Diff of the two buildlogs: -- --- b1/build.log 2024-10-19 03:09:30.102480465 +0000 +++ b2/build.log 2024-10-19 03:18:53.918528297 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Oct 18 14:57:58 -12 2024 -I: pbuilder-time-stamp: 1729306678 +I: Current time: Fri Nov 21 23:32:33 +14 2025 +I: pbuilder-time-stamp: 1763717553 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -32,52 +32,84 @@ dpkg-source: info: applying 0001-src-Makefile.Linux-Do-not-set-CFLAGS-and-CXXFLAGS-to.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3497738/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2151443/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +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 Nov 21 09:32 /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/2151443/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2151443/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + 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]="x86_64-pc-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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='2b422b662b844a3fb59f60dadd4307b7' - 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='3497738' - PS1='# ' - PS2='> ' + INVOCATION_ID=f7a2d69a74944f95b7e80db80bfbf556 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-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=2151443 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.1FVjAW8P/pbuilderrc_hIeJ --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.1FVjAW8P/b1 --logfile b1/build.log subread_2.0.7+dfsg-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.1FVjAW8P/pbuilderrc_NSE5 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.1FVjAW8P/b2 --logfile b2/build.log subread_2.0.7+dfsg-1.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-26-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3497738/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2151443/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -175,7 +207,7 @@ Get: 52 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] -Fetched 27.9 MB in 1s (21.8 MB/s) +Fetched 27.9 MB in 3s (10.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (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 ... 19944 files and directories currently installed.) @@ -372,8 +404,8 @@ Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Oct 19 02:59:45 UTC 2024. -Universal Time is now: Sat Oct 19 02:59:45 UTC 2024. +Local time is now: Fri Nov 21 09:33:30 UTC 2025. +Universal Time is now: Fri Nov 21 09:33:30 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -420,7 +452,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/subread-2.0.7+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 > ../subread_2.0.7+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/2151443/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2151443/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/subread-2.0.7+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 > ../subread_2.0.7+dfsg-1_source.changes dpkg-buildpackage: info: source package subread dpkg-buildpackage: info: source version 2.0.7+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -436,7 +472,7 @@ rm -rf bin src/longread-one/make.version find . -name "*.o" -delete dh_auto_clean --sourcedirectory=src -- -f Makefile.Linux - cd src && make -j20 clean -f Makefile.Linux + cd src && make -j42 clean -f Makefile.Linux make[2]: Entering directory '/build/reproducible-path/subread-2.0.7+dfsg/src' rm -f core featureCounts exactSNP removeDup subread-buildindex core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o make[2]: Leaving directory '/build/reproducible-path/subread-2.0.7+dfsg/src' @@ -464,7 +500,7 @@ make[1]: Entering directory '/build/reproducible-path/subread-2.0.7+dfsg' dh_auto_build --sourcedirectory=src -- -f Makefile.Linux CC=x86_64-linux-gnu-gcc ; \ - cd src && make -j20 "INSTALL=install --strip-program=true" -f Makefile.Linux CC=x86_64-linux-gnu-gcc + cd src && make -j42 "INSTALL=install --strip-program=true" -f Makefile.Linux CC=x86_64-linux-gnu-gcc make[2]: Entering directory '/build/reproducible-path/subread-2.0.7+dfsg/src' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core.o core.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-junction.o core-junction.c @@ -483,6 +519,10 @@ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seek-zlib.o seek-zlib.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-blc.o input-blc.c +input-blc.c: In function 'iCache_continuous_read_lanes': +input-blc.c:580:59: warning: unused variable 'npos' [-Wunused-variable] + 580 | long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET); + | ^~~~ gene-value-index.c: In function 'is_offset_in_chro': gene-value-index.c:85:33: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 85 | if( pos < chros -> padding || pos >= ( chros->read_offsets[n] - chros->read_offsets[n-1] - chros -> padding )) @@ -502,18 +542,6 @@ core-junction.c:2103:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 2103 | if( (end_site_mismatches + start_site_mismatches) * 500 + insertion_in_between_i < best_testing_score ){ | ^~ -input-blc.c: In function 'iCache_continuous_read_lanes': -input-blc.c:580:59: warning: unused variable 'npos' [-Wunused-variable] - 580 | long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET); - | ^~~~ -input-files.c: In function 'reduce_SAM_to_BAM': -input-files.c:3240:13: warning: unused variable 'seq_len' [-Wunused-variable] - 3240 | int seq_len = qual - seq - 1; - | ^~~~~~~ -input-files.c: In function 'SAM_pairer_fix_format': -input-files.c:4830:50: warning: variable 'readname' set but not used [-Wunused-but-set-variable] - 4830 | char tmpfname [MAX_FILE_NAME_LENGTH+14], readname[256]; - | ^~~~~~~~ gene-algorithms.c: In function 'miltime': gene-algorithms.c:1395:17: warning: 'ftime' is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 1395 | ftime(&trp); @@ -522,6 +550,14 @@ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ +input-files.c: In function 'reduce_SAM_to_BAM': +input-files.c:3240:13: warning: unused variable 'seq_len' [-Wunused-variable] + 3240 | int seq_len = qual - seq - 1; + | ^~~~~~~ +input-files.c: In function 'SAM_pairer_fix_format': +input-files.c:4830:50: warning: variable 'readname' set but not used [-Wunused-but-set-variable] + 4830 | char tmpfname [MAX_FILE_NAME_LENGTH+14], readname[256]; + | ^~~~~~~~ sambam-file.c: In function 'PBam_chunk_headers': sambam-file.c:564:41: warning: '__builtin___strcpy_chk' writing 256 bytes into a region of size 200 [-Wstringop-overflow=] 564 | strcpy(new_event->chro_name, chro_name); @@ -554,26 +590,28 @@ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o detectionCall detection-calls.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm echo " " > longread-one/make.version x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o repair read-repair.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -rm -f longread-one/*.o x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o txUnique tx-unique.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -cd longread-one && make x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o removeDup removeDupReads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +rm -f longread-one/*.o +x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o exactSNP SNPCalling.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-buildindex index-builder.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subindel SUBindel.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +cd longread-one && make +x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-fullscan fullscan.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o flattenGTF flattenAnnotations.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm make[3]: Entering directory '/build/reproducible-path/subread-2.0.7+dfsg/src/longread-one' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMsorted-hashtable.o -c LRMsorted-hashtable.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMbase-index.o -c LRMbase-index.c -x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o exactSNP SNPCalling.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMchro-event.o -c LRMchro-event.c -x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-buildindex index-builder.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhelper.o -c LRMhelper.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMseek-zlib.o -c LRMseek-zlib.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMfile-io.o -c LRMfile-io.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhashtable.o -c LRMhashtable.c -x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subindel SUBindel.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-fullscan fullscan.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm detection-calls.c: In function 'DTCwrite_annotations': detection-calls.c:155:9: warning: dangling pointer 'gc_2int' to an unnamed temporary may be used [-Wdangling-pointer=] 155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0); @@ -587,22 +625,6 @@ detection-calls.c:154:48: note: unnamed temporary defined here 154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0}; | ^ -In file included from readSummary.c:41: -readSummary.c: In function 'get_RG_tables': -readSummary.c:2505:31: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] - 2505 | SUBREADprintf("cannot allocate memory for %s (%d)\n", rg_name, strlen(rg_name)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~ - | | - | size_t {aka long unsigned int} -subread.h:142:44: note: in definition of macro 'SUBREADprintf' - 142 | #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__) - | ^~~~~~~~~~~ -readSummary.c:2505:64: note: format string is defined here - 2505 | SUBREADprintf("cannot allocate memory for %s (%d)\n", rg_name, strlen(rg_name)); - | ~^ - | | - | int - | %ld SUBindel.c: In function 'load_global_context_forindel': SUBindel.c:66:31: warning: '.reads' directive writing 6 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 66 | sprintf(tmp_fname, "%s.reads", context->config.index_prefix); @@ -676,10 +698,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -readSummary.c: In function 'vote_and_add_count': -readSummary.c:3819:58: warning: variable 'assignment_target_number' set but not used [-Wunused-but-set-variable] - 3819 | srInt_64 assignment_target_number = tmp_voter_id; - | ^~~~~~~~~~~~~~~~~~~~~~~~ SUBindel.c: In function 'load_indexes_forindel': SUBindel.c:110:40: warning: '%02d' directive writing between 2 and 10 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 110 | sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, block_no, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b'); @@ -696,13 +714,31 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +In file included from readSummary.c:41: +readSummary.c: In function 'get_RG_tables': +readSummary.c:2505:31: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] + 2505 | SUBREADprintf("cannot allocate memory for %s (%d)\n", rg_name, strlen(rg_name)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~ + | | + | size_t {aka long unsigned int} +subread.h:142:44: note: in definition of macro 'SUBREADprintf' + 142 | #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__) + | ^~~~~~~~~~~ +readSummary.c:2505:64: note: format string is defined here + 2505 | SUBREADprintf("cannot allocate memory for %s (%d)\n", rg_name, strlen(rg_name)); + | ~^ + | | + | int + | %ld +readSummary.c: In function 'vote_and_add_count': +readSummary.c:3819:58: warning: variable 'assignment_target_number' set but not used [-Wunused-but-set-variable] + 3819 | srInt_64 assignment_target_number = tmp_voter_id; + | ^~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c: In function 'fc_thread_merge_results': readSummary.c:3889:32: warning: unused variable 'sample_i' [-Wunused-variable] 3889 | int xk1, xk2, ret = 0, sample_i; | ^~~~~~~~ -x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm readSummary.c: In function 'readSummary': -x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o flattenGTF flattenAnnotations.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm readSummary.c:5650:52: warning: variable 'scrna_total_BAM_no' set but not used [-Wunused-but-set-variable] 5650 | int isGTF, n_input_files=0,is_dual_index, scrna_total_BAM_no; | ^~~~~~~~~~~~~~~~~~ @@ -777,7 +813,7 @@ || Repeat threshold : 100 repeats || || Gapped index : no || || || -|| Free / total memory : 69.3GB / 79.0GB || +|| Free / total memory : 71.0GB / 78.5GB || || || || Input files : 1 file in total || || o chr901.fa || @@ -793,30 +829,30 @@ || 52 uninformative subreads were found. || || These subreads were excluded from index building. || || Estimate the index size... || -|| 8%, 0 mins elapsed, rate=197.3k bps/s || -|| 16%, 0 mins elapsed, rate=370.1k bps/s || -|| 25%, 0 mins elapsed, rate=522.9k bps/s || -|| 33%, 0 mins elapsed, rate=653.7k bps/s || -|| 41%, 0 mins elapsed, rate=771.9k bps/s || -|| 50%, 0 mins elapsed, rate=880.9k bps/s || -|| 58%, 0 mins elapsed, rate=971.6k bps/s || -|| 66%, 0 mins elapsed, rate=1061.2k bps/s || -|| 75%, 0 mins elapsed, rate=1117.8k bps/s || -|| 83%, 0 mins elapsed, rate=1161.1k bps/s || -|| 91%, 0 mins elapsed, rate=1210.2k bps/s || +|| 8%, 0 mins elapsed, rate=603.1k bps/s || +|| 16%, 0 mins elapsed, rate=1110.4k bps/s || +|| 25%, 0 mins elapsed, rate=1562.1k bps/s || +|| 33%, 0 mins elapsed, rate=1949.6k bps/s || +|| 41%, 0 mins elapsed, rate=2290.5k bps/s || +|| 50%, 0 mins elapsed, rate=2592.7k bps/s || +|| 58%, 0 mins elapsed, rate=2862.6k bps/s || +|| 66%, 0 mins elapsed, rate=3133.9k bps/s || +|| 75%, 0 mins elapsed, rate=3368.3k bps/s || +|| 83%, 0 mins elapsed, rate=3582.6k bps/s || +|| 91%, 0 mins elapsed, rate=3810.5k bps/s || || 3.0 GB of memory is needed for index building. || || Build the index... || -|| 8%, 0 mins elapsed, rate=13.5k bps/s || -|| 16%, 0 mins elapsed, rate=26.7k bps/s || -|| 25%, 0 mins elapsed, rate=39.4k bps/s || -|| 33%, 0 mins elapsed, rate=52.1k bps/s || -|| 41%, 0 mins elapsed, rate=64.4k bps/s || -|| 50%, 0 mins elapsed, rate=76.5k bps/s || -|| 58%, 0 mins elapsed, rate=88.3k bps/s || -|| 66%, 0 mins elapsed, rate=100.0k bps/s || -|| 75%, 0 mins elapsed, rate=111.3k bps/s || -|| 83%, 0 mins elapsed, rate=122.4k bps/s || -|| 91%, 0 mins elapsed, rate=133.2k bps/s || +|| 8%, 0 mins elapsed, rate=57.9k bps/s || +|| 16%, 0 mins elapsed, rate=114.0k bps/s || +|| 25%, 0 mins elapsed, rate=168.5k bps/s || +|| 33%, 0 mins elapsed, rate=221.2k bps/s || +|| 41%, 0 mins elapsed, rate=272.4k bps/s || +|| 50%, 0 mins elapsed, rate=322.0k bps/s || +|| 58%, 0 mins elapsed, rate=370.5k bps/s || +|| 66%, 0 mins elapsed, rate=417.6k bps/s || +|| 75%, 0 mins elapsed, rate=463.4k bps/s || +|| 83%, 0 mins elapsed, rate=507.8k bps/s || +|| 91%, 0 mins elapsed, rate=552.2k bps/s || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || @@ -830,7 +866,7 @@ || [ 90.0% finished ] || || [ 100.0% finished ] || || || -|| Total running time: 0.6 minutes. || +|| Total running time: 0.1 minutes. || || Index ../small1 was successfully built. || || || \\============================================================================// @@ -863,7 +899,7 @@ || || \\============================================================================// -//=============== Running (18-Oct-2024 15:01:25, pid=3534813) ================\\ +//=============== Running (21-Nov-2025 23:34:03, pid=2164633) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -877,10 +913,10 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.9 mins elapsed, rate=28.5k reads per second || +|| 33% completed, 0.9 mins elapsed, rate=66.0k reads per second || || 74% completed, 0.9 mins elapsed, rate=0.3k reads per second || || 83% completed, 0.9 mins elapsed, rate=0.3k reads per second || -|| 91% completed, 0.9 mins elapsed, rate=0.3k reads per second || +|| 91% completed, 1.0 mins elapsed, rate=0.3k reads per second || || || || Completed successfully. || || || @@ -897,7 +933,7 @@ || || || Indels : 0 || || || -|| Running time : 0.9 minutes || +|| Running time : 1.0 minutes || || || \\============================================================================// @@ -929,7 +965,7 @@ || || \\============================================================================// -//=============== Running (18-Oct-2024 15:02:19, pid=3543827) ================\\ +//=============== Running (21-Nov-2025 23:35:01, pid=2172396) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -943,10 +979,10 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 1.5 mins elapsed, rate=29.9k reads per second || -|| 74% completed, 1.6 mins elapsed, rate=0.2k reads per second || -|| 83% completed, 1.6 mins elapsed, rate=0.2k reads per second || -|| 91% completed, 1.6 mins elapsed, rate=0.2k reads per second || +|| 33% completed, 0.9 mins elapsed, rate=67.3k reads per second || +|| 74% completed, 0.9 mins elapsed, rate=0.3k reads per second || +|| 83% completed, 0.9 mins elapsed, rate=0.3k reads per second || +|| 91% completed, 0.9 mins elapsed, rate=0.3k reads per second || || || || Completed successfully. || || || @@ -963,7 +999,7 @@ || || || Indels : 0 || || || -|| Running time : 1.6 minutes || +|| Running time : 1.0 minutes || || || \\============================================================================// @@ -1000,7 +1036,7 @@ || || \\============================================================================// -//=============== Running (18-Oct-2024 15:03:53, pid=3561733) ================\\ +//=============== Running (21-Nov-2025 23:35:58, pid=2180698) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1014,9 +1050,9 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 1.0 mins elapsed, rate=11.9k fragments per second || +|| 33% completed, 0.9 mins elapsed, rate=27.6k fragments per second || || Estimated fragment length : 495 bp || -|| 74% completed, 1.0 mins elapsed, rate=0.2k fragments per second || +|| 74% completed, 1.0 mins elapsed, rate=0.3k fragments per second || || 83% completed, 1.0 mins elapsed, rate=0.3k fragments per second || || 91% completed, 1.0 mins elapsed, rate=0.3k fragments per second || || || @@ -1043,7 +1079,7 @@ || || || Indels : 0 || || || -|| Running time : 1.1 minutes || +|| Running time : 1.0 minutes || || || \\============================================================================// @@ -1080,7 +1116,7 @@ || || \\============================================================================// -//=============== Running (18-Oct-2024 15:04:57, pid=3578935) ================\\ +//=============== Running (21-Nov-2025 23:36:58, pid=2192262) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1094,9 +1130,9 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 1.0 mins elapsed, rate=14.9k fragments per second || +|| 33% completed, 1.0 mins elapsed, rate=31.3k fragments per second || || Estimated fragment length : 495 bp || -|| 74% completed, 1.0 mins elapsed, rate=0.2k fragments per second || +|| 74% completed, 1.0 mins elapsed, rate=0.3k fragments per second || || 83% completed, 1.0 mins elapsed, rate=0.3k fragments per second || || 91% completed, 1.0 mins elapsed, rate=0.3k fragments per second || || || @@ -1160,7 +1196,7 @@ || || \\============================================================================// -//=============== Running (18-Oct-2024 15:06:01, pid=3595774) ================\\ +//=============== Running (21-Nov-2025 23:37:56, pid=2216259) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1174,7 +1210,7 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 1.0 mins elapsed, rate=17.2k fragments per second || +|| 33% completed, 1.1 mins elapsed, rate=23.0k fragments per second || || Estimated fragment length : 497 bp || || 74% completed, 1.1 mins elapsed, rate=0.2k fragments per second || || 83% completed, 1.1 mins elapsed, rate=0.3k fragments per second || @@ -1241,7 +1277,7 @@ || || \\============================================================================// -//=============== Running (18-Oct-2024 15:07:07, pid=3616521) ================\\ +//=============== Running (21-Nov-2025 23:39:03, pid=2232020) ================\\ || || ERROR: unable to open file 'data/test-err-mut-r1.fq.gz'. File name might be incorrect, or you do not have the permission to read the file. ERROR: unable to open file 'data/test-err-mut-r2.fq.gz'. File name might be incorrect, or you do not have the permission to read the file. @@ -1311,7 +1347,7 @@ || Repeat threshold : 100 repeats || || Gapped index : yes || || || -|| Free / total memory : 70.9GB / 79.0GB || +|| Free / total memory : 59.5GB / 78.5GB || || || || Input files : 1 file in total || || o chr901.fa || @@ -1327,30 +1363,30 @@ || 2 uninformative subreads were found. || || These subreads were excluded from index building. || || Estimate the index size... || -|| 8%, 0 mins elapsed, rate=388.1k bps/s || -|| 16%, 0 mins elapsed, rate=722.7k bps/s || -|| 25%, 0 mins elapsed, rate=1035.0k bps/s || -|| 33%, 0 mins elapsed, rate=1341.3k bps/s || -|| 41%, 0 mins elapsed, rate=1631.0k bps/s || -|| 50%, 0 mins elapsed, rate=1890.9k bps/s || -|| 58%, 0 mins elapsed, rate=2149.5k bps/s || -|| 66%, 0 mins elapsed, rate=2395.2k bps/s || -|| 75%, 0 mins elapsed, rate=2628.9k bps/s || -|| 83%, 0 mins elapsed, rate=2851.4k bps/s || -|| 91%, 0 mins elapsed, rate=3053.5k bps/s || +|| 8%, 0 mins elapsed, rate=3224.3k bps/s || +|| 16%, 0 mins elapsed, rate=4931.3k bps/s || +|| 25%, 0 mins elapsed, rate=5988.0k bps/s || +|| 33%, 0 mins elapsed, rate=6706.6k bps/s || +|| 41%, 0 mins elapsed, rate=7226.9k bps/s || +|| 50%, 0 mins elapsed, rate=7621.1k bps/s || +|| 58%, 0 mins elapsed, rate=7930.1k bps/s || +|| 66%, 0 mins elapsed, rate=8279.7k bps/s || +|| 75%, 0 mins elapsed, rate=8477.4k bps/s || +|| 83%, 0 mins elapsed, rate=8642.5k bps/s || +|| 91%, 0 mins elapsed, rate=8782.4k bps/s || || 0.8 GB of memory is needed for index building. || || Build the index... || -|| 8%, 0 mins elapsed, rate=129.8k bps/s || -|| 16%, 0 mins elapsed, rate=254.4k bps/s || -|| 25%, 0 mins elapsed, rate=367.7k bps/s || -|| 33%, 0 mins elapsed, rate=472.3k bps/s || -|| 41%, 0 mins elapsed, rate=568.7k bps/s || -|| 50%, 0 mins elapsed, rate=659.2k bps/s || -|| 58%, 0 mins elapsed, rate=713.9k bps/s || -|| 66%, 0 mins elapsed, rate=790.9k bps/s || -|| 75%, 0 mins elapsed, rate=863.3k bps/s || -|| 83%, 0 mins elapsed, rate=936.7k bps/s || -|| 91%, 0 mins elapsed, rate=1000.2k bps/s || +|| 8%, 0 mins elapsed, rate=237.5k bps/s || +|| 16%, 0 mins elapsed, rate=436.6k bps/s || +|| 25%, 0 mins elapsed, rate=613.4k bps/s || +|| 33%, 0 mins elapsed, rate=787.2k bps/s || +|| 41%, 0 mins elapsed, rate=952.6k bps/s || +|| 50%, 0 mins elapsed, rate=1105.5k bps/s || +|| 58%, 0 mins elapsed, rate=1251.2k bps/s || +|| 66%, 0 mins elapsed, rate=1388.5k bps/s || +|| 75%, 0 mins elapsed, rate=1518.1k bps/s || +|| 83%, 0 mins elapsed, rate=1640.5k bps/s || +|| 91%, 0 mins elapsed, rate=1756.5k bps/s || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || @@ -1402,7 +1438,7 @@ || || \\============================================================================// -//=============== Running (18-Oct-2024 15:07:17, pid=3618047) ================\\ +//=============== Running (21-Nov-2025 23:39:12, pid=2233129) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1416,11 +1452,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 41% completed, 0.3 mins elapsed, rate=4.2k fragments per second || +|| 41% completed, 0.2 mins elapsed, rate=10.6k fragments per second || || Estimated fragment length : 173 bp || -|| 77% completed, 0.3 mins elapsed, rate=0.7k fragments per second || -|| 87% completed, 0.3 mins elapsed, rate=0.7k fragments per second || -|| 97% completed, 0.3 mins elapsed, rate=0.8k fragments per second || +|| 77% completed, 0.2 mins elapsed, rate=1.0k fragments per second || +|| 87% completed, 0.2 mins elapsed, rate=1.1k fragments per second || +|| 97% completed, 0.2 mins elapsed, rate=1.1k fragments per second || || || || Completed successfully. || || || @@ -1446,7 +1482,7 @@ || Junctions : 419 || || Indels : 177 || || || -|| Running time : 0.3 minutes || +|| Running time : 0.2 minutes || || || \\============================================================================// @@ -1483,7 +1519,7 @@ || || \\============================================================================// -//=============== Running (18-Oct-2024 15:07:38, pid=3620207) ================\\ +//=============== Running (21-Nov-2025 23:39:26, pid=2234349) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1497,11 +1533,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 41% completed, 0.3 mins elapsed, rate=2.3k fragments per second || +|| 41% completed, 0.2 mins elapsed, rate=5.1k fragments per second || || Estimated fragment length : 174 bp || -|| 77% completed, 0.3 mins elapsed, rate=0.6k fragments per second || -|| 87% completed, 0.3 mins elapsed, rate=0.7k fragments per second || -|| 97% completed, 0.4 mins elapsed, rate=0.7k fragments per second || +|| 77% completed, 0.2 mins elapsed, rate=0.8k fragments per second || +|| 87% completed, 0.3 mins elapsed, rate=0.9k fragments per second || +|| 97% completed, 0.3 mins elapsed, rate=0.9k fragments per second || || || || Completed successfully. || || || @@ -1528,7 +1564,7 @@ || Fusions : 33 || || Indels : 180 || || || -|| Running time : 0.4 minutes || +|| Running time : 0.3 minutes || || || \\============================================================================// @@ -1702,9 +1738,9 @@ || || \\============================================================================// -//====================== Running (18-Oct-2024 15:08:18) ======================\\ +//====================== Running (21-Nov-2025 23:39:51) ======================\\ || || -|| Split BAM file into result/temp-snps-3625517-5DD7DB620909-* ... || +|| Split BAM file into result/temp-snps-2238234-50D45716792A-* ... || || processed block chr901@999950 by thread 1/1 [block number=1/1] || || || || Completed successfully. || @@ -1768,10 +1804,10 @@ install -m0755 -d debian/subread-data/usr/share/doc/subread-data install -p -m0644 debian/copyright debian/subread-data/usr/share/doc/subread-data/copyright dh_installchangelogs -O--buildsystem=makefile - install -m0755 -d debian/subread-data/usr/share/doc/subread-data - install -p -m0644 debian/.debhelper/generated/subread-data/dh_installchangelogs.dch.trimmed debian/subread-data/usr/share/doc/subread-data/changelog.Debian install -m0755 -d debian/subread/usr/share/doc/subread install -p -m0644 debian/.debhelper/generated/subread/dh_installchangelogs.dch.trimmed debian/subread/usr/share/doc/subread/changelog.Debian + install -m0755 -d debian/subread-data/usr/share/doc/subread-data + install -p -m0644 debian/.debhelper/generated/subread-data/dh_installchangelogs.dch.trimmed debian/subread-data/usr/share/doc/subread-data/changelog.Debian rm -f debian/subread-data.debhelper.log debian/subread.debhelper.log debian/rules override_dh_installexamples-indep make[1]: Entering directory '/build/reproducible-path/subread-2.0.7+dfsg' @@ -1812,44 +1848,44 @@ install -p -m0644 ./debian/subread-fullscan.1 debian/subread/usr/share/man/man1/subread-fullscan.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/exactSNP.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/featureCounts.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/flattenGTF.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/genRandomReads.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/propmapped.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/qualityScores.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/genRandomReads.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/flattenGTF.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/removeDup.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/repair.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subjunc.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/sublong.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subindel.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-align.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subjunc.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-fullscan.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/qualityScores.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/sublong.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 mv debian/subread/usr/share/man/man1/propmapped.1.dh-new debian/subread/usr/share/man/man1/propmapped.1 chmod 0644 -- debian/subread/usr/share/man/man1/propmapped.1 - mv debian/subread/usr/share/man/man1/exactSNP.1.dh-new debian/subread/usr/share/man/man1/exactSNP.1 - chmod 0644 -- debian/subread/usr/share/man/man1/exactSNP.1 mv debian/subread/usr/share/man/man1/flattenGTF.1.dh-new debian/subread/usr/share/man/man1/flattenGTF.1 chmod 0644 -- debian/subread/usr/share/man/man1/flattenGTF.1 - mv debian/subread/usr/share/man/man1/subread-align.1.dh-new debian/subread/usr/share/man/man1/subread-align.1 - chmod 0644 -- debian/subread/usr/share/man/man1/subread-align.1 - mv debian/subread/usr/share/man/man1/qualityScores.1.dh-new debian/subread/usr/share/man/man1/qualityScores.1 - chmod 0644 -- debian/subread/usr/share/man/man1/qualityScores.1 mv debian/subread/usr/share/man/man1/repair.1.dh-new debian/subread/usr/share/man/man1/repair.1 chmod 0644 -- debian/subread/usr/share/man/man1/repair.1 mv debian/subread/usr/share/man/man1/genRandomReads.1.dh-new debian/subread/usr/share/man/man1/genRandomReads.1 chmod 0644 -- debian/subread/usr/share/man/man1/genRandomReads.1 - mv debian/subread/usr/share/man/man1/subindel.1.dh-new debian/subread/usr/share/man/man1/subindel.1 - chmod 0644 -- debian/subread/usr/share/man/man1/subindel.1 - mv debian/subread/usr/share/man/man1/sublong.1.dh-new debian/subread/usr/share/man/man1/sublong.1 - chmod 0644 -- debian/subread/usr/share/man/man1/sublong.1 mv debian/subread/usr/share/man/man1/featureCounts.1.dh-new debian/subread/usr/share/man/man1/featureCounts.1 chmod 0644 -- debian/subread/usr/share/man/man1/featureCounts.1 + mv debian/subread/usr/share/man/man1/exactSNP.1.dh-new debian/subread/usr/share/man/man1/exactSNP.1 + chmod 0644 -- debian/subread/usr/share/man/man1/exactSNP.1 + mv debian/subread/usr/share/man/man1/subread-align.1.dh-new debian/subread/usr/share/man/man1/subread-align.1 + chmod 0644 -- debian/subread/usr/share/man/man1/subread-align.1 mv debian/subread/usr/share/man/man1/subread-buildindex.1.dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 chmod 0644 -- debian/subread/usr/share/man/man1/subread-buildindex.1 - mv debian/subread/usr/share/man/man1/removeDup.1.dh-new debian/subread/usr/share/man/man1/removeDup.1 - chmod 0644 -- debian/subread/usr/share/man/man1/removeDup.1 + mv debian/subread/usr/share/man/man1/sublong.1.dh-new debian/subread/usr/share/man/man1/sublong.1 + chmod 0644 -- debian/subread/usr/share/man/man1/sublong.1 + mv debian/subread/usr/share/man/man1/subindel.1.dh-new debian/subread/usr/share/man/man1/subindel.1 + chmod 0644 -- debian/subread/usr/share/man/man1/subindel.1 mv debian/subread/usr/share/man/man1/subjunc.1.dh-new debian/subread/usr/share/man/man1/subjunc.1 chmod 0644 -- debian/subread/usr/share/man/man1/subjunc.1 + mv debian/subread/usr/share/man/man1/removeDup.1.dh-new debian/subread/usr/share/man/man1/removeDup.1 + chmod 0644 -- debian/subread/usr/share/man/man1/removeDup.1 + mv debian/subread/usr/share/man/man1/qualityScores.1.dh-new debian/subread/usr/share/man/man1/qualityScores.1 + chmod 0644 -- debian/subread/usr/share/man/man1/qualityScores.1 mv debian/subread/usr/share/man/man1/subread-fullscan.1.dh-new debian/subread/usr/share/man/man1/subread-fullscan.1 chmod 0644 -- debian/subread/usr/share/man/man1/subread-fullscan.1 dh_installsystemduser -O--buildsystem=makefile @@ -1859,23 +1895,23 @@ Using 1725095375 as canonical time Normalizing debian/subread-data/usr/share/doc/subread/examples/annotation/mm39_RefSeq_exon.txt.gz using File::StripNondeterminism::handlers::gzip dh_compress -O--buildsystem=makefile - cd debian/subread cd debian/subread-data - chmod a-x usr/share/doc/subread/changelog.Debian usr/share/man/man1/exactSNP.1 usr/share/man/man1/featureCounts.1 usr/share/man/man1/flattenGTF.1 usr/share/man/man1/genRandomReads.1 usr/share/man/man1/propmapped.1 usr/share/man/man1/qualityScores.1 usr/share/man/man1/removeDup.1 usr/share/man/man1/repair.1 usr/share/man/man1/subindel.1 usr/share/man/man1/subjunc.1 usr/share/man/man1/sublong.1 usr/share/man/man1/subread-align.1 usr/share/man/man1/subread-buildindex.1 usr/share/man/man1/subread-fullscan.1 - gzip -9nf usr/share/doc/subread/changelog.Debian usr/share/man/man1/exactSNP.1 usr/share/man/man1/featureCounts.1 usr/share/man/man1/flattenGTF.1 usr/share/man/man1/genRandomReads.1 usr/share/man/man1/propmapped.1 usr/share/man/man1/qualityScores.1 usr/share/man/man1/removeDup.1 usr/share/man/man1/repair.1 usr/share/man/man1/subindel.1 usr/share/man/man1/subjunc.1 usr/share/man/man1/sublong.1 usr/share/man/man1/subread-align.1 usr/share/man/man1/subread-buildindex.1 usr/share/man/man1/subread-fullscan.1 + cd debian/subread chmod a-x usr/share/doc/subread-data/changelog.Debian usr/share/doc/subread/examples/annotation/hg19_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/hg38_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm10_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm9_RefSeq_exon.txt + chmod a-x usr/share/doc/subread/changelog.Debian usr/share/man/man1/exactSNP.1 usr/share/man/man1/featureCounts.1 usr/share/man/man1/flattenGTF.1 usr/share/man/man1/genRandomReads.1 usr/share/man/man1/propmapped.1 usr/share/man/man1/qualityScores.1 usr/share/man/man1/removeDup.1 usr/share/man/man1/repair.1 usr/share/man/man1/subindel.1 usr/share/man/man1/subjunc.1 usr/share/man/man1/sublong.1 usr/share/man/man1/subread-align.1 usr/share/man/man1/subread-buildindex.1 usr/share/man/man1/subread-fullscan.1 gzip -9nf usr/share/doc/subread-data/changelog.Debian usr/share/doc/subread/examples/annotation/hg19_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/hg38_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm10_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm9_RefSeq_exon.txt + gzip -9nf usr/share/doc/subread/changelog.Debian usr/share/man/man1/exactSNP.1 usr/share/man/man1/featureCounts.1 usr/share/man/man1/flattenGTF.1 usr/share/man/man1/genRandomReads.1 usr/share/man/man1/propmapped.1 usr/share/man/man1/qualityScores.1 usr/share/man/man1/removeDup.1 usr/share/man/man1/repair.1 usr/share/man/man1/subindel.1 usr/share/man/man1/subjunc.1 usr/share/man/man1/sublong.1 usr/share/man/man1/subread-align.1 usr/share/man/man1/subread-buildindex.1 usr/share/man/man1/subread-fullscan.1 cd '/build/reproducible-path/subread-2.0.7+dfsg' cd '/build/reproducible-path/subread-2.0.7+dfsg' dh_fixperms -O--buildsystem=makefile find debian/subread ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/subread-data ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s - find debian/subread-data/usr/share/doc -type f -a -true -a ! -regex 'debian/subread-data/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread/usr/share/doc -type f -a -true -a ! -regex 'debian/subread/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/subread-data/usr/share/doc -type f -a -true -a ! -regex 'debian/subread-data/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread-data/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/subread/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 - find debian/subread-data -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/subread-data -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/subread/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w @@ -1886,81 +1922,81 @@ objcopy --compress-debug-sections debian/subread/usr/lib/debug/.dwz/x86_64-linux-gnu/subread.debug chmod 0644 -- debian/subread/usr/lib/debug/.dwz/x86_64-linux-gnu/subread.debug dh_strip -a -O--buildsystem=makefile - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bd - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/txUnique debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bd/f218b30dc2ccd20e6171c4234ba462a823fd7a.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bd/f218b30dc2ccd20e6171c4234ba462a823fd7a.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/txUnique - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bd/f218b30dc2ccd20e6171c4234ba462a823fd7a.debug debian/subread/usr/lib/subread/txUnique - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1b - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1b/fcf2cb4d5a2d54d51d31db675a14723b111c8b.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1b/fcf2cb4d5a2d54d51d31db675a14723b111c8b.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/removeDup - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1b/fcf2cb4d5a2d54d51d31db675a14723b111c8b.debug debian/subread/usr/lib/subread/removeDup - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/96 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/flattenGTF debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/96/5444e09d5b0427514a4543a44c7bed649ae8e6.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/96/5444e09d5b0427514a4543a44c7bed649ae8e6.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/flattenGTF - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/96/5444e09d5b0427514a4543a44c7bed649ae8e6.debug debian/subread/usr/lib/subread/flattenGTF - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/genRandomReads debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5/1fd53992f76374b37e0c2efddb6d6b4b293a7c.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5/1fd53992f76374b37e0c2efddb6d6b4b293a7c.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/genRandomReads - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5/1fd53992f76374b37e0c2efddb6d6b4b293a7c.debug debian/subread/usr/lib/subread/genRandomReads install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4c objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/subread-fullscan debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4c/15320a1ae4109a52cf0dd43569aefe69adc9aa.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4c/15320a1ae4109a52cf0dd43569aefe69adc9aa.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/subread-fullscan objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4c/15320a1ae4109a52cf0dd43569aefe69adc9aa.debug debian/subread/usr/lib/subread/subread-fullscan - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/3e - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/repair debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/3e/66ddc7b4f8959cbf2a3aa6c058d4f1273a8406.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/3e/66ddc7b4f8959cbf2a3aa6c058d4f1273a8406.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/repair - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/3e/66ddc7b4f8959cbf2a3aa6c058d4f1273a8406.debug debian/subread/usr/lib/subread/repair - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/84 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/84/98beefce2f0918c24dce282a664e0b2567bde2.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/84/98beefce2f0918c24dce282a664e0b2567bde2.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/propmapped - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/84/98beefce2f0918c24dce282a664e0b2567bde2.debug debian/subread/usr/lib/subread/propmapped install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/81 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/81/7fb4aabf4aef51299f1c2bd2f88ca78baa47b0.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/81/7fb4aabf4aef51299f1c2bd2f88ca78baa47b0.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/qualityScores objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/81/7fb4aabf4aef51299f1c2bd2f88ca78baa47b0.debug debian/subread/usr/lib/subread/qualityScores + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/84 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/84/98beefce2f0918c24dce282a664e0b2567bde2.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/84/98beefce2f0918c24dce282a664e0b2567bde2.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/propmapped + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/84/98beefce2f0918c24dce282a664e0b2567bde2.debug debian/subread/usr/lib/subread/propmapped + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/96 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/flattenGTF debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/96/5444e09d5b0427514a4543a44c7bed649ae8e6.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/96/5444e09d5b0427514a4543a44c7bed649ae8e6.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/flattenGTF + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/96/5444e09d5b0427514a4543a44c7bed649ae8e6.debug debian/subread/usr/lib/subread/flattenGTF + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/3e + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/repair debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/3e/66ddc7b4f8959cbf2a3aa6c058d4f1273a8406.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/3e/66ddc7b4f8959cbf2a3aa6c058d4f1273a8406.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/repair + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/3e/66ddc7b4f8959cbf2a3aa6c058d4f1273a8406.debug debian/subread/usr/lib/subread/repair + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bd + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/txUnique debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bd/f218b30dc2ccd20e6171c4234ba462a823fd7a.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bd/f218b30dc2ccd20e6171c4234ba462a823fd7a.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/txUnique + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bd/f218b30dc2ccd20e6171c4234ba462a823fd7a.debug debian/subread/usr/lib/subread/txUnique + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/genRandomReads debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5/1fd53992f76374b37e0c2efddb6d6b4b293a7c.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5/1fd53992f76374b37e0c2efddb6d6b4b293a7c.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/genRandomReads + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5/1fd53992f76374b37e0c2efddb6d6b4b293a7c.debug debian/subread/usr/lib/subread/genRandomReads + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1b + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1b/fcf2cb4d5a2d54d51d31db675a14723b111c8b.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1b/fcf2cb4d5a2d54d51d31db675a14723b111c8b.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/removeDup + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1b/fcf2cb4d5a2d54d51d31db675a14723b111c8b.debug debian/subread/usr/lib/subread/removeDup install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d0 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-buildindex debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d0/31013018e5ed86a4ae4007dbe754faedbcea12.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d0/31013018e5ed86a4ae4007dbe754faedbcea12.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subread-buildindex objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d0/31013018e5ed86a4ae4007dbe754faedbcea12.debug debian/subread/usr/bin/subread-buildindex - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d5 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d5/f99e2fddd3d9ae85e78b5dc97f6088b2485549.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d5/f99e2fddd3d9ae85e78b5dc97f6088b2485549.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subjunc - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d5/f99e2fddd3d9ae85e78b5dc97f6088b2485549.debug debian/subread/usr/bin/subjunc - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e6 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e6/7198c7d34591a61569012b88204afa443b77e7.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e6/7198c7d34591a61569012b88204afa443b77e7.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subindel - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e6/7198c7d34591a61569012b88204afa443b77e7.debug debian/subread/usr/bin/subindel + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b5 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b5/7648fafbdbce385f719e668c186fc3880e8646.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b5/7648fafbdbce385f719e668c186fc3880e8646.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subread-align + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b5/7648fafbdbce385f719e668c186fc3880e8646.debug debian/subread/usr/bin/subread-align install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f8 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/featureCounts debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f8/94817af898b56d7ded768ab06cd2d0f1341b08.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f8/94817af898b56d7ded768ab06cd2d0f1341b08.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/featureCounts objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f8/94817af898b56d7ded768ab06cd2d0f1341b08.debug debian/subread/usr/bin/featureCounts - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/50 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/50/d1c65acf2c1f508173caa517c76ce2d4e96d95.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/50/d1c65acf2c1f508173caa517c76ce2d4e96d95.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/sublong - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/50/d1c65acf2c1f508173caa517c76ce2d4e96d95.debug debian/subread/usr/bin/sublong + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e6 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e6/7198c7d34591a61569012b88204afa443b77e7.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e6/7198c7d34591a61569012b88204afa443b77e7.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subindel + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e6/7198c7d34591a61569012b88204afa443b77e7.debug debian/subread/usr/bin/subindel + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d5 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d5/f99e2fddd3d9ae85e78b5dc97f6088b2485549.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d5/f99e2fddd3d9ae85e78b5dc97f6088b2485549.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subjunc + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d5/f99e2fddd3d9ae85e78b5dc97f6088b2485549.debug debian/subread/usr/bin/subjunc install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/16 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/16/f27dc3db5e1f3eb54c77699f1ac55b2870e682.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/16/f27dc3db5e1f3eb54c77699f1ac55b2870e682.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/exactSNP objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/16/f27dc3db5e1f3eb54c77699f1ac55b2870e682.debug debian/subread/usr/bin/exactSNP - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b5 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b5/7648fafbdbce385f719e668c186fc3880e8646.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b5/7648fafbdbce385f719e668c186fc3880e8646.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subread-align - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b5/7648fafbdbce385f719e668c186fc3880e8646.debug debian/subread/usr/bin/subread-align + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/50 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/50/d1c65acf2c1f508173caa517c76ce2d4e96d95.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/50/d1c65acf2c1f508173caa517c76ce2d4e96d95.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/sublong + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/50/d1c65acf2c1f508173caa517c76ce2d4e96d95.debug debian/subread/usr/bin/sublong install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/subread/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/subread/usr/lib/debug/.dwz @@ -1972,7 +2008,7 @@ rm -f debian/subread/DEBIAN/shlibs dh_shlibdeps -a -O--buildsystem=makefile install -m0755 -d debian/subread/DEBIAN - dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/lib/subread/txUnique debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/qualityScores debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/subjunc debian/subread/usr/bin/subindel debian/subread/usr/bin/featureCounts debian/subread/usr/bin/sublong debian/subread/usr/bin/exactSNP debian/subread/usr/bin/subread-align + dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/txUnique debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/removeDup debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/subread-align debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subindel debian/subread/usr/bin/subjunc debian/subread/usr/bin/exactSNP debian/subread/usr/bin/sublong dh_installdeb -O--buildsystem=makefile install -m0755 -d debian/subread/DEBIAN install -m0755 -d debian/subread-data/DEBIAN @@ -1993,8 +2029,8 @@ chmod 0644 -- debian/subread/DEBIAN/control dh_md5sums -O--buildsystem=makefile install -m0755 -d debian/subread/DEBIAN - install -m0755 -d debian/subread-data/DEBIAN cd debian/subread >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums + install -m0755 -d debian/subread-data/DEBIAN cd debian/subread-data >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/subread/DEBIAN/md5sums install -m0755 -d debian/.debhelper/subread/dbgsym-root/DEBIAN @@ -2005,9 +2041,9 @@ dpkg-deb --root-owner-group --build debian/subread .. dpkg-deb --root-owner-group --build debian/.debhelper/subread/dbgsym-root .. dpkg-deb --root-owner-group --build debian/subread-data .. -dpkg-deb: building package 'subread-data' in '../subread-data_2.0.7+dfsg-1_all.deb'. -dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_2.0.7+dfsg-1_amd64.deb'. dpkg-deb: building package 'subread' in '../subread_2.0.7+dfsg-1_amd64.deb'. +dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_2.0.7+dfsg-1_amd64.deb'. +dpkg-deb: building package 'subread-data' in '../subread-data_2.0.7+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../subread_2.0.7+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../subread_2.0.7+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2015,12 +2051,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2151443/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2151443/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/3497738 and its subdirectories -I: Current time: Fri Oct 18 15:09:29 -12 2024 -I: pbuilder-time-stamp: 1729307369 +I: removing directory /srv/workspace/pbuilder/2151443 and its subdirectories +I: Current time: Fri Nov 21 23:41:52 +14 2025 +I: pbuilder-time-stamp: 1763718112