Diff of the two buildlogs: -- --- b1/build.log 2024-05-18 20:01:07.319101713 +0000 +++ b2/build.log 2024-05-18 20:18:11.243536675 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Jun 20 14:20:06 -12 2025 -I: pbuilder-time-stamp: 1750472406 +I: Current time: Sun May 19 10:01:22 +14 2024 +I: pbuilder-time-stamp: 1716062482 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying 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/1324575/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1747975/tmp/hooks/D01_modify_environment starting +debug: Running on codethink02-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 May 18 20:01 /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/1747975/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1747975/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]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=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='1fecc16c5af545c2a70361f4641d33e9' - 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='1324575' - PS1='# ' - PS2='> ' + INVOCATION_ID=6e8455739d5d4c15a3d7ef7fd68dbc92 + 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=1747975 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.nBCD9UlQ/pbuilderrc_QDG8 --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.nBCD9UlQ/b1 --logfile b1/build.log subread_2.0.6+dfsg-3.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.nBCD9UlQ/pbuilderrc_KOK7 --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.nBCD9UlQ/b2 --logfile b2/build.log subread_2.0.6+dfsg-3.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 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 18 17:46 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1324575/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 18 11:24 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1747975/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -166,7 +198,7 @@ Get: 44 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3.1 [915 kB] -Fetched 25.3 MB in 0s (140 MB/s) +Fetched 25.3 MB in 1s (48.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-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 ... 19745 files and directories currently installed.) @@ -333,8 +365,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Jun 21 02:20:25 UTC 2025. -Universal Time is now: Sat Jun 21 02:20:25 UTC 2025. +Local time is now: Sat May 18 20:02:12 UTC 2024. +Universal Time is now: Sat May 18 20:02:12 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -377,7 +409,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/subread-2.0.6+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_2.0.6+dfsg-3_source.changes +I: user script /srv/workspace/pbuilder/1747975/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1747975/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/subread-2.0.6+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_2.0.6+dfsg-3_source.changes dpkg-buildpackage: info: source package subread dpkg-buildpackage: info: source version 2.0.6+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -436,6 +472,13 @@ aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+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=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -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) + | ^~ +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 ){ + | ^~ 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 )) @@ -448,13 +491,6 @@ gene-value-index.c:87:41: note: in expansion of macro 'SUBREADprintf' 87 | SUBREADprintf("INCHRO:%d ; POS:%d\n", ret, pos); | ^~~~~~~~~~~~~ -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) - | ^~ -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 ){ - | ^~ 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); @@ -521,19 +557,19 @@ aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+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=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -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 -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+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=\""2.0.6"\" -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 -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+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=\""2.0.6"\" -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 rm -f longread-one/*.o -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+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=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -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 cd longread-one && make -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+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=\""2.0.6"\" -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 make[3]: Entering directory '/build/reproducible-path/subread-2.0.6+dfsg/src/longread-one' aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+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=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -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 +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+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=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMfile-io.o -c LRMfile-io.c 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); @@ -547,6 +583,26 @@ 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:2641:31: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] + 2641 | SUBREADprintf("cannot allocate memory for %s (%d)\n", rg_name, strlen(rg_name)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~ + | | + | size_t {aka long unsigned int} +subread.h:143:44: note: in definition of macro 'SUBREADprintf' + 143 | #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__) + | ^~~~~~~~~~~ +readSummary.c:2641:64: note: format string is defined here + 2641 | SUBREADprintf("cannot allocate memory for %s (%d)\n", rg_name, strlen(rg_name)); + | ~^ + | | + | int + | %ld +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+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=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -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 +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+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=\""2.0.6"\" -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 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); @@ -620,6 +676,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+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=\""2.0.6"\" -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 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'); @@ -636,32 +693,11 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -In file included from readSummary.c:41: -readSummary.c: In function 'get_RG_tables': -readSummary.c:2641:31: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] - 2641 | SUBREADprintf("cannot allocate memory for %s (%d)\n", rg_name, strlen(rg_name)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~ - | | - | size_t {aka long unsigned int} -subread.h:143:44: note: in definition of macro 'SUBREADprintf' - 143 | #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__) - | ^~~~~~~~~~~ -readSummary.c:2641:64: note: format string is defined here - 2641 | SUBREADprintf("cannot allocate memory for %s (%d)\n", rg_name, strlen(rg_name)); - | ~^ - | | - | int - | %ld +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+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=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -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-2.0.6+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=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -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 longread-mapping.c: In function 'LRMmiltime': longread-mapping.c:234:9: warning: 'ftime' is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] @@ -733,7 +769,7 @@ || Repeat threshold : 100 repeats || || Gapped index : no || || || -|| Free / total memory : 56.3GB / 58.8GB || +|| Free / total memory : 31.1GB / 58.8GB || || || || Input files : 1 file in total || || o chr901.fa || @@ -749,30 +785,30 @@ || 52 uninformative subreads were found. || || These subreads were excluded from index building. || || Estimate the index size... || -|| 8%, 0 mins elapsed, rate=2465.7k bps/s || -|| 16%, 0 mins elapsed, rate=3810.6k bps/s || -|| 25%, 0 mins elapsed, rate=4657.3k bps/s || -|| 33%, 0 mins elapsed, rate=5239.5k bps/s || -|| 41%, 0 mins elapsed, rate=5588.8k bps/s || -|| 50%, 0 mins elapsed, rate=5917.6k bps/s || -|| 58%, 0 mins elapsed, rate=6177.1k bps/s || -|| 66%, 0 mins elapsed, rate=6326.9k bps/s || -|| 75%, 0 mins elapsed, rate=6504.2k bps/s || -|| 83%, 0 mins elapsed, rate=6653.3k bps/s || -|| 91%, 0 mins elapsed, rate=6780.5k bps/s || +|| 8%, 0 mins elapsed, rate=408.9k bps/s || +|| 16%, 0 mins elapsed, rate=654.9k bps/s || +|| 25%, 0 mins elapsed, rate=766.8k bps/s || +|| 33%, 0 mins elapsed, rate=866.5k bps/s || +|| 41%, 0 mins elapsed, rate=979.3k bps/s || +|| 50%, 0 mins elapsed, rate=1047.9k bps/s || +|| 58%, 0 mins elapsed, rate=1137.3k bps/s || +|| 66%, 0 mins elapsed, rate=1197.6k bps/s || +|| 75%, 0 mins elapsed, rate=1240.9k bps/s || +|| 83%, 0 mins elapsed, rate=1276.0k bps/s || +|| 91%, 0 mins elapsed, rate=1293.3k bps/s || || 3.0 GB of memory is needed for index building. || || Build the index... || -|| 8%, 0 mins elapsed, rate=90.3k bps/s || -|| 16%, 0 mins elapsed, rate=177.2k bps/s || -|| 25%, 0 mins elapsed, rate=261.4k bps/s || -|| 33%, 0 mins elapsed, rate=342.5k bps/s || -|| 41%, 0 mins elapsed, rate=420.4k bps/s || -|| 50%, 0 mins elapsed, rate=496.0k bps/s || -|| 58%, 0 mins elapsed, rate=568.6k bps/s || -|| 66%, 0 mins elapsed, rate=639.3k bps/s || -|| 75%, 0 mins elapsed, rate=707.1k bps/s || -|| 83%, 0 mins elapsed, rate=772.6k bps/s || -|| 91%, 0 mins elapsed, rate=836.0k bps/s || +|| 8%, 0 mins elapsed, rate=17.0k bps/s || +|| 16%, 0 mins elapsed, rate=33.6k bps/s || +|| 25%, 0 mins elapsed, rate=50.1k bps/s || +|| 33%, 0 mins elapsed, rate=66.2k bps/s || +|| 41%, 0 mins elapsed, rate=81.9k bps/s || +|| 50%, 0 mins elapsed, rate=97.5k bps/s || +|| 58%, 0 mins elapsed, rate=112.7k bps/s || +|| 66%, 0 mins elapsed, rate=127.6k bps/s || +|| 75%, 0 mins elapsed, rate=142.5k bps/s || +|| 83%, 0 mins elapsed, rate=156.9k bps/s || +|| 91%, 0 mins elapsed, rate=171.2k bps/s || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || @@ -786,7 +822,7 @@ || [ 90.0% finished ] || || [ 100.0% finished ] || || || -|| Total running time: 0.1 minutes. || +|| Total running time: 0.5 minutes. || || Index ../small1 was successfully built. || || || \\============================================================================// @@ -819,7 +855,7 @@ || || \\============================================================================// -//=============== Running (20-Jun-2025 14:20:59, pid=1327920) ================\\ +//=============== Running (19-May-2024 10:04:32, pid=1804240) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -833,10 +869,10 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.4 mins elapsed, rate=80.3k reads per second || -|| 74% completed, 0.4 mins elapsed, rate=0.6k reads per second || -|| 83% completed, 0.4 mins elapsed, rate=0.7k reads per second || -|| 91% completed, 0.4 mins elapsed, rate=0.8k reads per second || +|| 33% completed, 1.9 mins elapsed, rate=16.0k reads per second || +|| 74% completed, 1.9 mins elapsed, rate=0.1k reads per second || +|| 83% completed, 1.9 mins elapsed, rate=0.1k reads per second || +|| 91% completed, 1.9 mins elapsed, rate=0.2k reads per second || || || || Completed successfully. || || || @@ -853,7 +889,7 @@ || || || Indels : 0 || || || -|| Running time : 0.4 minutes || +|| Running time : 1.9 minutes || || || \\============================================================================// @@ -885,7 +921,7 @@ || || \\============================================================================// -//=============== Running (20-Jun-2025 14:21:23, pid=1332749) ================\\ +//=============== Running (19-May-2024 10:06:28, pid=1832404) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -899,10 +935,10 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.4 mins elapsed, rate=76.6k reads per second || -|| 74% completed, 0.4 mins elapsed, rate=0.6k reads per second || -|| 83% completed, 0.4 mins elapsed, rate=0.7k reads per second || -|| 91% completed, 0.4 mins elapsed, rate=0.7k reads per second || +|| 33% completed, 2.0 mins elapsed, rate=15.6k reads per second || +|| 74% completed, 2.0 mins elapsed, rate=0.1k reads per second || +|| 83% completed, 2.0 mins elapsed, rate=0.1k reads per second || +|| 91% completed, 2.0 mins elapsed, rate=0.2k reads per second || || || || Completed successfully. || || || @@ -919,7 +955,7 @@ || || || Indels : 0 || || || -|| Running time : 0.4 minutes || +|| Running time : 2.0 minutes || || || \\============================================================================// @@ -956,7 +992,7 @@ || || \\============================================================================// -//=============== Running (20-Jun-2025 14:21:49, pid=1341340) ================\\ +//=============== Running (19-May-2024 10:08:29, pid=1871372) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -970,11 +1006,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.4 mins elapsed, rate=38.8k fragments per second || +|| 33% completed, 1.7 mins elapsed, rate=6.4k fragments per second || || Estimated fragment length : 495 bp || -|| 74% completed, 0.4 mins elapsed, rate=0.6k fragments per second || -|| 83% completed, 0.4 mins elapsed, rate=0.6k fragments per second || -|| 91% completed, 0.4 mins elapsed, rate=0.7k fragments per second || +|| 74% completed, 1.8 mins elapsed, rate=0.1k fragments per second || +|| 83% completed, 1.8 mins elapsed, rate=0.2k fragments per second || +|| 91% completed, 1.8 mins elapsed, rate=0.2k fragments per second || || || || Completed successfully. || || || @@ -999,7 +1035,7 @@ || || || Indels : 0 || || || -|| Running time : 0.4 minutes || +|| Running time : 1.8 minutes || || || \\============================================================================// @@ -1036,7 +1072,7 @@ || || \\============================================================================// -//=============== Running (20-Jun-2025 14:22:15, pid=1348923) ================\\ +//=============== Running (19-May-2024 10:10:16, pid=1898306) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1050,11 +1086,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.4 mins elapsed, rate=39.0k fragments per second || +|| 33% completed, 1.8 mins elapsed, rate=5.6k fragments per second || || Estimated fragment length : 495 bp || -|| 74% completed, 0.4 mins elapsed, rate=0.6k fragments per second || -|| 83% completed, 0.4 mins elapsed, rate=0.7k fragments per second || -|| 91% completed, 0.4 mins elapsed, rate=0.7k 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. || || || @@ -1079,7 +1115,7 @@ || || || Indels : 0 || || || -|| Running time : 0.4 minutes || +|| Running time : 1.9 minutes || || || \\============================================================================// @@ -1116,7 +1152,7 @@ || || \\============================================================================// -//=============== Running (20-Jun-2025 14:22:40, pid=1353783) ================\\ +//=============== Running (19-May-2024 10:12:10, pid=1920549) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1130,11 +1166,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.4 mins elapsed, rate=43.3k fragments per second || +|| 33% completed, 1.3 mins elapsed, rate=4.7k fragments per second || || Estimated fragment length : 497 bp || -|| 74% completed, 0.4 mins elapsed, rate=0.6k fragments per second || -|| 83% completed, 0.4 mins elapsed, rate=0.7k fragments per second || -|| 91% completed, 0.4 mins elapsed, rate=0.7k fragments per second || +|| 74% completed, 1.4 mins elapsed, rate=0.2k fragments per second || +|| 83% completed, 1.4 mins elapsed, rate=0.2k fragments per second || +|| 91% completed, 1.4 mins elapsed, rate=0.2k fragments per second || || || || Completed successfully. || || || @@ -1159,7 +1195,7 @@ || || || Indels : 15 || || || -|| Running time : 0.4 minutes || +|| Running time : 1.4 minutes || || || \\============================================================================// @@ -1197,7 +1233,7 @@ || || \\============================================================================// -//=============== Running (20-Jun-2025 14:23:05, pid=1358169) ================\\ +//=============== Running (19-May-2024 10:13:33, pid=1933540) ================\\ || || 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. @@ -1267,7 +1303,7 @@ || Repeat threshold : 100 repeats || || Gapped index : yes || || || -|| Free / total memory : 52.7GB / 58.8GB || +|| Free / total memory : 30.0GB / 58.8GB || || || || Input files : 1 file in total || || o chr901.fa || @@ -1283,30 +1319,30 @@ || 2 uninformative subreads were found. || || These subreads were excluded from index building. || || Estimate the index size... || -|| 8%, 0 mins elapsed, rate=11976.1k bps/s || -|| 16%, 0 mins elapsed, rate=13971.9k bps/s || -|| 25%, 0 mins elapsed, rate=10059.8k bps/s || -|| 33%, 0 mins elapsed, rate=11563.0k bps/s || -|| 41%, 0 mins elapsed, rate=12328.2k bps/s || -|| 50%, 0 mins elapsed, rate=13236.6k bps/s || -|| 58%, 0 mins elapsed, rate=13647.1k bps/s || -|| 66%, 0 mins elapsed, rate=14269.2k bps/s || -|| 75%, 0 mins elapsed, rate=14509.4k bps/s || -|| 83%, 0 mins elapsed, rate=13521.3k bps/s || -|| 91%, 0 mins elapsed, rate=13972.0k bps/s || +|| 8%, 0 mins elapsed, rate=2328.7k bps/s || +|| 16%, 0 mins elapsed, rate=3287.5k bps/s || +|| 25%, 0 mins elapsed, rate=4572.7k bps/s || +|| 33%, 0 mins elapsed, rate=3644.9k bps/s || +|| 41%, 0 mins elapsed, rate=3151.6k bps/s || +|| 50%, 0 mins elapsed, rate=3287.5k bps/s || +|| 58%, 0 mins elapsed, rate=3451.9k bps/s || +|| 66%, 0 mins elapsed, rate=3529.8k bps/s || +|| 75%, 0 mins elapsed, rate=3644.9k bps/s || +|| 83%, 0 mins elapsed, rate=3676.8k bps/s || +|| 91%, 0 mins elapsed, rate=3842.3k bps/s || || 0.8 GB of memory is needed for index building. || || Build the index... || -|| 8%, 0 mins elapsed, rate=578.2k bps/s || -|| 16%, 0 mins elapsed, rate=1110.4k bps/s || -|| 25%, 0 mins elapsed, rate=1591.7k bps/s || -|| 33%, 0 mins elapsed, rate=2044.7k bps/s || -|| 41%, 0 mins elapsed, rate=2315.8k bps/s || -|| 50%, 0 mins elapsed, rate=2689.8k bps/s || -|| 58%, 0 mins elapsed, rate=2994.0k bps/s || -|| 66%, 0 mins elapsed, rate=3320.1k bps/s || -|| 75%, 0 mins elapsed, rate=3575.8k bps/s || -|| 83%, 0 mins elapsed, rate=3776.2k bps/s || -|| 91%, 0 mins elapsed, rate=4044.5k bps/s || +|| 8%, 0 mins elapsed, rate=106.4k bps/s || +|| 16%, 0 mins elapsed, rate=204.0k bps/s || +|| 25%, 0 mins elapsed, rate=278.5k bps/s || +|| 33%, 0 mins elapsed, rate=354.8k bps/s || +|| 41%, 0 mins elapsed, rate=413.0k bps/s || +|| 50%, 0 mins elapsed, rate=479.5k bps/s || +|| 58%, 0 mins elapsed, rate=520.2k bps/s || +|| 66%, 0 mins elapsed, rate=575.2k bps/s || +|| 75%, 0 mins elapsed, rate=612.4k bps/s || +|| 83%, 0 mins elapsed, rate=664.3k bps/s || +|| 91%, 0 mins elapsed, rate=693.9k bps/s || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || @@ -1320,7 +1356,7 @@ || [ 90.0% finished ] || || [ 100.0% finished ] || || || -|| Total running time: 0.0 minutes. || +|| Total running time: 0.1 minutes. || || Index ../small1 was successfully built. || || || \\============================================================================// @@ -1358,7 +1394,7 @@ || || \\============================================================================// -//=============== Running (20-Jun-2025 14:23:07, pid=1358415) ================\\ +//=============== Running (19-May-2024 10:13:42, pid=1934534) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1372,11 +1408,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 41% completed, 0.1 mins elapsed, rate=25.7k fragments per second || +|| 41% completed, 0.3 mins elapsed, rate=3.5k fragments per second || || Estimated fragment length : 173 bp || -|| 77% completed, 0.1 mins elapsed, rate=3.3k fragments per second || -|| 87% completed, 0.1 mins elapsed, rate=3.6k fragments per second || -|| 97% completed, 0.1 mins elapsed, rate=4.0k 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. || || || @@ -1402,7 +1438,7 @@ || Junctions : 419 || || Indels : 177 || || || -|| Running time : 0.1 minutes || +|| Running time : 0.4 minutes || || || \\============================================================================// @@ -1439,7 +1475,7 @@ || || \\============================================================================// -//=============== Running (20-Jun-2025 14:23:11, pid=1359125) ================\\ +//=============== Running (19-May-2024 10:14:03, pid=1936181) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1453,11 +1489,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 41% completed, 0.1 mins elapsed, rate=14.2k fragments per second || +|| 41% completed, 0.3 mins elapsed, rate=2.3k fragments per second || || Estimated fragment length : 174 bp || -|| 77% completed, 0.1 mins elapsed, rate=3.1k fragments per second || -|| 87% completed, 0.1 mins elapsed, rate=3.4k fragments per second || -|| 97% completed, 0.1 mins elapsed, rate=3.7k fragments per second || +|| 77% completed, 0.4 mins elapsed, rate=0.6k fragments per second || +|| 87% completed, 0.4 mins elapsed, rate=0.6k fragments per second || +|| 97% completed, 0.4 mins elapsed, rate=0.7k fragments per second || || || || Completed successfully. || || || @@ -1484,7 +1520,7 @@ || Fusions : 33 || || Indels : 180 || || || -|| Running time : 0.1 minutes || +|| Running time : 0.4 minutes || || || \\============================================================================// @@ -1657,9 +1693,9 @@ || || \\============================================================================// -//====================== Running (20-Jun-2025 14:23:18) ======================\\ +//====================== Running (19-May-2024 10:14:33) ======================\\ || || -|| Split BAM file into result/temp-snps-1361435-64729A075C90-* ... || +|| Split BAM file into result/temp-snps-1938281-7A579ACA7359-* ... || || processed block chr901@999950 by thread 1/1 [block number=1/1] || || || || Completed successfully. || @@ -1672,7 +1708,7 @@ || Reported SNPs : 416 || || Reported indels : 22 || || || -|| Running time : 0.0 minutes || +|| Running time : 0.1 minutes || || || \\============================================================================// @@ -1766,33 +1802,33 @@ 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/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/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/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/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/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/subindel.1 debian/subread/usr/share/man/man1/subjunc.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 + 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/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/exactSNP.1 debian/subread/usr/share/man/man1/featureCounts.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/exactSNP.1.dh-new debian/subread/usr/share/man/man1/exactSNP.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/exactSNP.1 debian/subread/usr/share/man/man1/featureCounts.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 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/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/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 + 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/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/exactSNP.1.dh-new debian/subread/usr/share/man/man1/exactSNP.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/exactSNP.1 debian/subread/usr/share/man/man1/featureCounts.1 dh_installsystemduser -O--buildsystem=makefile dh_perl -O--buildsystem=makefile dh_link -O--buildsystem=makefile @@ -1800,22 +1836,22 @@ Using 1714041519 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-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 + cd debian/subread 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-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-2.0.6+dfsg' + 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 cd '/build/reproducible-path/subread-2.0.6+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-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 f -a -true -a ! -regex 'debian/subread/usr/share/doc/[^/]*/examples/.*' -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-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 -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 @@ -1842,11 +1878,11 @@ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/69/bb2ca97d148b2c8ee517d720bf09b0c3199d28.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/69/bb2ca97d148b2c8ee517d720bf09b0c3199d28.debug debian/subread/usr/lib/subread/repair - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/92 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/92/9d7dc7e9fd5d66d4ff1a3c5b0b03cdbab734af.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/92/9d7dc7e9fd5d66d4ff1a3c5b0b03cdbab734af.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/92/9d7dc7e9fd5d66d4ff1a3c5b0b03cdbab734af.debug debian/subread/usr/lib/subread/removeDup + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bb + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bb/5c8e5ef75d720d0e273fa65b90245e8d18c07d.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bb/5c8e5ef75d720d0e273fa65b90245e8d18c07d.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/bb/5c8e5ef75d720d0e273fa65b90245e8d18c07d.debug debian/subread/usr/lib/subread/propmapped install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0e objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0e/4b49bc638b781cc7356b4ff3d7b3eeed121047.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0e/4b49bc638b781cc7356b4ff3d7b3eeed121047.debug @@ -1857,16 +1893,16 @@ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/20/a5e0f54c768ba366c8e6579038e9a09d260de0.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/20/a5e0f54c768ba366c8e6579038e9a09d260de0.debug debian/subread/usr/lib/subread/genRandomReads + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/92 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/92/9d7dc7e9fd5d66d4ff1a3c5b0b03cdbab734af.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/92/9d7dc7e9fd5d66d4ff1a3c5b0b03cdbab734af.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/92/9d7dc7e9fd5d66d4ff1a3c5b0b03cdbab734af.debug debian/subread/usr/lib/subread/removeDup install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a8 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/flattenGTF debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a8/92d3bb6910a95b7555ae774dacbe9ec6b509b6.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a8/92d3bb6910a95b7555ae774dacbe9ec6b509b6.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/a8/92d3bb6910a95b7555ae774dacbe9ec6b509b6.debug debian/subread/usr/lib/subread/flattenGTF - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bb - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bb/5c8e5ef75d720d0e273fa65b90245e8d18c07d.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bb/5c8e5ef75d720d0e273fa65b90245e8d18c07d.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/bb/5c8e5ef75d720d0e273fa65b90245e8d18c07d.debug debian/subread/usr/lib/subread/propmapped install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0c objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-buildindex debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0c/8cf6c7c75e74dac06b4291ac8ba2961adcb739.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0c/8cf6c7c75e74dac06b4291ac8ba2961adcb739.debug @@ -1887,16 +1923,16 @@ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ac/2092b635ef07cc4244cbc4b2da8ee9bfc7f993.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/ac/2092b635ef07cc4244cbc4b2da8ee9bfc7f993.debug debian/subread/usr/bin/exactSNP - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/db - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/db/0318ef4ab41fc803959a54de83a22cdc11a2f0.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/db/0318ef4ab41fc803959a54de83a22cdc11a2f0.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/db/0318ef4ab41fc803959a54de83a22cdc11a2f0.debug debian/subread/usr/bin/subindel install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f3 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f3/98b563c5f154b324deeb171314131a17185c75.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f3/98b563c5f154b324deeb171314131a17185c75.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/f3/98b563c5f154b324deeb171314131a17185c75.debug debian/subread/usr/bin/subjunc + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/db + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/db/0318ef4ab41fc803959a54de83a22cdc11a2f0.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/db/0318ef4ab41fc803959a54de83a22cdc11a2f0.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/db/0318ef4ab41fc803959a54de83a22cdc11a2f0.debug debian/subread/usr/bin/subindel install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/64 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/64/27c5758f0fa133d04bf43e5266034c3566235d.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/64/27c5758f0fa133d04bf43e5266034c3566235d.debug @@ -1913,38 +1949,38 @@ 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/subread-fullscan debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/genRandomReads 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/exactSNP debian/subread/usr/bin/subindel debian/subread/usr/bin/subjunc debian/subread/usr/bin/sublong + dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/lib/subread/txUnique 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/lib/subread/genRandomReads debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subread-align debian/subread/usr/bin/exactSNP debian/subread/usr/bin/subjunc debian/subread/usr/bin/subindel debian/subread/usr/bin/sublong dh_installdeb -O--buildsystem=makefile install -m0755 -d debian/subread/DEBIAN install -m0755 -d debian/subread-data/DEBIAN dh_gencontrol -O--buildsystem=makefile + install -m0755 -d debian/subread-data/DEBIAN + echo misc:Depends= >> debian/subread-data.substvars + echo misc:Pre-Depends= >> debian/subread-data.substvars + dpkg-gencontrol -psubread-data -ldebian/changelog -Tdebian/subread-data.substvars -cdebian/control -Pdebian/subread-data install -m0755 -d debian/subread/DEBIAN echo misc:Depends= >> debian/subread.substvars echo misc:Pre-Depends= >> debian/subread.substvars install -m0755 -d debian/.debhelper/subread/dbgsym-root/DEBIAN dpkg-gencontrol -psubread -ldebian/changelog -Tdebian/subread.substvars -cdebian/control -Pdebian/.debhelper/subread/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=subread-dbgsym "-DDepends=subread (= \${binary:Version})" "-DDescription=debug symbols for subread" "-DBuild-Ids=0c8cf6c7c75e74dac06b4291ac8ba2961adcb739 0dc4183459c49ee8d62f32fdf6de05348f076fdf 0e4b49bc638b781cc7356b4ff3d7b3eeed121047 20a5e0f54c768ba366c8e6579038e9a09d260de0 2557c676f18b4718b9a0af0a4a1d0562410b8388 6427c5758f0fa133d04bf43e5266034c3566235d 69bb2ca97d148b2c8ee517d720bf09b0c3199d28 748f8fa6f6b2b26225856e43692ab2f32798c693 929d7dc7e9fd5d66d4ff1a3c5b0b03cdbab734af a892d3bb6910a95b7555ae774dacbe9ec6b509b6 ac2092b635ef07cc4244cbc4b2da8ee9bfc7f993 b0529ac7758295d2143e59eb73accfc9e60e6dcd bb5c8e5ef75d720d0e273fa65b90245e8d18c07d db0318ef4ab41fc803959a54de83a22cdc11a2f0 f398b563c5f154b324deeb171314131a17185c75" -DSection=debug -UMulti-Arch -UReplaces -UBreaks - install -m0755 -d debian/subread-data/DEBIAN - echo misc:Depends= >> debian/subread-data.substvars - echo misc:Pre-Depends= >> debian/subread-data.substvars - dpkg-gencontrol -psubread-data -ldebian/changelog -Tdebian/subread-data.substvars -cdebian/control -Pdebian/subread-data chmod 0644 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/control dpkg-gencontrol -psubread -ldebian/changelog -Tdebian/subread.substvars -cdebian/control -Pdebian/subread 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/subread/DEBIAN/control dh_md5sums -O--buildsystem=makefile - install -m0755 -d debian/subread-data/DEBIAN install -m0755 -d debian/subread/DEBIAN - cd debian/subread-data >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums 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 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 .. dpkg-deb --root-owner-group --build debian/subread-data .. dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_2.0.6+dfsg-3_arm64.deb'. dpkg-deb: building package 'subread' in '../subread_2.0.6+dfsg-3_arm64.deb'. @@ -1956,12 +1992,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1747975/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1747975/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/1324575 and its subdirectories -I: Current time: Fri Jun 20 14:24:05 -12 2025 -I: pbuilder-time-stamp: 1750472645 +I: removing directory /srv/workspace/pbuilder/1747975 and its subdirectories +I: Current time: Sun May 19 10:18:09 +14 2024 +I: pbuilder-time-stamp: 1716063489