Diff of the two buildlogs: -- --- b1/build.log 2025-03-09 14:54:01.113358426 +0000 +++ b2/build.log 2025-03-09 15:08:37.285921788 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Apr 11 09:11:36 -12 2026 -I: pbuilder-time-stamp: 1775941896 +I: Current time: Mon Mar 10 04:54:06 +14 2025 +I: pbuilder-time-stamp: 1741532046 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -28,52 +28,84 @@ 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/697129/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1731606/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Mar 9 14:54 /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/1731606/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1731606/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='b092b92e3e8b4018804c72b7859f6056' - 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='697129' - PS1='# ' - PS2='> ' + INVOCATION_ID=c9802bf1883c420dbf309d11baaa46b8 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1731606 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.0RYDLhAF/pbuilderrc_DiEr --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.0RYDLhAF/b1 --logfile b1/build.log subread_2.0.8+dfsg-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.0RYDLhAF/pbuilderrc_Klbr --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.0RYDLhAF/b2 --logfile b2/build.log subread_2.0.8+dfsg-1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/697129/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1731606/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -164,7 +196,7 @@ Get: 45 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.1 [920 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] -Fetched 27.3 MB in 0s (231 MB/s) +Fetched 27.3 MB in 0s (117 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19914 files and directories currently installed.) @@ -334,8 +366,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Apr 11 21:11:56 UTC 2026. -Universal Time is now: Sat Apr 11 21:11:56 UTC 2026. +Local time is now: Sun Mar 9 14:54:45 UTC 2025. +Universal Time is now: Sun Mar 9 14:54:45 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -379,7 +411,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/subread-2.0.8+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_2.0.8+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/1731606/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1731606/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/subread-2.0.8+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_2.0.8+dfsg-1_source.changes dpkg-buildpackage: info: source package subread dpkg-buildpackage: info: source version 2.0.8+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -437,7 +473,6 @@ aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-value-index.o gene-value-index.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o exon-algorithms.o exon-algorithms.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HelperFunctions.o HelperFunctions.c -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o interval_merge.o interval_merge.c core-junction.c: In function 'find_donor_receptor': core-junction.c:2099:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 2099 | if(0&& FIXLENstrcmp("V0112_0155:7:1101:12618:2466#ACTTGA", rname) == 0) @@ -445,6 +480,7 @@ 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 ){ | ^~ +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o interval_merge.o interval_merge.c 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 )) @@ -465,16 +501,16 @@ /usr/include/aarch64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o long-hashtable.o long-hashtable.c 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; | ^~~~~~~ +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o long-hashtable.o long-hashtable.c +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.c 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]; | ^~~~~~~~ -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.c 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); @@ -512,19 +548,19 @@ aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o genRandomReads gen_rand_reads.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 aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -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 -rm -f longread-one/*.o aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -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 cd longread-one && make -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -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 make[3]: Entering directory '/build/reproducible-path/subread-2.0.8+dfsg/src/longread-one' +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -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 aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMsorted-hashtable.o -c LRMsorted-hashtable.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -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 aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMbase-index.o -c LRMbase-index.c -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -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 aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMchro-event.o -c LRMchro-event.c -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhelper.o -c LRMhelper.c +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -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 aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -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 -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMseek-zlib.o -c LRMseek-zlib.c +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhelper.o -c LRMhelper.c +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -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 detection-calls.c: In function 'DTCwrite_annotations': detection-calls.c:155:109: 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); @@ -558,19 +594,12 @@ 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; | ^~~~~~~~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -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 readSummary.c: In function 'fc_thread_merge_results': -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -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 readSummary.c:3889:32: warning: unused variable 'sample_i' [-Wunused-variable] 3889 | int xk1, xk2, ret = 0, sample_i; | ^~~~~~~~ -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMfile-io.o -c LRMfile-io.c -readSummary.c: In function 'readSummary': -readSummary.c:5645:52: warning: variable 'scrna_total_BAM_no' set but not used [-Wunused-but-set-variable] - 5645 | int isGTF, n_input_files=0,is_dual_index, scrna_total_BAM_no; - | ^~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhashtable.o -c LRMhashtable.c -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -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 -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -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 +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMseek-zlib.o -c LRMseek-zlib.c 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); @@ -660,9 +689,16 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +readSummary.c: In function 'readSummary': +readSummary.c:5645:52: warning: variable 'scrna_total_BAM_no' set but not used [-Wunused-but-set-variable] + 5645 | int isGTF, n_input_files=0,is_dual_index, scrna_total_BAM_no; + | ^~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -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 +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMfile-io.o -c LRMfile-io.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -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 aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -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 aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -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 +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhashtable.o -c LRMhashtable.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -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 aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -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 aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRM longread-mapping.c LRMsorted-hashtable.o LRMbase-index.o LRMchro-event.o LRMhelper.o LRMseek-zlib.o LRMfile-io.o LRMhashtable.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE @@ -674,6 +710,7 @@ /usr/include/aarch64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ +make[3]: Leaving directory '/build/reproducible-path/subread-2.0.8+dfsg/src/longread-one' readSummary.c: In function 'vote_and_add_count': readSummary.c:3752:66: warning: 'longest_overlap_score' may be used uninitialized [-Wmaybe-uninitialized] 3752 | if(longest_overlap_score > scoring_numbers[score_x1]) scoring_numbers[score_x1] = 0; @@ -681,7 +718,6 @@ readSummary.c:3521:51: note: 'longest_overlap_score' was declared here 3521 | int scoring_count = 0, score_x1, longest_overlap_score; | ^~~~~~~~~~~~~~~~~~~~~ -make[3]: Leaving directory '/build/reproducible-path/subread-2.0.8+dfsg/src/longread-one' mkdir -p ../bin/utilities mv longread-one/LRM longread-one/sublong mv longread-one/sublong subread-align subjunc featureCounts subindel exactSNP subread-buildindex ../bin/ @@ -736,7 +772,7 @@ || Repeat threshold : 100 repeats || || Gapped index : no || || || -|| Free / total memory : 33.2GB / 58.8GB || +|| Free / total memory : 40.4GB / 58.8GB || || || || Input files : 1 file in total || || o chr901.fa || @@ -752,30 +788,30 @@ || 52 uninformative subreads were found. || || These subreads were excluded from index building. || || Estimate the index size... || -|| 8%, 0 mins elapsed, rate=2328.7k bps/s || -|| 16%, 0 mins elapsed, rate=3493.0k bps/s || -|| 25%, 0 mins elapsed, rate=4191.6k bps/s || -|| 33%, 0 mins elapsed, rate=4722.9k bps/s || -|| 41%, 0 mins elapsed, rate=5050.1k bps/s || -|| 50%, 0 mins elapsed, rate=5294.7k bps/s || -|| 58%, 0 mins elapsed, rate=5484.3k bps/s || -|| 66%, 0 mins elapsed, rate=5635.8k bps/s || -|| 75%, 0 mins elapsed, rate=5759.4k bps/s || -|| 83%, 0 mins elapsed, rate=5862.4k bps/s || -|| 91%, 0 mins elapsed, rate=5988.0k bps/s || +|| 8%, 0 mins elapsed, rate=644.9k bps/s || +|| 16%, 0 mins elapsed, rate=921.2k bps/s || +|| 25%, 0 mins elapsed, rate=1112.8k bps/s || +|| 33%, 0 mins elapsed, rate=1223.8k bps/s || +|| 41%, 0 mins elapsed, rate=1305.8k bps/s || +|| 50%, 0 mins elapsed, rate=1348.5k bps/s || +|| 58%, 0 mins elapsed, rate=1384.0k bps/s || +|| 66%, 0 mins elapsed, rate=1448.5k bps/s || +|| 75%, 0 mins elapsed, rate=1479.4k bps/s || +|| 83%, 0 mins elapsed, rate=1491.7k bps/s || +|| 91%, 0 mins elapsed, rate=1521.7k bps/s || || 3.0 GB of memory is needed for index building. || || Build the index... || -|| 8%, 0 mins elapsed, rate=80.3k bps/s || -|| 16%, 0 mins elapsed, rate=157.9k bps/s || -|| 25%, 0 mins elapsed, rate=232.7k bps/s || -|| 33%, 0 mins elapsed, rate=304.8k bps/s || -|| 41%, 0 mins elapsed, rate=373.9k bps/s || -|| 50%, 0 mins elapsed, rate=441.2k bps/s || -|| 58%, 0 mins elapsed, rate=506.8k bps/s || -|| 66%, 0 mins elapsed, rate=569.8k bps/s || -|| 75%, 0 mins elapsed, rate=630.8k bps/s || -|| 83%, 0 mins elapsed, rate=690.0k bps/s || -|| 91%, 0 mins elapsed, rate=747.3k bps/s || +|| 8%, 0 mins elapsed, rate=50.5k bps/s || +|| 16%, 0 mins elapsed, rate=100.0k bps/s || +|| 25%, 0 mins elapsed, rate=148.4k bps/s || +|| 33%, 0 mins elapsed, rate=195.6k bps/s || +|| 41%, 0 mins elapsed, rate=242.0k bps/s || +|| 50%, 0 mins elapsed, rate=287.4k bps/s || +|| 58%, 0 mins elapsed, rate=331.9k bps/s || +|| 66%, 0 mins elapsed, rate=375.5k bps/s || +|| 75%, 0 mins elapsed, rate=418.0k bps/s || +|| 83%, 0 mins elapsed, rate=459.9k bps/s || +|| 91%, 0 mins elapsed, rate=500.9k bps/s || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || @@ -789,7 +825,7 @@ || [ 90.0% finished ] || || [ 100.0% finished ] || || || -|| Total running time: 0.1 minutes. || +|| Total running time: 0.3 minutes. || || Index ../small1 was successfully built. || || || \\============================================================================// @@ -822,7 +858,7 @@ || || \\============================================================================// -//================ Running (11-Apr-2026 09:12:34, pid=718679) ================\\ +//=============== Running (10-Mar-2025 04:56:06, pid=1739671) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -836,10 +872,10 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.5 mins elapsed, rate=77.5k reads per second || -|| 74% completed, 0.5 mins elapsed, rate=0.5k reads per second || -|| 83% completed, 0.5 mins elapsed, rate=0.6k reads per second || -|| 91% completed, 0.5 mins elapsed, rate=0.6k reads per second || +|| 33% completed, 1.3 mins elapsed, rate=23.4k reads per second || +|| 74% completed, 1.3 mins elapsed, rate=0.2k reads per second || +|| 83% completed, 1.3 mins elapsed, rate=0.2k reads per second || +|| 91% completed, 1.3 mins elapsed, rate=0.2k reads per second || || || || Completed successfully. || || || @@ -856,7 +892,7 @@ || || || Indels : 0 || || || -|| Running time : 0.5 minutes || +|| Running time : 1.3 minutes || || || \\============================================================================// @@ -888,7 +924,7 @@ || || \\============================================================================// -//================ Running (11-Apr-2026 09:13:02, pid=731360) ================\\ +//=============== Running (10-Mar-2025 04:57:25, pid=1745911) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -902,10 +938,10 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.6 mins elapsed, rate=56.5k reads per second || -|| 74% completed, 0.6 mins elapsed, rate=0.4k reads per second || -|| 83% completed, 0.6 mins elapsed, rate=0.4k reads per second || -|| 91% completed, 0.6 mins elapsed, rate=0.5k reads per second || +|| 33% completed, 1.1 mins elapsed, rate=23.8k reads per second || +|| 74% completed, 1.1 mins elapsed, rate=0.2k reads per second || +|| 83% completed, 1.1 mins elapsed, rate=0.2k reads per second || +|| 91% completed, 1.1 mins elapsed, rate=0.3k reads per second || || || || Completed successfully. || || || @@ -922,7 +958,7 @@ || || || Indels : 0 || || || -|| Running time : 0.6 minutes || +|| Running time : 1.1 minutes || || || \\============================================================================// @@ -959,7 +995,7 @@ || || \\============================================================================// -//================ Running (11-Apr-2026 09:13:40, pid=740442) ================\\ +//=============== Running (10-Mar-2025 04:58:34, pid=1750368) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -973,11 +1009,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.7 mins elapsed, rate=24.8k fragments per second || +|| 33% completed, 2.0 mins elapsed, rate=6.7k fragments per second || || Estimated fragment length : 495 bp || -|| 74% completed, 0.7 mins elapsed, rate=0.4k fragments per second || -|| 83% completed, 0.7 mins elapsed, rate=0.4k fragments per second || -|| 91% completed, 0.7 mins elapsed, rate=0.5k fragments per second || +|| 74% completed, 2.0 mins elapsed, rate=0.1k fragments per second || +|| 83% completed, 2.0 mins elapsed, rate=0.1k fragments per second || +|| 91% completed, 2.0 mins elapsed, rate=0.2k fragments per second || || || || Completed successfully. || || || @@ -1002,7 +1038,7 @@ || || || Indels : 0 || || || -|| Running time : 0.7 minutes || +|| Running time : 2.0 minutes || || || \\============================================================================// @@ -1039,7 +1075,7 @@ || || \\============================================================================// -//================ Running (11-Apr-2026 09:14:21, pid=750141) ================\\ +//=============== Running (10-Mar-2025 05:00:35, pid=1753884) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1053,11 +1089,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.6 mins elapsed, rate=23.6k fragments per second || +|| 33% completed, 2.6 mins elapsed, rate=7.0k fragments per second || || Estimated fragment length : 495 bp || -|| 74% completed, 0.6 mins elapsed, rate=0.4k fragments per second || -|| 83% completed, 0.6 mins elapsed, rate=0.4k fragments per second || -|| 91% completed, 0.6 mins elapsed, rate=0.5k fragments per second || +|| 74% completed, 2.7 mins elapsed, rate=0.1k fragments per second || +|| 83% completed, 2.7 mins elapsed, rate=0.1k fragments per second || +|| 91% completed, 2.7 mins elapsed, rate=0.1k fragments per second || || || || Completed successfully. || || || @@ -1082,7 +1118,7 @@ || || || Indels : 0 || || || -|| Running time : 0.6 minutes || +|| Running time : 2.7 minutes || || || \\============================================================================// @@ -1119,7 +1155,7 @@ || || \\============================================================================// -//================ Running (11-Apr-2026 09:14:59, pid=762935) ================\\ +//=============== Running (10-Mar-2025 05:03:16, pid=1761112) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1133,11 +1169,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.7 mins elapsed, rate=29.1k fragments per second || +|| 33% completed, 1.9 mins elapsed, rate=6.2k fragments per second || || Estimated fragment length : 497 bp || -|| 74% completed, 0.7 mins elapsed, rate=0.4k fragments per second || -|| 83% completed, 0.7 mins elapsed, rate=0.4k fragments per second || -|| 91% completed, 0.7 mins elapsed, rate=0.5k fragments per second || +|| 74% completed, 1.9 mins elapsed, rate=0.1k fragments per second || +|| 83% completed, 1.9 mins elapsed, rate=0.1k fragments per second || +|| 91% completed, 1.9 mins elapsed, rate=0.2k fragments per second || || || || Completed successfully. || || || @@ -1162,7 +1198,7 @@ || || || Indels : 15 || || || -|| Running time : 0.7 minutes || +|| Running time : 1.9 minutes || || || \\============================================================================// @@ -1200,7 +1236,7 @@ || || \\============================================================================// -//================ Running (11-Apr-2026 09:15:40, pid=774216) ================\\ +//=============== Running (10-Mar-2025 05:05:10, pid=1772595) ================\\ || || 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. @@ -1270,7 +1306,7 @@ || Repeat threshold : 100 repeats || || Gapped index : yes || || || -|| Free / total memory : 32.7GB / 58.8GB || +|| Free / total memory : 39.6GB / 58.8GB || || || || Input files : 1 file in total || || o chr901.fa || @@ -1286,30 +1322,30 @@ || 2 uninformative subreads were found. || || These subreads were excluded from index building. || || Estimate the index size... || -|| 8%, 0 mins elapsed, rate=5239.6k bps/s || -|| 16%, 0 mins elapsed, rate=5781.6k bps/s || -|| 25%, 0 mins elapsed, rate=5988.0k bps/s || -|| 33%, 0 mins elapsed, rate=7289.8k bps/s || -|| 41%, 0 mins elapsed, rate=7104.4k bps/s || -|| 50%, 0 mins elapsed, rate=7859.3k bps/s || -|| 58%, 0 mins elapsed, rate=7721.4k bps/s || -|| 66%, 0 mins elapsed, rate=8279.7k bps/s || -|| 75%, 0 mins elapsed, rate=8876.4k bps/s || -|| 83%, 0 mins elapsed, rate=9314.7k bps/s || -|| 91%, 0 mins elapsed, rate=9810.1k bps/s || +|| 8%, 0 mins elapsed, rate=9314.6k bps/s || +|| 16%, 0 mins elapsed, rate=12897.2k bps/s || +|| 25%, 0 mins elapsed, rate=13972.1k bps/s || +|| 33%, 0 mins elapsed, rate=13413.1k bps/s || +|| 41%, 0 mins elapsed, rate=13972.0k bps/s || +|| 50%, 0 mins elapsed, rate=14371.2k bps/s || +|| 58%, 0 mins elapsed, rate=12485.6k bps/s || +|| 66%, 0 mins elapsed, rate=10994.3k bps/s || +|| 75%, 0 mins elapsed, rate=11261.0k bps/s || +|| 83%, 0 mins elapsed, rate=9980.0k bps/s || +|| 91%, 0 mins elapsed, rate=9506.7k bps/s || || 0.8 GB of memory is needed for index building. || || Build the index... || -|| 8%, 0 mins elapsed, rate=540.9k bps/s || -|| 16%, 0 mins elapsed, rate=1035.0k bps/s || -|| 25%, 0 mins elapsed, rate=1497.0k bps/s || -|| 33%, 0 mins elapsed, rate=1927.2k bps/s || -|| 41%, 0 mins elapsed, rate=2217.8k bps/s || -|| 50%, 0 mins elapsed, rate=2566.3k bps/s || -|| 58%, 0 mins elapsed, rate=2821.3k bps/s || -|| 66%, 0 mins elapsed, rate=3048.4k bps/s || -|| 75%, 0 mins elapsed, rate=3252.1k bps/s || -|| 83%, 0 mins elapsed, rate=3478.5k bps/s || -|| 91%, 0 mins elapsed, rate=3703.4k bps/s || +|| 8%, 0 mins elapsed, rate=202.5k bps/s || +|| 16%, 0 mins elapsed, rate=398.3k bps/s || +|| 25%, 0 mins elapsed, rate=587.6k bps/s || +|| 33%, 0 mins elapsed, rate=772.6k bps/s || +|| 41%, 0 mins elapsed, rate=948.3k bps/s || +|| 50%, 0 mins elapsed, rate=1122.8k bps/s || +|| 58%, 0 mins elapsed, rate=1278.5k bps/s || +|| 66%, 0 mins elapsed, rate=1426.9k bps/s || +|| 75%, 0 mins elapsed, rate=1539.8k bps/s || +|| 83%, 0 mins elapsed, rate=1690.2k bps/s || +|| 91%, 0 mins elapsed, rate=1790.6k bps/s || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || @@ -1323,7 +1359,7 @@ || [ 90.0% finished ] || || [ 100.0% finished ] || || || -|| Total running time: 0.0 minutes. || +|| Total running time: 0.1 minutes. || || Index ../small1 was successfully built. || || || \\============================================================================// @@ -1361,7 +1397,7 @@ || || \\============================================================================// -//================ Running (11-Apr-2026 09:15:42, pid=774837) ================\\ +//=============== Running (10-Mar-2025 05:05:14, pid=1773787) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1375,11 +1411,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 41% completed, 0.1 mins elapsed, rate=12.9k fragments per second || +|| 41% completed, 0.3 mins elapsed, rate=4.8k fragments per second || || Estimated fragment length : 173 bp || -|| 77% completed, 0.1 mins elapsed, rate=1.7k fragments per second || -|| 87% completed, 0.1 mins elapsed, rate=1.9k fragments per second || -|| 97% completed, 0.1 mins elapsed, rate=2.1k fragments per second || +|| 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 || || || || Completed successfully. || || || @@ -1405,7 +1441,7 @@ || Junctions : 419 || || Indels : 177 || || || -|| Running time : 0.1 minutes || +|| Running time : 0.3 minutes || || || \\============================================================================// @@ -1442,7 +1478,7 @@ || || \\============================================================================// -//================ Running (11-Apr-2026 09:15:50, pid=776388) ================\\ +//=============== Running (10-Mar-2025 05:05:34, pid=1776851) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1456,11 +1492,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 41% completed, 0.1 mins elapsed, rate=6.9k fragments per second || +|| 41% completed, 0.3 mins elapsed, rate=2.6k fragments per second || || Estimated fragment length : 174 bp || -|| 77% completed, 0.1 mins elapsed, rate=1.5k fragments per second || -|| 87% completed, 0.1 mins elapsed, rate=1.7k fragments per second || -|| 97% completed, 0.1 mins elapsed, rate=1.8k fragments per second || +|| 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 || || || || Completed successfully. || || || @@ -1487,7 +1523,7 @@ || Fusions : 33 || || Indels : 180 || || || -|| Running time : 0.1 minutes || +|| Running time : 0.4 minutes || || || \\============================================================================// @@ -1661,9 +1697,9 @@ || || \\============================================================================// -//====================== Running (11-Apr-2026 09:16:06) ======================\\ +//====================== Running (10-Mar-2025 05:06:06) ======================\\ || || -|| Split BAM file into result/temp-snps-779554-FAEBE1F927D3-* ... || +|| Split BAM file into result/temp-snps-1781946-1E9AB6867E7D-* ... || || processed block chr901@999950 by thread 1/1 [block number=1/1] || || || || Completed successfully. || @@ -1769,16 +1805,22 @@ install -p -m0644 ./debian/subread-buildindex.1 debian/subread/usr/share/man/man1/subread-buildindex.1 install -m0755 -d debian/subread/usr/share/man/man1/ 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/propmapped.1 debian/subread/usr/share/man/man1/qualityScores.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/flattenGTF.1 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 debian/subread/usr/share/man/man1/qualityScores.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/exactSNP.1 debian/subread/usr/share/man/man1/featureCounts.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/removeDup.1 debian/subread/usr/share/man/man1/repair.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/sublong.1 debian/subread/usr/share/man/man1/subread-align.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-buildindex.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/subindel.1 debian/subread/usr/share/man/man1/subjunc.1 - mv debian/subread/usr/share/man/man1/sublong.1.dh-new debian/subread/usr/share/man/man1/sublong.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/sublong.1 debian/subread/usr/share/man/man1/subread-align.1 + mv debian/subread/usr/share/man/man1/removeDup.1.dh-new debian/subread/usr/share/man/man1/removeDup.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/removeDup.1 debian/subread/usr/share/man/man1/repair.1 + mv debian/subread/usr/share/man/man1/subread-buildindex.1.dh-new debian/subread/usr/share/man/man1/subread-buildindex.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-buildindex.1 debian/subread/usr/share/man/man1/subread-fullscan.1 + mv debian/subread/usr/share/man/man1/propmapped.1.dh-new debian/subread/usr/share/man/man1/propmapped.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/propmapped.1 debian/subread/usr/share/man/man1/qualityScores.1 mv debian/subread/usr/share/man/man1/flattenGTF.1.dh-new debian/subread/usr/share/man/man1/flattenGTF.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/flattenGTF.1 debian/subread/usr/share/man/man1/genRandomReads.1 @@ -1788,15 +1830,9 @@ mv debian/subread/usr/share/man/man1/subindel.1.dh-new 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/subindel.1 debian/subread/usr/share/man/man1/subjunc.1 - mv debian/subread/usr/share/man/man1/subread-buildindex.1.dh-new debian/subread/usr/share/man/man1/subread-buildindex.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-buildindex.1 debian/subread/usr/share/man/man1/subread-fullscan.1 - mv debian/subread/usr/share/man/man1/propmapped.1.dh-new debian/subread/usr/share/man/man1/propmapped.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/propmapped.1 debian/subread/usr/share/man/man1/qualityScores.1 - mv debian/subread/usr/share/man/man1/removeDup.1.dh-new debian/subread/usr/share/man/man1/removeDup.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/removeDup.1 debian/subread/usr/share/man/man1/repair.1 + mv debian/subread/usr/share/man/man1/sublong.1.dh-new debian/subread/usr/share/man/man1/sublong.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/sublong.1 debian/subread/usr/share/man/man1/subread-align.1 dh_installsystemduser -O--buildsystem=makefile dh_perl -O--buildsystem=makefile dh_link -O--buildsystem=makefile @@ -1807,8 +1843,8 @@ cd debian/subread cd debian/subread-data 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 + 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 '/build/reproducible-path/subread-2.0.8+dfsg' cd '/build/reproducible-path/subread-2.0.8+dfsg' @@ -1817,8 +1853,8 @@ 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/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/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 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/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 @@ -1836,46 +1872,41 @@ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7a/355268e47ac3211c919a5bf5eaf9c733b8d493.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/7a/355268e47ac3211c919a5bf5eaf9c733b8d493.debug debian/subread/usr/lib/subread/subread-fullscan - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/cf - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/repair debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/cf/a531b23598bbd633f5417a7b1eb0bffad34eba.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/cf/a531b23598bbd633f5417a7b1eb0bffad34eba.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/cf/a531b23598bbd633f5417a7b1eb0bffad34eba.debug debian/subread/usr/lib/subread/repair install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/57 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/txUnique debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/57/846aa70ff8ce80187304c85703defe4555d9b6.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/57/846aa70ff8ce80187304c85703defe4555d9b6.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/57/846aa70ff8ce80187304c85703defe4555d9b6.debug debian/subread/usr/lib/subread/txUnique - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/fc - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/fc/53d34e4d2cf9941d5065d7205a822ba24cad0d.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/fc/53d34e4d2cf9941d5065d7205a822ba24cad0d.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/fc/53d34e4d2cf9941d5065d7205a822ba24cad0d.debug debian/subread/usr/lib/subread/propmapped 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/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4c/85524aaf8b66ce87c3202af55f76ec86032ee2.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4c/85524aaf8b66ce87c3202af55f76ec86032ee2.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/4c/85524aaf8b66ce87c3202af55f76ec86032ee2.debug debian/subread/usr/lib/subread/removeDup - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/genRandomReads debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26/f7dec03fa98302965f62db032372a431c91d1d.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26/f7dec03fa98302965f62db032372a431c91d1d.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/26/f7dec03fa98302965f62db032372a431c91d1d.debug debian/subread/usr/lib/subread/genRandomReads install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/12 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/12/b4c201361ce68da63d176abea17cea7d74dda3.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/12/b4c201361ce68da63d176abea17cea7d74dda3.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/12/b4c201361ce68da63d176abea17cea7d74dda3.debug debian/subread/usr/lib/subread/qualityScores + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/genRandomReads debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26/f7dec03fa98302965f62db032372a431c91d1d.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26/f7dec03fa98302965f62db032372a431c91d1d.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/26/f7dec03fa98302965f62db032372a431c91d1d.debug debian/subread/usr/lib/subread/genRandomReads + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/cf + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/repair debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/cf/a531b23598bbd633f5417a7b1eb0bffad34eba.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/cf/a531b23598bbd633f5417a7b1eb0bffad34eba.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/cf/a531b23598bbd633f5417a7b1eb0bffad34eba.debug debian/subread/usr/lib/subread/repair install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/fa objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/flattenGTF debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/fa/ee0944cff27afebcb68fb6763eaaadf0db80b2.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/fa/ee0944cff27afebcb68fb6763eaaadf0db80b2.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/fa/ee0944cff27afebcb68fb6763eaaadf0db80b2.debug debian/subread/usr/lib/subread/flattenGTF - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0d - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0d/168d14fad890098a321382a9001f4d988218f8.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0d/168d14fad890098a321382a9001f4d988218f8.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/0d/168d14fad890098a321382a9001f4d988218f8.debug debian/subread/usr/bin/subread-align + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/fc + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/fc/53d34e4d2cf9941d5065d7205a822ba24cad0d.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/fc/53d34e4d2cf9941d5065d7205a822ba24cad0d.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/fc/53d34e4d2cf9941d5065d7205a822ba24cad0d.debug debian/subread/usr/lib/subread/propmapped install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0b objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-buildindex debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0b/88a80efcfdea13836cc341de7b58caf28ed7bf.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0b/88a80efcfdea13836cc341de7b58caf28ed7bf.debug @@ -1886,21 +1917,26 @@ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/58/bf60d80eaadde6888c8fea390648e76ee2633b.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/58/bf60d80eaadde6888c8fea390648e76ee2633b.debug debian/subread/usr/bin/featureCounts + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0d + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0d/168d14fad890098a321382a9001f4d988218f8.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0d/168d14fad890098a321382a9001f4d988218f8.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/0d/168d14fad890098a321382a9001f4d988218f8.debug debian/subread/usr/bin/subread-align install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/05 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/05/e87849b985b0cb8bc62dcc95c714898fa4fbc6.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/05/e87849b985b0cb8bc62dcc95c714898fa4fbc6.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/05/e87849b985b0cb8bc62dcc95c714898fa4fbc6.debug debian/subread/usr/bin/subindel - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a9 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a9/bffd025987c729942f9b18d298a34985901a47.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a9/bffd025987c729942f9b18d298a34985901a47.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/a9/bffd025987c729942f9b18d298a34985901a47.debug debian/subread/usr/bin/subjunc install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/51 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/51/dbdc1aa3b9416c89daf5e249ebc0c7db83b3f5.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/51/dbdc1aa3b9416c89daf5e249ebc0c7db83b3f5.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/51/dbdc1aa3b9416c89daf5e249ebc0c7db83b3f5.debug debian/subread/usr/bin/exactSNP + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a9 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a9/bffd025987c729942f9b18d298a34985901a47.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a9/bffd025987c729942f9b18d298a34985901a47.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/a9/bffd025987c729942f9b18d298a34985901a47.debug debian/subread/usr/bin/subjunc install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ef objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ef/8f0bbdd96d83cc5e8443181a7b449fd307f12e.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ef/8f0bbdd96d83cc5e8443181a7b449fd307f12e.debug @@ -1917,7 +1953,7 @@ 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/subread-fullscan debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/txUnique debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/bin/subread-align debian/subread/usr/bin/subread-buildindex 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 + dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/txUnique debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/propmapped debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subread-align debian/subread/usr/bin/subindel debian/subread/usr/bin/exactSNP debian/subread/usr/bin/subjunc debian/subread/usr/bin/sublong dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect @@ -1936,26 +1972,26 @@ echo misc:Pre-Depends= >> debian/subread-data.substvars dpkg-gencontrol -psubread-data -ldebian/changelog -Tdebian/subread-data.substvars -cdebian/control -Pdebian/subread-data dpkg-gencontrol: warning: Depends field of package subread-data: substitution variable ${shlibs:Depends} used, but is not defined + chmod 0644 -- debian/subread-data/DEBIAN/control chmod 0644 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/control dpkg-gencontrol -psubread -ldebian/changelog -Tdebian/subread.substvars -cdebian/control -Pdebian/subread - chmod 0644 -- debian/subread-data/DEBIAN/control 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-data >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums + install -m0755 -d debian/subread/DEBIAN cd debian/subread >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums + 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 cd debian/.debhelper/subread/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/subread-data/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/md5sums dh_builddeb -O--buildsystem=makefile - 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' in '../subread_2.0.8+dfsg-1_arm64.deb'. + dpkg-deb --root-owner-group --build debian/.debhelper/subread/dbgsym-root .. + dpkg-deb --root-owner-group --build debian/subread .. dpkg-deb: building package 'subread-data' in '../subread-data_2.0.8+dfsg-1_all.deb'. +dpkg-deb: building package 'subread' in '../subread_2.0.8+dfsg-1_arm64.deb'. dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_2.0.8+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../subread_2.0.8+dfsg-1_arm64.buildinfo dpkg-genchanges --build=binary -O../subread_2.0.8+dfsg-1_arm64.changes @@ -1964,12 +2000,14 @@ 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/1731606/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1731606/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/697129 and its subdirectories -I: Current time: Sat Apr 11 09:16:57 -12 2026 -I: pbuilder-time-stamp: 1775942217 +I: removing directory /srv/workspace/pbuilder/1731606 and its subdirectories +I: Current time: Mon Mar 10 05:08:36 +14 2025 +I: pbuilder-time-stamp: 1741532916