from ./gclib/gff.h:9: -/usr/include/c++/13/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -tablemaker.cpp:212:29: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = double]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 212 | bind2nd( minus(), mavg)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -./gclib/gff.h:1165:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] - 1165 | struct { - | ^ In static member function 'static GStr::Data* GStr::new_data(const char*, uint)', inlined from 'GStr::GStr(const char*, uint)' at gclib/GStr.cpp:157:19: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] @@ -646,14 +556,6 @@ gclib/GStr.cpp:38:15: note: 'data' was declared here 38 | Data* data; | ^~~~ -In file included from rlink.h:6: -./gclib/GSam.h:32:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] - 32 | struct { - | ^ -In file included from rlink.h:6: -./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::trim(char)' at gclib/GStr.cpp:463:23: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] @@ -738,6 +640,7 @@ 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 -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 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] @@ -750,6 +653,7 @@ 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 -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 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] @@ -774,6 +678,22 @@ gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ +In file included from gclib/gff.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 static member function 'static GStr::Data* GStr::new_data(uint, uint)', inlined from 'GStr& GStr::insert(const GStr&, int)' at gclib/GStr.cpp:975:30: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] @@ -786,6 +706,10 @@ gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ +gclib/gff.cpp: In constructor 'GffLine::GffLine(GffReader*, const char*)': +gclib/gff.cpp:426:19: warning: unknown escape sequence: '\%' + 426 | GMessage("Warning: unexpected tab character in last column, line truncated:\n\%s\n",l); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static GStr::Data* GStr::new_data(uint, uint)', inlined from 'GStr& GStr::insert(const char*, int)' at gclib/GStr.cpp:1000:30: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] @@ -798,6 +722,130 @@ 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 -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 -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 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] + 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ + | ^~ +gclib/GStr.cpp:21:9: note: in expansion of macro 'GMALLOC' + 21 | GMALLOC(data, sizeof(Data)+len+addcap); + | ^~~~~~~ +gclib/GStr.cpp: In member function 'size_t GStr::read(FILE*, const char*, size_t)': +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 -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 tablemaker.cpp:2: +./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 { + | ^ +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 { + | ^ +In file included from rlink.h:5, + from rlink.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:1165:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] + 1165 | struct { + | ^ +tablemaker.cpp: In function 'void rc_update_exons(RC_BundleData&)': +tablemaker.cpp:205:29: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = double]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 205 | bind2nd( minus(), avg)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_function.h:1438, + from /usr/include/c++/13/functional:49, + from ./gclib/khashl.hh:25, + from ./gclib/GHashMap.hh:8, + from ./gclib/GFastaIndex.h:11, + from ./gclib/GFaSeqGet.h:3, + from ./gclib/gff.h:9: +/usr/include/c++/13/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +tablemaker.cpp:212:29: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = double]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 212 | bind2nd( minus(), mavg)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +./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 { + | ^ +In file included from rlink.h:6: +./gclib/GSam.h:32:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] + 32 | struct { + | ^ +In file included from rlink.h:5, + from stringtie.cpp:2: +./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 { + | ^ +stringtie.cpp: In function 'int main(int, char**)': +stringtie.cpp:468:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + 468 | if (tstackSize