Diff of the two buildlogs: -- --- b1/build.log 2025-01-10 19:45:37.386761079 +0000 +++ b2/build.log 2025-01-10 20:01:16.419783987 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Feb 12 14:02:00 -12 2026 -I: pbuilder-time-stamp: 1770948120 +I: Current time: Fri Feb 13 16:08:42 +14 2026 +I: pbuilder-time-stamp: 1770948522 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/55943/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1959700/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-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 Feb 13 02:08 /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/1959700/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1959700/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='1e7bd00a023f400a8525d10c8cdea4fc' - 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='55943' - PS1='# ' - PS2='> ' + INVOCATION_ID=7aaa8ac774db4e14b6ae5a0c4ce694f7 + 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=1959700 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.QwNBIXaM/pbuilderrc_gJby --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.QwNBIXaM/b1 --logfile b1/build.log subread_2.0.7+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.QwNBIXaM/pbuilderrc_EjOr --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.QwNBIXaM/b2 --logfile b2/build.log subread_2.0.7+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 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/55943/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/1959700/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -173,7 +205,7 @@ Get: 54 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.23 [919 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] -Fetched 27.6 MB in 0s (83.4 MB/s) +Fetched 27.6 MB in 1s (34.3 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.12-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 ... 19969 files and directories currently installed.) @@ -376,8 +408,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Feb 13 02:02:39 UTC 2026. -Universal Time is now: Fri Feb 13 02:02:39 UTC 2026. +Local time is now: Fri Feb 13 02:09:47 UTC 2026. +Universal Time is now: Fri Feb 13 02:09:47 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -426,7 +458,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/subread-2.0.7+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../subread_2.0.7+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/1959700/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1959700/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/subread-2.0.7+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../subread_2.0.7+dfsg-1_source.changes dpkg-buildpackage: info: source package subread dpkg-buildpackage: info: source version 2.0.7+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -480,10 +516,6 @@ aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-algorithms.o gene-algorithms.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-files.o input-files.c -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sorted-hashtable.o sorted-hashtable.c -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o 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-2.0.7+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=\""2.0.7"\" -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-2.0.7+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=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HelperFunctions.o HelperFunctions.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) @@ -491,20 +523,11 @@ 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-2.0.7+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=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sorted-hashtable.o sorted-hashtable.c +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o 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-2.0.7+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=\""2.0.7"\" -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-2.0.7+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=\""2.0.7"\" -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-2.0.7+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=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o interval_merge.o interval_merge.c -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o long-hashtable.o long-hashtable.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 )) - | ^~ -In file included from gene-value-index.h:24, - from gene-value-index.c:25: -subread.h:142:28: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 142 | #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__) - | ^~~~~~~ -gene-value-index.c:87:41: note: in expansion of macro 'SUBREADprintf' - 87 | SUBREADprintf("INCHRO:%d ; POS:%d\n", ret, pos); - | ^~~~~~~~~~~~~ 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); @@ -517,13 +540,25 @@ 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-2.0.7+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=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.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 )) + | ^~ +In file included from gene-value-index.h:24, + from gene-value-index.c:25: +subread.h:142:28: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 142 | #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__) + | ^~~~~~~ +gene-value-index.c:87:41: note: in expansion of macro 'SUBREADprintf' + 87 | SUBREADprintf("INCHRO:%d ; POS:%d\n", ret, pos); + | ^~~~~~~~~~~~~ +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o long-hashtable.o long-hashtable.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-2.0.7+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=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seek-zlib.o seek-zlib.c -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-blc.o input-blc.c 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); @@ -539,6 +574,7 @@ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: warning: '__builtin___memcpy_chk' writing 256 bytes into a region of size 200 overflows the destination [-Wstringop-overflow=] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-blc.o input-blc.c input-blc.c: In function 'iCache_continuous_read_lanes': input-blc.c:580:59: warning: unused variable 'npos' [-Wunused-variable] 580 | long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET); @@ -560,18 +596,18 @@ aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o detectionCall detection-calls.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm echo " " > longread-one/make.version rm -f longread-one/*.o -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o repair read-repair.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o txUnique tx-unique.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm cd longread-one && make -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o repair read-repair.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm make[3]: Entering directory '/build/reproducible-path/subread-2.0.7+dfsg/src/longread-one' aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMsorted-hashtable.o -c LRMsorted-hashtable.c +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o txUnique tx-unique.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMbase-index.o -c LRMbase-index.c +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o removeDup removeDupReads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMchro-event.o -c LRMchro-event.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o exactSNP SNPCalling.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMbase-index.o -c LRMbase-index.c +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhelper.o -c LRMhelper.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-buildindex index-builder.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMchro-event.o -c LRMchro-event.c -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subindel SUBindel.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm 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); @@ -585,6 +621,38 @@ detection-calls.c:154:48: note: unnamed temporary defined here 154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0}; | ^ +In file included from readSummary.c:41: +readSummary.c: In function 'get_RG_tables': +readSummary.c:2505:31: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] + 2505 | SUBREADprintf("cannot allocate memory for %s (%d)\n", rg_name, strlen(rg_name)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~ + | | + | size_t {aka long unsigned int} +subread.h:142:44: note: in definition of macro 'SUBREADprintf' + 142 | #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__) + | ^~~~~~~~~~~ +readSummary.c:2505:64: note: format string is defined here + 2505 | SUBREADprintf("cannot allocate memory for %s (%d)\n", rg_name, strlen(rg_name)); + | ~^ + | | + | int + | %ld +readSummary.c: In function 'vote_and_add_count': +readSummary.c:3819:58: warning: variable 'assignment_target_number' set but not used [-Wunused-but-set-variable] + 3819 | srInt_64 assignment_target_number = tmp_voter_id; + | ^~~~~~~~~~~~~~~~~~~~~~~~ +readSummary.c: In function 'fc_thread_merge_results': +readSummary.c:3889:32: warning: unused variable 'sample_i' [-Wunused-variable] + 3889 | int xk1, xk2, ret = 0, sample_i; + | ^~~~~~~~ +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subindel SUBindel.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMseek-zlib.o -c LRMseek-zlib.c +readSummary.c: In function 'readSummary': +readSummary.c:5650:52: warning: variable 'scrna_total_BAM_no' set but not used [-Wunused-but-set-variable] + 5650 | int isGTF, n_input_files=0,is_dual_index, scrna_total_BAM_no; + | ^~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMfile-io.o -c LRMfile-io.c 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); @@ -658,22 +726,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -In file included from readSummary.c:41: -readSummary.c: In function 'get_RG_tables': -readSummary.c:2505:31: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] - 2505 | SUBREADprintf("cannot allocate memory for %s (%d)\n", rg_name, strlen(rg_name)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~ - | | - | size_t {aka long unsigned int} -subread.h:142:44: note: in definition of macro 'SUBREADprintf' - 142 | #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__) - | ^~~~~~~~~~~ -readSummary.c:2505:64: note: format string is defined here - 2505 | SUBREADprintf("cannot allocate memory for %s (%d)\n", rg_name, strlen(rg_name)); - | ~^ - | | - | int - | %ld 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'); @@ -690,28 +742,12 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -readSummary.c: In function 'vote_and_add_count': -readSummary.c:3819:58: warning: variable 'assignment_target_number' set but not used [-Wunused-but-set-variable] - 3819 | srInt_64 assignment_target_number = tmp_voter_id; - | ^~~~~~~~~~~~~~~~~~~~~~~~ -readSummary.c: In function 'fc_thread_merge_results': -readSummary.c:3889:32: warning: unused variable 'sample_i' [-Wunused-variable] - 3889 | int xk1, xk2, ret = 0, sample_i; - | ^~~~~~~~ -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -readSummary.c: In function 'readSummary': -readSummary.c:5650:52: warning: variable 'scrna_total_BAM_no' set but not used [-Wunused-but-set-variable] - 5650 | int isGTF, n_input_files=0,is_dual_index, scrna_total_BAM_no; - | ^~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhashtable.o -c LRMhashtable.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhelper.o -c LRMhelper.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-fullscan fullscan.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMseek-zlib.o -c LRMseek-zlib.c -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMfile-io.o -c LRMfile-io.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o flattenGTF flattenAnnotations.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhashtable.o -c LRMhashtable.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.7"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o 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] @@ -783,7 +819,7 @@ || Repeat threshold : 100 repeats || || Gapped index : no || || || -|| Free / total memory : 49.8GB / 58.8GB || +|| Free / total memory : 42.3GB / 58.8GB || || || || Input files : 1 file in total || || o chr901.fa || @@ -799,30 +835,30 @@ || 52 uninformative subreads were found. || || These subreads were excluded from index building. || || Estimate the index size... || -|| 8%, 0 mins elapsed, rate=963.6k bps/s || -|| 16%, 0 mins elapsed, rate=1341.3k bps/s || -|| 25%, 0 mins elapsed, rate=1581.7k bps/s || -|| 33%, 0 mins elapsed, rate=1755.6k bps/s || -|| 41%, 0 mins elapsed, rate=1914.0k bps/s || -|| 50%, 0 mins elapsed, rate=1972.5k bps/s || -|| 58%, 0 mins elapsed, rate=2044.7k bps/s || -|| 66%, 0 mins elapsed, rate=2102.4k bps/s || -|| 75%, 0 mins elapsed, rate=2149.5k bps/s || -|| 83%, 0 mins elapsed, rate=2144.0k bps/s || -|| 91%, 0 mins elapsed, rate=2200.8k bps/s || +|| 8%, 0 mins elapsed, rate=298.3k bps/s || +|| 16%, 0 mins elapsed, rate=477.7k bps/s || +|| 25%, 0 mins elapsed, rate=566.4k bps/s || +|| 33%, 0 mins elapsed, rate=598.8k bps/s || +|| 41%, 0 mins elapsed, rate=649.9k bps/s || +|| 50%, 0 mins elapsed, rate=686.2k bps/s || +|| 58%, 0 mins elapsed, rate=714.8k bps/s || +|| 66%, 0 mins elapsed, rate=740.2k bps/s || +|| 75%, 0 mins elapsed, rate=756.8k bps/s || +|| 83%, 0 mins elapsed, rate=767.7k bps/s || +|| 91%, 0 mins elapsed, rate=780.8k bps/s || || 3.0 GB of memory is needed for index building. || || Build the index... || -|| 8%, 0 mins elapsed, rate=25.6k bps/s || -|| 16%, 0 mins elapsed, rate=50.7k bps/s || -|| 25%, 0 mins elapsed, rate=75.4k bps/s || -|| 33%, 0 mins elapsed, rate=99.4k bps/s || -|| 41%, 0 mins elapsed, rate=122.5k bps/s || -|| 50%, 0 mins elapsed, rate=145.5k bps/s || -|| 58%, 0 mins elapsed, rate=167.4k bps/s || -|| 66%, 0 mins elapsed, rate=188.9k bps/s || -|| 75%, 0 mins elapsed, rate=209.8k bps/s || -|| 83%, 0 mins elapsed, rate=230.2k bps/s || -|| 91%, 0 mins elapsed, rate=250.0k bps/s || +|| 8%, 0 mins elapsed, rate=9.8k bps/s || +|| 16%, 0 mins elapsed, rate=19.2k bps/s || +|| 25%, 0 mins elapsed, rate=28.3k bps/s || +|| 33%, 0 mins elapsed, rate=37.1k bps/s || +|| 41%, 0 mins elapsed, rate=45.8k bps/s || +|| 50%, 0 mins elapsed, rate=54.0k bps/s || +|| 58%, 0 mins elapsed, rate=62.0k bps/s || +|| 66%, 0 mins elapsed, rate=69.7k bps/s || +|| 75%, 0 mins elapsed, rate=77.0k bps/s || +|| 83%, 0 mins elapsed, rate=84.7k bps/s || +|| 91%, 0 mins elapsed, rate=92.3k bps/s || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || @@ -836,7 +872,7 @@ || [ 90.0% finished ] || || [ 100.0% finished ] || || || -|| Total running time: 0.3 minutes. || +|| Total running time: 0.6 minutes. || || Index ../small1 was successfully built. || || || \\============================================================================// @@ -869,7 +905,7 @@ || || \\============================================================================// -//================ Running (12-Feb-2026 14:03:47, pid=70568) =================\\ +//=============== Running (13-Feb-2026 16:12:02, pid=2016601) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -883,10 +919,10 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.8 mins elapsed, rate=43.0k reads per second || -|| 74% completed, 0.8 mins elapsed, rate=0.3k reads per second || -|| 83% completed, 0.8 mins elapsed, rate=0.4k reads per second || -|| 91% completed, 0.8 mins elapsed, rate=0.4k reads per second || +|| 33% completed, 1.7 mins elapsed, rate=20.3k reads per second || +|| 74% completed, 1.7 mins elapsed, rate=0.1k reads per second || +|| 83% completed, 1.7 mins elapsed, rate=0.2k reads per second || +|| 91% completed, 1.7 mins elapsed, rate=0.2k reads per second || || || || Completed successfully. || || || @@ -903,7 +939,7 @@ || || || Indels : 0 || || || -|| Running time : 0.8 minutes || +|| Running time : 1.7 minutes || || || \\============================================================================// @@ -935,7 +971,7 @@ || || \\============================================================================// -//================ Running (12-Feb-2026 14:04:33, pid=73726) =================\\ +//=============== Running (13-Feb-2026 16:13:44, pid=2041246) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -949,10 +985,10 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.5 mins elapsed, rate=67.3k reads per second || -|| 74% completed, 0.5 mins elapsed, rate=0.5k reads per second || -|| 83% completed, 0.5 mins elapsed, rate=0.5k reads per second || -|| 91% completed, 0.5 mins elapsed, rate=0.6k reads per second || +|| 33% completed, 1.8 mins elapsed, rate=11.1k reads per second || +|| 74% completed, 1.8 mins elapsed, rate=0.1k reads per second || +|| 83% completed, 1.8 mins elapsed, rate=0.2k reads per second || +|| 91% completed, 1.8 mins elapsed, rate=0.2k reads per second || || || || Completed successfully. || || || @@ -969,7 +1005,7 @@ || || || Indels : 0 || || || -|| Running time : 0.5 minutes || +|| Running time : 1.8 minutes || || || \\============================================================================// @@ -1006,7 +1042,7 @@ || || \\============================================================================// -//================ Running (12-Feb-2026 14:05:06, pid=75795) =================\\ +//=============== Running (13-Feb-2026 16:15:34, pid=2084171) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1020,11 +1056,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.6 mins elapsed, rate=11.3k fragments per second || +|| 33% completed, 1.8 mins elapsed, rate=8.4k 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=0.5k fragments per second || -|| 91% completed, 0.6 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. || || || @@ -1049,7 +1085,7 @@ || || || Indels : 0 || || || -|| Running time : 0.6 minutes || +|| Running time : 1.9 minutes || || || \\============================================================================// @@ -1086,7 +1122,7 @@ || || \\============================================================================// -//================ Running (12-Feb-2026 14:05:42, pid=78300) =================\\ +//=============== Running (13-Feb-2026 16:17:28, pid=2125709) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1100,11 +1136,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.9 mins elapsed, rate=12.8k fragments per second || +|| 33% completed, 1.6 mins elapsed, rate=8.1k fragments per second || || Estimated fragment length : 495 bp || -|| 74% completed, 0.9 mins elapsed, rate=0.3k fragments per second || -|| 83% completed, 0.9 mins elapsed, rate=0.3k fragments per second || -|| 91% completed, 0.9 mins elapsed, rate=0.3k fragments per second || +|| 74% completed, 1.6 mins elapsed, rate=0.2k fragments per second || +|| 83% completed, 1.6 mins elapsed, rate=0.2k fragments per second || +|| 91% completed, 1.6 mins elapsed, rate=0.2k fragments per second || || || || Completed successfully. || || || @@ -1129,7 +1165,7 @@ || || || Indels : 0 || || || -|| Running time : 0.9 minutes || +|| Running time : 1.6 minutes || || || \\============================================================================// @@ -1166,7 +1202,7 @@ || || \\============================================================================// -//================ Running (12-Feb-2026 14:06:36, pid=82497) =================\\ +//=============== Running (13-Feb-2026 16:19:05, pid=2187470) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1180,11 +1216,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.7 mins elapsed, rate=17.9k fragments per second || +|| 33% completed, 1.7 mins elapsed, rate=4.9k 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, 1.8 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. || || || @@ -1209,7 +1245,7 @@ || || || Indels : 15 || || || -|| Running time : 0.7 minutes || +|| Running time : 1.8 minutes || || || \\============================================================================// @@ -1247,7 +1283,7 @@ || || \\============================================================================// -//================ Running (12-Feb-2026 14:07:16, pid=84709) =================\\ +//=============== Running (13-Feb-2026 16:20:52, pid=2227027) ================\\ || || 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. @@ -1317,7 +1353,7 @@ || Repeat threshold : 100 repeats || || Gapped index : yes || || || -|| Free / total memory : 51.7GB / 58.8GB || +|| Free / total memory : 42.8GB / 58.8GB || || || || Input files : 1 file in total || || o chr901.fa || @@ -1333,30 +1369,30 @@ || 2 uninformative subreads were found. || || These subreads were excluded from index building. || || Estimate the index size... || -|| 8%, 0 mins elapsed, rate=10478.8k bps/s || -|| 16%, 0 mins elapsed, rate=12897.2k bps/s || -|| 25%, 0 mins elapsed, rate=14793.9k bps/s || -|| 33%, 0 mins elapsed, rate=15242.1k bps/s || -|| 41%, 0 mins elapsed, rate=15524.5k bps/s || -|| 50%, 0 mins elapsed, rate=15718.5k bps/s || -|| 58%, 0 mins elapsed, rate=15860.1k bps/s || -|| 66%, 0 mins elapsed, rate=15968.0k bps/s || -|| 75%, 0 mins elapsed, rate=16052.9k bps/s || -|| 83%, 0 mins elapsed, rate=16121.5k bps/s || -|| 91%, 0 mins elapsed, rate=14408.6k bps/s || +|| 8%, 0 mins elapsed, rate=2890.8k bps/s || +|| 16%, 0 mins elapsed, rate=4931.3k bps/s || +|| 25%, 0 mins elapsed, rate=3929.6k bps/s || +|| 33%, 0 mins elapsed, rate=4139.9k bps/s || +|| 41%, 0 mins elapsed, rate=4150.1k bps/s || +|| 50%, 0 mins elapsed, rate=4157.0k bps/s || +|| 58%, 0 mins elapsed, rate=4283.4k bps/s || +|| 66%, 0 mins elapsed, rate=4722.9k bps/s || +|| 75%, 0 mins elapsed, rate=4361.2k bps/s || +|| 83%, 0 mins elapsed, rate=4343.6k bps/s || +|| 91%, 0 mins elapsed, rate=4329.4k bps/s || || 0.8 GB of memory is needed for index building. || || Build the index... || -|| 8%, 0 mins elapsed, rate=350.8k bps/s || -|| 16%, 0 mins elapsed, rate=657.5k bps/s || -|| 25%, 0 mins elapsed, rate=941.9k bps/s || -|| 33%, 0 mins elapsed, rate=1201.9k bps/s || -|| 41%, 0 mins elapsed, rate=1440.4k bps/s || -|| 50%, 0 mins elapsed, rate=1638.4k bps/s || -|| 58%, 0 mins elapsed, rate=1839.6k bps/s || -|| 66%, 0 mins elapsed, rate=2026.2k bps/s || -|| 75%, 0 mins elapsed, rate=2174.3k bps/s || -|| 83%, 0 mins elapsed, rate=2335.2k bps/s || -|| 91%, 0 mins elapsed, rate=2485.6k bps/s || +|| 8%, 0 mins elapsed, rate=172.1k bps/s || +|| 16%, 0 mins elapsed, rate=335.3k bps/s || +|| 25%, 0 mins elapsed, rate=476.3k bps/s || +|| 33%, 0 mins elapsed, rate=609.7k bps/s || +|| 41%, 0 mins elapsed, rate=723.9k bps/s || +|| 50%, 0 mins elapsed, rate=836.9k bps/s || +|| 58%, 0 mins elapsed, rate=951.1k bps/s || +|| 66%, 0 mins elapsed, rate=1038.2k bps/s || +|| 75%, 0 mins elapsed, rate=1127.8k bps/s || +|| 83%, 0 mins elapsed, rate=1227.4k bps/s || +|| 91%, 0 mins elapsed, rate=1317.4k bps/s || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || @@ -1370,7 +1406,7 @@ || [ 90.0% finished ] || || [ 100.0% finished ] || || || -|| Total running time: 0.0 minutes. || +|| Total running time: 0.1 minutes. || || Index ../small1 was successfully built. || || || \\============================================================================// @@ -1408,7 +1444,7 @@ || || \\============================================================================// -//================ Running (12-Feb-2026 14:07:19, pid=84759) =================\\ +//=============== Running (13-Feb-2026 16:20:59, pid=2228775) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1422,11 +1458,11 @@ || 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=4.5k 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=0.8k fragments per second || +|| 97% completed, 0.3 mins elapsed, rate=0.8k fragments per second || || || || Completed successfully. || || || @@ -1452,7 +1488,7 @@ || Junctions : 419 || || Indels : 177 || || || -|| Running time : 0.1 minutes || +|| Running time : 0.3 minutes || || || \\============================================================================// @@ -1489,7 +1525,7 @@ || || \\============================================================================// -//================ Running (12-Feb-2026 14:07:26, pid=84991) =================\\ +//=============== Running (13-Feb-2026 16:21:18, pid=2235032) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1503,11 +1539,11 @@ || 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, 0.2 mins elapsed, rate=4.2k fragments per second || || Estimated fragment length : 174 bp || -|| 77% completed, 0.1 mins elapsed, rate=1.4k fragments per second || -|| 87% completed, 0.1 mins elapsed, rate=1.6k fragments per second || -|| 97% completed, 0.2 mins elapsed, rate=1.7k fragments per second || +|| 77% completed, 0.3 mins elapsed, rate=0.7k fragments per second || +|| 87% completed, 0.3 mins elapsed, rate=0.8k fragments per second || +|| 97% completed, 0.3 mins elapsed, rate=0.9k fragments per second || || || || Completed successfully. || || || @@ -1534,7 +1570,7 @@ || Fusions : 33 || || Indels : 180 || || || -|| Running time : 0.2 minutes || +|| Running time : 0.3 minutes || || || \\============================================================================// @@ -1708,9 +1744,9 @@ || || \\============================================================================// -//====================== Running (12-Feb-2026 14:07:44) ======================\\ +//====================== Running (13-Feb-2026 16:21:51) ======================\\ || || -|| Split BAM file into result/temp-snps-086045-7CDD167CE8B5-* ... || +|| Split BAM file into result/temp-snps-2244231-F0A09277AEDE-* ... || || processed block chr901@999950 by thread 1/1 [block number=1/1] || || || || Completed successfully. || @@ -1723,7 +1759,7 @@ || Reported SNPs : 416 || || Reported indels : 22 || || || -|| Running time : 0.1 minutes || +|| Running time : 0.2 minutes || || || \\============================================================================// @@ -1816,19 +1852,22 @@ 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/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/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 + 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/subindel.1 debian/subread/usr/share/man/man1/subjunc.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/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/sublong.1 debian/subread/usr/share/man/man1/subread-align.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 - 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/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/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 @@ -1838,12 +1877,9 @@ 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/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/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 dh_installsystemduser -O--buildsystem=makefile dh_perl -O--buildsystem=makefile dh_link -O--buildsystem=makefile @@ -1853,10 +1889,10 @@ dh_compress -O--buildsystem=makefile cd debian/subread-data 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 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 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-2.0.7+dfsg' cd '/build/reproducible-path/subread-2.0.7+dfsg' dh_fixperms -O--buildsystem=makefile @@ -1864,10 +1900,10 @@ 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-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-data/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 find debian/subread/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/subread/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w @@ -1883,71 +1919,71 @@ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/35/4c9e65306f4eada614ff5c057b5c16591d7b6c.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/35/4c9e65306f4eada614ff5c057b5c16591d7b6c.debug debian/subread/usr/lib/subread/txUnique - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f6 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/repair debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f6/dcead2b0a158db462d3e7388b7ac81cb48352a.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f6/dcead2b0a158db462d3e7388b7ac81cb48352a.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/f6/dcead2b0a158db462d3e7388b7ac81cb48352a.debug debian/subread/usr/lib/subread/repair - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ef - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ef/c169972f84dda8a37e9bba7ca6e69acce977e4.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ef/c169972f84dda8a37e9bba7ca6e69acce977e4.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/ef/c169972f84dda8a37e9bba7ca6e69acce977e4.debug debian/subread/usr/lib/subread/removeDup install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/87 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/subread-fullscan debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/87/f373cc2d1dafb8f1cb2ceb75ca2927a7a24d5a.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/87/f373cc2d1dafb8f1cb2ceb75ca2927a7a24d5a.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/87/f373cc2d1dafb8f1cb2ceb75ca2927a7a24d5a.debug debian/subread/usr/lib/subread/subread-fullscan + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f6 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/repair debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f6/dcead2b0a158db462d3e7388b7ac81cb48352a.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f6/dcead2b0a158db462d3e7388b7ac81cb48352a.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/f6/dcead2b0a158db462d3e7388b7ac81cb48352a.debug debian/subread/usr/lib/subread/repair 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/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a8/7967aed6806de38d3406057f0e1fc3a480a123.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a8/7967aed6806de38d3406057f0e1fc3a480a123.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/a8/7967aed6806de38d3406057f0e1fc3a480a123.debug debian/subread/usr/lib/subread/qualityScores + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ef + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ef/c169972f84dda8a37e9bba7ca6e69acce977e4.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ef/c169972f84dda8a37e9bba7ca6e69acce977e4.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/ef/c169972f84dda8a37e9bba7ca6e69acce977e4.debug debian/subread/usr/lib/subread/removeDup install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d2 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/genRandomReads debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d2/de57d33df2dafd25ea2bad2091db812f550652.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d2/de57d33df2dafd25ea2bad2091db812f550652.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/d2/de57d33df2dafd25ea2bad2091db812f550652.debug debian/subread/usr/lib/subread/genRandomReads - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1d - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/flattenGTF debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1d/b770f6b40e05c207bde76b0e0e50dc6a371896.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1d/b770f6b40e05c207bde76b0e0e50dc6a371896.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/1d/b770f6b40e05c207bde76b0e0e50dc6a371896.debug debian/subread/usr/lib/subread/flattenGTF install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/69 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/69/3e726b320e05d270b12ebbbb08ceab67605291.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/69/3e726b320e05d270b12ebbbb08ceab67605291.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/69/3e726b320e05d270b12ebbbb08ceab67605291.debug debian/subread/usr/lib/subread/propmapped - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/21 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/featureCounts debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/21/8a86191b9c0fed8d7ca67cc1df1305af62bb6e.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/21/8a86191b9c0fed8d7ca67cc1df1305af62bb6e.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/21/8a86191b9c0fed8d7ca67cc1df1305af62bb6e.debug debian/subread/usr/bin/featureCounts + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1d + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/flattenGTF debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1d/b770f6b40e05c207bde76b0e0e50dc6a371896.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1d/b770f6b40e05c207bde76b0e0e50dc6a371896.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/1d/b770f6b40e05c207bde76b0e0e50dc6a371896.debug debian/subread/usr/lib/subread/flattenGTF install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/13 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-buildindex debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/13/dc8c246b1bcbd2eeae374969c9ac31cdf80b39.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/13/dc8c246b1bcbd2eeae374969c9ac31cdf80b39.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subread-buildindex objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/13/dc8c246b1bcbd2eeae374969c9ac31cdf80b39.debug debian/subread/usr/bin/subread-buildindex - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b3 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b3/8287c090f9df37c51bb9fdacf1c28279863a72.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b3/8287c090f9df37c51bb9fdacf1c28279863a72.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/b3/8287c090f9df37c51bb9fdacf1c28279863a72.debug debian/subread/usr/bin/subindel - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c9 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c9/0d2a5f35e81f7cd5616f54b982a4caeb801912.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c9/0d2a5f35e81f7cd5616f54b982a4caeb801912.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/c9/0d2a5f35e81f7cd5616f54b982a4caeb801912.debug debian/subread/usr/bin/subread-align install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9d objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9d/762dfabdb96f73335bc38237efb06c785fd862.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9d/762dfabdb96f73335bc38237efb06c785fd862.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/9d/762dfabdb96f73335bc38237efb06c785fd862.debug debian/subread/usr/bin/exactSNP + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c9 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c9/0d2a5f35e81f7cd5616f54b982a4caeb801912.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c9/0d2a5f35e81f7cd5616f54b982a4caeb801912.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/c9/0d2a5f35e81f7cd5616f54b982a4caeb801912.debug debian/subread/usr/bin/subread-align install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a7 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a7/fa63b61aa5f493f1aa5b9daa8f09242acd5652.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a7/fa63b61aa5f493f1aa5b9daa8f09242acd5652.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/a7/fa63b61aa5f493f1aa5b9daa8f09242acd5652.debug debian/subread/usr/bin/subjunc + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/21 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/featureCounts debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/21/8a86191b9c0fed8d7ca67cc1df1305af62bb6e.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/21/8a86191b9c0fed8d7ca67cc1df1305af62bb6e.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/21/8a86191b9c0fed8d7ca67cc1df1305af62bb6e.debug debian/subread/usr/bin/featureCounts + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b3 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b3/8287c090f9df37c51bb9fdacf1c28279863a72.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b3/8287c090f9df37c51bb9fdacf1c28279863a72.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/b3/8287c090f9df37c51bb9fdacf1c28279863a72.debug debian/subread/usr/bin/subindel install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/da objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/da/1abd0f8f1df614cfdd17a41f0381824a09c571.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/da/1abd0f8f1df614cfdd17a41f0381824a09c571.debug @@ -1964,7 +2000,7 @@ rm -f debian/subread/DEBIAN/shlibs dh_shlibdeps -a -O--buildsystem=makefile install -m0755 -d debian/subread/DEBIAN - dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/lib/subread/txUnique debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/subread-fullscan 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/featureCounts debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/subindel debian/subread/usr/bin/subread-align debian/subread/usr/bin/exactSNP 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/qualityScores debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/exactSNP debian/subread/usr/bin/subread-align debian/subread/usr/bin/subjunc debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subindel 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 @@ -1973,37 +2009,37 @@ 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=13dc8c246b1bcbd2eeae374969c9ac31cdf80b39 1db770f6b40e05c207bde76b0e0e50dc6a371896 218a86191b9c0fed8d7ca67cc1df1305af62bb6e 354c9e65306f4eada614ff5c057b5c16591d7b6c 693e726b320e05d270b12ebbbb08ceab67605291 87f373cc2d1dafb8f1cb2ceb75ca2927a7a24d5a 9d762dfabdb96f73335bc38237efb06c785fd862 a7fa63b61aa5f493f1aa5b9daa8f09242acd5652 a87967aed6806de38d3406057f0e1fc3a480a123 b38287c090f9df37c51bb9fdacf1c28279863a72 c90d2a5f35e81f7cd5616f54b982a4caeb801912 d2de57d33df2dafd25ea2bad2091db812f550652 da1abd0f8f1df614cfdd17a41f0381824a09c571 efc169972f84dda8a37e9bba7ca6e69acce977e4 f6dcead2b0a158db462d3e7388b7ac81cb48352a" -DSection=debug -UMulti-Arch -UReplaces -UBreaks - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/control - dpkg-gencontrol -psubread -ldebian/changelog -Tdebian/subread.substvars -cdebian/control -Pdebian/subread + 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 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/DEBIAN/control dh_md5sums -O--buildsystem=makefile - 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 + install -m0755 -d debian/subread-data/DEBIAN cd debian/subread >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums - chmod 0644 -- debian/subread-data/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/.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' in '../subread_2.0.7+dfsg-1_arm64.deb'. + dpkg-deb --root-owner-group --build debian/subread .. dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_2.0.7+dfsg-1_arm64.deb'. dpkg-deb: building package 'subread-data' in '../subread-data_2.0.7+dfsg-1_all.deb'. +dpkg-deb: building package 'subread' in '../subread_2.0.7+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../subread_2.0.7+dfsg-1_arm64.buildinfo dpkg-genchanges --build=binary -O../subread_2.0.7+dfsg-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2011,12 +2047,14 @@ 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/1959700/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1959700/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/55943 and its subdirectories -I: Current time: Thu Feb 12 14:08:35 -12 2026 -I: pbuilder-time-stamp: 1770948515 +I: removing directory /srv/workspace/pbuilder/1959700 and its subdirectories +I: Current time: Fri Feb 13 16:24:14 +14 2026 +I: pbuilder-time-stamp: 1770949454