Diff of the two buildlogs: -- --- b1/build.log 2025-03-06 05:43:43.144520621 +0000 +++ b2/build.log 2025-03-06 05:50:20.026481679 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Apr 8 00:02:48 -12 2026 -I: pbuilder-time-stamp: 1775649768 +I: Current time: Thu Mar 6 19:43:47 +14 2025 +I: pbuilder-time-stamp: 1741239827 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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/3921293/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1362745/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Mar 6 05:43 /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/1362745/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1362745/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='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='4c2fe3a1d8a34f37a8713d255b2bb3d9' - 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='3921293' - PS1='# ' - PS2='> ' + INVOCATION_ID=68be2d9082cb4ae2afe6863cbc506305 + 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=1362745 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.vjbawvei/pbuilderrc_FZXX --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.vjbawvei/b1 --logfile b1/build.log subread_2.0.8+dfsg-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.vjbawvei/pbuilderrc_mOg2 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.vjbawvei/b2 --logfile b2/build.log subread_2.0.8+dfsg-1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3921293/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1362745/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -164,7 +196,7 @@ Get: 45 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] -Fetched 27.3 MB in 0s (131 MB/s) +Fetched 27.3 MB in 0s (94.9 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19897 files and directories currently installed.) @@ -334,8 +366,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Apr 8 12:03:16 UTC 2026. -Universal Time is now: Wed Apr 8 12:03:16 UTC 2026. +Local time is now: Thu Mar 6 05:44:24 UTC 2025. +Universal Time is now: Thu Mar 6 05:44:24 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -379,7 +411,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/subread-2.0.8+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../subread_2.0.8+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/1362745/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1362745/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/subread-2.0.8+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../subread_2.0.8+dfsg-1_source.changes dpkg-buildpackage: info: source package subread dpkg-buildpackage: info: source version 2.0.8+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -457,6 +493,10 @@ gene-value-index.c:87:41: note: in expansion of macro 'SUBREADprintf' 87 | SUBREADprintf("INCHRO:%d ; POS:%d\n", ret, pos); | ^~~~~~~~~~~~~ +input-files.c: In function 'reduce_SAM_to_BAM': +input-files.c:3240:13: warning: unused variable 'seq_len' [-Wunused-variable] + 3240 | int seq_len = qual - seq - 1; + | ^~~~~~~ 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); @@ -465,16 +505,14 @@ /usr/include/aarch64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ -input-files.c: In function 'reduce_SAM_to_BAM': -input-files.c:3240:13: warning: unused variable 'seq_len' [-Wunused-variable] - 3240 | int seq_len = qual - seq - 1; - | ^~~~~~~ aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o long-hashtable.o long-hashtable.c +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.c input-files.c: In function 'SAM_pairer_fix_format': input-files.c:4830:50: warning: variable 'readname' set but not used [-Wunused-but-set-variable] 4830 | char tmpfname [MAX_FILE_NAME_LENGTH+14], readname[256]; | ^~~~~~~~ -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.c +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seek-zlib.o seek-zlib.c +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o 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); @@ -490,8 +528,6 @@ /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-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seek-zlib.o seek-zlib.c -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o 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); @@ -513,18 +549,18 @@ aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o detectionCall detection-calls.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm echo " " > longread-one/make.version rm -f longread-one/*.o -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o repair read-repair.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o txUnique tx-unique.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm cd longread-one && make -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o 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 make[3]: Entering directory '/build/reproducible-path/subread-2.0.8+dfsg/src/longread-one' +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o 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-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMsorted-hashtable.o -c LRMsorted-hashtable.c -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o removeDup removeDupReads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o txUnique tx-unique.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMbase-index.o -c LRMbase-index.c -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o exactSNP SNPCalling.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMchro-event.o -c LRMchro-event.c -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o 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-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o removeDup removeDupReads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhelper.o -c LRMhelper.c +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o exactSNP SNPCalling.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-buildindex index-builder.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm detection-calls.c: In function 'DTCwrite_annotations': detection-calls.c:155:109: warning: dangling pointer 'gc_2int' to an unnamed temporary may be used [-Wdangling-pointer=] 155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0); @@ -563,6 +599,8 @@ 3889 | int xk1, xk2, ret = 0, sample_i; | ^~~~~~~~ aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subindel SUBindel.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMseek-zlib.o -c LRMseek-zlib.c +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMfile-io.o -c LRMfile-io.c readSummary.c: In function 'readSummary': readSummary.c:5645:52: warning: variable 'scrna_total_BAM_no' set but not used [-Wunused-but-set-variable] 5645 | int isGTF, n_input_files=0,is_dual_index, scrna_total_BAM_no; @@ -640,12 +678,11 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMseek-zlib.o -c LRMseek-zlib.c +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm SUBindel.c: In function 'load_indexes_forindel': SUBindel.c:110:40: warning: '%02d' directive writing between 2 and 10 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 110 | sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, block_no, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b'); | ^~~~ -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm SUBindel.c:110:36: note: directive argument in the range [0, 2147483646] 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'); | ^~~~~~~~~~~~~~~~~~ @@ -659,7 +696,6 @@ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMfile-io.o -c LRMfile-io.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhashtable.o -c LRMhashtable.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-fullscan fullscan.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm @@ -674,6 +710,7 @@ /usr/include/aarch64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ +make[3]: Leaving directory '/build/reproducible-path/subread-2.0.8+dfsg/src/longread-one' readSummary.c: In function 'vote_and_add_count': readSummary.c:3752:66: warning: 'longest_overlap_score' may be used uninitialized [-Wmaybe-uninitialized] 3752 | if(longest_overlap_score > scoring_numbers[score_x1]) scoring_numbers[score_x1] = 0; @@ -681,7 +718,6 @@ readSummary.c:3521:51: note: 'longest_overlap_score' was declared here 3521 | int scoring_count = 0, score_x1, longest_overlap_score; | ^~~~~~~~~~~~~~~~~~~~~ -make[3]: Leaving directory '/build/reproducible-path/subread-2.0.8+dfsg/src/longread-one' mkdir -p ../bin/utilities mv longread-one/LRM longread-one/sublong mv longread-one/sublong subread-align subjunc featureCounts subindel exactSNP subread-buildindex ../bin/ @@ -736,7 +772,7 @@ || Repeat threshold : 100 repeats || || Gapped index : no || || || -|| Free / total memory : 51.8GB / 58.8GB || +|| Free / total memory : 45.9GB / 58.8GB || || || || Input files : 1 file in total || || o chr901.fa || @@ -752,30 +788,30 @@ || 52 uninformative subreads were found. || || These subreads were excluded from index building. || || Estimate the index size... || -|| 8%, 0 mins elapsed, rate=2540.4k bps/s || +|| 8%, 0 mins elapsed, rate=2465.7k bps/s || || 16%, 0 mins elapsed, rate=3810.5k bps/s || -|| 25%, 0 mins elapsed, rate=4657.3k bps/s || -|| 33%, 0 mins elapsed, rate=5239.5k bps/s || -|| 41%, 0 mins elapsed, rate=5588.8k bps/s || -|| 50%, 0 mins elapsed, rate=5917.6k bps/s || -|| 58%, 0 mins elapsed, rate=6177.1k bps/s || -|| 66%, 0 mins elapsed, rate=6326.9k bps/s || -|| 75%, 0 mins elapsed, rate=6504.2k bps/s || -|| 83%, 0 mins elapsed, rate=6600.9k bps/s || -|| 91%, 0 mins elapsed, rate=6731.0k bps/s || +|| 25%, 0 mins elapsed, rate=3992.0k bps/s || +|| 33%, 0 mins elapsed, rate=4593.5k bps/s || +|| 41%, 0 mins elapsed, rate=4990.0k bps/s || +|| 50%, 0 mins elapsed, rate=5351.0k bps/s || +|| 58%, 0 mins elapsed, rate=5642.5k bps/s || +|| 66%, 0 mins elapsed, rate=5588.8k bps/s || +|| 75%, 0 mins elapsed, rate=5803.7k bps/s || +|| 83%, 0 mins elapsed, rate=5945.5k bps/s || +|| 91%, 0 mins elapsed, rate=6107.0k bps/s || || 3.0 GB of memory is needed for index building. || || Build the index... || -|| 8%, 0 mins elapsed, rate=92.5k bps/s || -|| 16%, 0 mins elapsed, rate=181.5k bps/s || -|| 25%, 0 mins elapsed, rate=267.3k bps/s || -|| 33%, 0 mins elapsed, rate=350.0k bps/s || -|| 41%, 0 mins elapsed, rate=429.5k bps/s || -|| 50%, 0 mins elapsed, rate=506.5k bps/s || -|| 58%, 0 mins elapsed, rate=580.4k bps/s || -|| 66%, 0 mins elapsed, rate=652.4k bps/s || -|| 75%, 0 mins elapsed, rate=721.3k bps/s || -|| 83%, 0 mins elapsed, rate=787.9k bps/s || -|| 91%, 0 mins elapsed, rate=852.3k bps/s || +|| 8%, 0 mins elapsed, rate=52.2k bps/s || +|| 16%, 0 mins elapsed, rate=101.1k bps/s || +|| 25%, 0 mins elapsed, rate=147.3k bps/s || +|| 33%, 0 mins elapsed, rate=191.0k bps/s || +|| 41%, 0 mins elapsed, rate=231.5k bps/s || +|| 50%, 0 mins elapsed, rate=270.0k bps/s || +|| 58%, 0 mins elapsed, rate=306.9k bps/s || +|| 66%, 0 mins elapsed, rate=341.0k bps/s || +|| 75%, 0 mins elapsed, rate=373.7k bps/s || +|| 83%, 0 mins elapsed, rate=404.8k bps/s || +|| 91%, 0 mins elapsed, rate=434.4k bps/s || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || @@ -789,7 +825,7 @@ || [ 90.0% finished ] || || [ 100.0% finished ] || || || -|| Total running time: 0.1 minutes. || +|| Total running time: 0.2 minutes. || || Index ../small1 was successfully built. || || || \\============================================================================// @@ -822,7 +858,7 @@ || || \\============================================================================// -//=============== Running (08-Apr-2026 00:03:53, pid=3923960) ================\\ +//=============== Running (06-Mar-2025 19:45:30, pid=1379815) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -836,10 +872,10 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.4 mins elapsed, rate=82.3k reads per second || -|| 74% completed, 0.4 mins elapsed, rate=0.6k reads per second || -|| 83% completed, 0.4 mins elapsed, rate=0.7k reads per second || -|| 91% completed, 0.4 mins elapsed, rate=0.7k reads per second || +|| 33% completed, 0.8 mins elapsed, rate=33.0k reads per second || +|| 74% completed, 0.8 mins elapsed, rate=0.3k reads per second || +|| 83% completed, 0.8 mins elapsed, rate=0.3k reads per second || +|| 91% completed, 0.9 mins elapsed, rate=0.4k reads per second || || || || Completed successfully. || || || @@ -856,7 +892,7 @@ || || || Indels : 0 || || || -|| Running time : 0.4 minutes || +|| Running time : 0.9 minutes || || || \\============================================================================// @@ -888,7 +924,7 @@ || || \\============================================================================// -//=============== Running (08-Apr-2026 00:04:18, pid=3924115) ================\\ +//=============== Running (06-Mar-2025 19:46:21, pid=1387168) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -902,10 +938,10 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.4 mins elapsed, rate=79.4k reads per second || -|| 74% completed, 0.4 mins elapsed, rate=0.6k reads per second || -|| 83% completed, 0.4 mins elapsed, rate=0.7k reads per second || -|| 91% completed, 0.4 mins elapsed, rate=0.7k reads per second || +|| 33% completed, 0.7 mins elapsed, rate=81.3k reads per second || +|| 74% completed, 0.7 mins elapsed, rate=0.4k reads per second || +|| 83% completed, 0.7 mins elapsed, rate=0.4k reads per second || +|| 91% completed, 0.7 mins elapsed, rate=0.5k reads per second || || || || Completed successfully. || || || @@ -922,7 +958,7 @@ || || || Indels : 0 || || || -|| Running time : 0.4 minutes || +|| Running time : 0.7 minutes || || || \\============================================================================// @@ -959,7 +995,7 @@ || || \\============================================================================// -//=============== Running (08-Apr-2026 00:04:42, pid=3924477) ================\\ +//=============== Running (06-Mar-2025 19:47:01, pid=1393224) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -973,11 +1009,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.4 mins elapsed, rate=38.8k fragments per second || +|| 33% completed, 0.9 mins elapsed, rate=22.8k fragments per second || || Estimated fragment length : 495 bp || -|| 74% completed, 0.4 mins elapsed, rate=0.6k fragments per second || -|| 83% completed, 0.4 mins elapsed, rate=0.7k fragments per second || -|| 91% completed, 0.4 mins elapsed, rate=0.7k fragments per second || +|| 74% completed, 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=0.4k fragments per second || || || || Completed successfully. || || || @@ -1002,7 +1038,7 @@ || || || Indels : 0 || || || -|| Running time : 0.4 minutes || +|| Running time : 0.9 minutes || || || \\============================================================================// @@ -1039,7 +1075,7 @@ || || \\============================================================================// -//=============== Running (08-Apr-2026 00:05:07, pid=3924493) ================\\ +//=============== Running (06-Mar-2025 19:47:54, pid=1399301) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1053,11 +1089,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.4 mins elapsed, rate=39.0k fragments per second || +|| 33% completed, 0.9 mins elapsed, rate=15.3k fragments per second || || Estimated fragment length : 495 bp || -|| 74% completed, 0.4 mins elapsed, rate=0.6k fragments per second || -|| 83% completed, 0.4 mins elapsed, rate=0.7k fragments per second || -|| 91% completed, 0.4 mins elapsed, rate=0.7k fragments per second || +|| 74% completed, 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 || || || || Completed successfully. || || || @@ -1082,7 +1118,7 @@ || || || Indels : 0 || || || -|| Running time : 0.4 minutes || +|| Running time : 0.9 minutes || || || \\============================================================================// @@ -1119,7 +1155,7 @@ || || \\============================================================================// -//=============== Running (08-Apr-2026 00:05:32, pid=3924611) ================\\ +//=============== Running (06-Mar-2025 19:48:48, pid=1409000) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1133,11 +1169,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.4 mins elapsed, rate=41.9k fragments per second || +|| 33% completed, 0.5 mins elapsed, rate=40.4k fragments per second || || Estimated fragment length : 497 bp || -|| 74% completed, 0.4 mins elapsed, rate=0.6k fragments per second || -|| 83% completed, 0.4 mins elapsed, rate=0.7k fragments per second || -|| 91% completed, 0.4 mins elapsed, rate=0.7k fragments per second || +|| 74% completed, 0.5 mins elapsed, rate=0.5k fragments per second || +|| 83% completed, 0.5 mins elapsed, rate=0.5k fragments per second || +|| 91% completed, 0.5 mins elapsed, rate=0.6k fragments per second || || || || Completed successfully. || || || @@ -1162,7 +1198,7 @@ || || || Indels : 15 || || || -|| Running time : 0.4 minutes || +|| Running time : 0.5 minutes || || || \\============================================================================// @@ -1200,7 +1236,7 @@ || || \\============================================================================// -//=============== Running (08-Apr-2026 00:05:58, pid=3925519) ================\\ +//=============== Running (06-Mar-2025 19:49:20, pid=1419894) ================\\ || || ERROR: unable to open file 'data/test-err-mut-r1.fq.gz'. File name might be incorrect, or you do not have the permission to read the file. ERROR: unable to open file 'data/test-err-mut-r2.fq.gz'. File name might be incorrect, or you do not have the permission to read the file. @@ -1270,7 +1306,7 @@ || Repeat threshold : 100 repeats || || Gapped index : yes || || || -|| Free / total memory : 52.0GB / 58.8GB || +|| Free / total memory : 51.6GB / 58.8GB || || || || Input files : 1 file in total || || o chr901.fa || @@ -1286,30 +1322,30 @@ || 2 uninformative subreads were found. || || These subreads were excluded from index building. || || Estimate the index size... || -|| 8%, 0 mins elapsed, rate=10478.8k bps/s || -|| 16%, 0 mins elapsed, rate=13971.9k bps/s || +|| 8%, 0 mins elapsed, rate=11976.1k bps/s || +|| 16%, 0 mins elapsed, rate=13972.2k bps/s || || 25%, 0 mins elapsed, rate=15718.5k bps/s || -|| 33%, 0 mins elapsed, rate=15968.1k bps/s || -|| 41%, 0 mins elapsed, rate=16766.3k bps/s || -|| 50%, 0 mins elapsed, rate=17344.5k bps/s || -|| 58%, 0 mins elapsed, rate=17259.6k bps/s || -|| 66%, 0 mins elapsed, rate=17196.3k bps/s || -|| 75%, 0 mins elapsed, rate=17546.2k bps/s || -|| 83%, 0 mins elapsed, rate=17465.0k bps/s || -|| 91%, 0 mins elapsed, rate=17733.7k bps/s || +|| 33%, 0 mins elapsed, rate=16766.4k bps/s || +|| 41%, 0 mins elapsed, rate=17465.1k bps/s || +|| 50%, 0 mins elapsed, rate=17344.7k bps/s || +|| 58%, 0 mins elapsed, rate=17782.5k bps/s || +|| 66%, 0 mins elapsed, rate=18125.9k bps/s || +|| 75%, 0 mins elapsed, rate=18402.2k bps/s || +|| 83%, 0 mins elapsed, rate=18629.4k bps/s || +|| 91%, 0 mins elapsed, rate=18443.1k bps/s || || 0.8 GB of memory is needed for index building. || || Build the index... || -|| 8%, 0 mins elapsed, rate=698.6k bps/s || -|| 16%, 0 mins elapsed, rate=1330.7k bps/s || -|| 25%, 0 mins elapsed, rate=1890.9k bps/s || -|| 33%, 0 mins elapsed, rate=2412.4k bps/s || -|| 41%, 0 mins elapsed, rate=2890.8k bps/s || -|| 50%, 0 mins elapsed, rate=3309.2k bps/s || -|| 58%, 0 mins elapsed, rate=3714.1k bps/s || -|| 66%, 0 mins elapsed, rate=4089.4k bps/s || -|| 75%, 0 mins elapsed, rate=4412.2k bps/s || -|| 83%, 0 mins elapsed, rate=4736.3k bps/s || -|| 91%, 0 mins elapsed, rate=5011.7k bps/s || +|| 8%, 0 mins elapsed, rate=716.5k bps/s || +|| 16%, 0 mins elapsed, rate=1363.1k bps/s || +|| 25%, 0 mins elapsed, rate=1934.6k bps/s || +|| 33%, 0 mins elapsed, rate=2465.6k bps/s || +|| 41%, 0 mins elapsed, rate=2951.8k bps/s || +|| 50%, 0 mins elapsed, rate=3398.6k bps/s || +|| 58%, 0 mins elapsed, rate=3810.5k bps/s || +|| 66%, 0 mins elapsed, rate=4191.6k bps/s || +|| 75%, 0 mins elapsed, rate=4545.1k bps/s || +|| 83%, 0 mins elapsed, rate=4845.8k bps/s || +|| 91%, 0 mins elapsed, rate=5151.7k bps/s || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || @@ -1361,7 +1397,7 @@ || || \\============================================================================// -//=============== Running (08-Apr-2026 00:05:59, pid=3926388) ================\\ +//=============== Running (06-Mar-2025 19:49:21, pid=1420872) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1375,11 +1411,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 41% completed, 0.1 mins elapsed, rate=26.7k fragments per second || +|| 41% completed, 0.1 mins elapsed, rate=26.0k fragments per second || || Estimated fragment length : 173 bp || -|| 77% completed, 0.1 mins elapsed, rate=3.4k fragments per second || +|| 77% completed, 0.1 mins elapsed, rate=3.3k fragments per second || || 87% completed, 0.1 mins elapsed, rate=3.7k fragments per second || -|| 97% completed, 0.1 mins elapsed, rate=4.1k fragments per second || +|| 97% completed, 0.1 mins elapsed, rate=4.0k fragments per second || || || || Completed successfully. || || || @@ -1442,7 +1478,7 @@ || || \\============================================================================// -//=============== Running (08-Apr-2026 00:06:03, pid=3927479) ================\\ +//=============== Running (06-Mar-2025 19:49:25, pid=1424234) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1456,11 +1492,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 41% completed, 0.1 mins elapsed, rate=15.1k fragments per second || +|| 41% completed, 0.1 mins elapsed, rate=12.7k fragments per second || || Estimated fragment length : 174 bp || -|| 77% completed, 0.1 mins elapsed, rate=3.1k fragments per second || -|| 87% completed, 0.1 mins elapsed, rate=3.4k fragments per second || -|| 97% completed, 0.1 mins elapsed, rate=3.7k fragments per second || +|| 77% completed, 0.1 mins elapsed, rate=3.0k fragments per second || +|| 87% completed, 0.1 mins elapsed, rate=3.2k fragments per second || +|| 97% completed, 0.1 mins elapsed, rate=3.5k fragments per second || || || || Completed successfully. || || || @@ -1661,9 +1697,9 @@ || || \\============================================================================// -//====================== Running (08-Apr-2026 00:06:08) ======================\\ +//====================== Running (06-Mar-2025 19:49:35) ======================\\ || || -|| Split BAM file into result/temp-snps-3931205-49DB981749A9-* ... || +|| Split BAM file into result/temp-snps-1430309-963FAEA94794-* ... || || processed block chr901@999950 by thread 1/1 [block number=1/1] || || || || Completed successfully. || @@ -1769,34 +1805,34 @@ 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/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/removeDup.1 debian/subread/usr/share/man/man1/repair.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/exactSNP.1 debian/subread/usr/share/man/man1/featureCounts.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/flattenGTF.1 debian/subread/usr/share/man/man1/genRandomReads.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/propmapped.1 debian/subread/usr/share/man/man1/qualityScores.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/removeDup.1 debian/subread/usr/share/man/man1/repair.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/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/sublong.1 debian/subread/usr/share/man/man1/subread-align.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 debian/subread/usr/share/man/man1/subread-fullscan.1 - mv debian/subread/usr/share/man/man1/propmapped.1.dh-new debian/subread/usr/share/man/man1/propmapped.1 - mv debian/subread/usr/share/man/man1/qualityScores.1.dh-new debian/subread/usr/share/man/man1/qualityScores.1 - chmod 0644 -- debian/subread/usr/share/man/man1/propmapped.1 debian/subread/usr/share/man/man1/qualityScores.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/sublong.1 debian/subread/usr/share/man/man1/subread-align.1 + mv debian/subread/usr/share/man/man1/subread-buildindex.1.dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 + mv debian/subread/usr/share/man/man1/subread-fullscan.1.dh-new debian/subread/usr/share/man/man1/subread-fullscan.1 + chmod 0644 -- debian/subread/usr/share/man/man1/subread-buildindex.1 debian/subread/usr/share/man/man1/subread-fullscan.1 mv debian/subread/usr/share/man/man1/exactSNP.1.dh-new debian/subread/usr/share/man/man1/exactSNP.1 mv debian/subread/usr/share/man/man1/featureCounts.1.dh-new debian/subread/usr/share/man/man1/featureCounts.1 chmod 0644 -- debian/subread/usr/share/man/man1/exactSNP.1 debian/subread/usr/share/man/man1/featureCounts.1 mv debian/subread/usr/share/man/man1/subindel.1.dh-new debian/subread/usr/share/man/man1/subindel.1 mv debian/subread/usr/share/man/man1/subjunc.1.dh-new debian/subread/usr/share/man/man1/subjunc.1 chmod 0644 -- debian/subread/usr/share/man/man1/subindel.1 debian/subread/usr/share/man/man1/subjunc.1 - mv debian/subread/usr/share/man/man1/subread-buildindex.1.dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 - mv debian/subread/usr/share/man/man1/subread-fullscan.1.dh-new debian/subread/usr/share/man/man1/subread-fullscan.1 - chmod 0644 -- debian/subread/usr/share/man/man1/subread-buildindex.1 debian/subread/usr/share/man/man1/subread-fullscan.1 + mv debian/subread/usr/share/man/man1/removeDup.1.dh-new debian/subread/usr/share/man/man1/removeDup.1 + mv debian/subread/usr/share/man/man1/repair.1.dh-new debian/subread/usr/share/man/man1/repair.1 + chmod 0644 -- debian/subread/usr/share/man/man1/removeDup.1 debian/subread/usr/share/man/man1/repair.1 mv debian/subread/usr/share/man/man1/sublong.1.dh-new debian/subread/usr/share/man/man1/sublong.1 mv debian/subread/usr/share/man/man1/subread-align.1.dh-new debian/subread/usr/share/man/man1/subread-align.1 chmod 0644 -- debian/subread/usr/share/man/man1/sublong.1 debian/subread/usr/share/man/man1/subread-align.1 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/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 dh_installsystemduser -O--buildsystem=makefile dh_perl -O--buildsystem=makefile dh_link -O--buildsystem=makefile @@ -1804,8 +1840,8 @@ Using 1741180806 as canonical time Normalizing debian/subread-data/usr/share/doc/subread/examples/annotation/mm39_RefSeq_exon.txt.gz using File::StripNondeterminism::handlers::gzip dh_compress -O--buildsystem=makefile - cd debian/subread-data cd debian/subread + cd debian/subread-data chmod a-x usr/share/doc/subread-data/changelog.Debian usr/share/doc/subread/examples/annotation/hg19_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/hg38_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm10_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm9_RefSeq_exon.txt chmod a-x usr/share/doc/subread/changelog.Debian usr/share/man/man1/exactSNP.1 usr/share/man/man1/featureCounts.1 usr/share/man/man1/flattenGTF.1 usr/share/man/man1/genRandomReads.1 usr/share/man/man1/propmapped.1 usr/share/man/man1/qualityScores.1 usr/share/man/man1/removeDup.1 usr/share/man/man1/repair.1 usr/share/man/man1/subindel.1 usr/share/man/man1/subjunc.1 usr/share/man/man1/sublong.1 usr/share/man/man1/subread-align.1 usr/share/man/man1/subread-buildindex.1 usr/share/man/man1/subread-fullscan.1 gzip -9nf usr/share/doc/subread-data/changelog.Debian usr/share/doc/subread/examples/annotation/hg19_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/hg38_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm10_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm9_RefSeq_exon.txt @@ -1815,12 +1851,12 @@ dh_fixperms -O--buildsystem=makefile find debian/subread ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/subread-data ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s - find debian/subread/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 f -a -true -a ! -regex 'debian/subread/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 - find debian/subread-data -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 @@ -1831,16 +1867,16 @@ objcopy --compress-debug-sections debian/subread/usr/lib/debug/.dwz/aarch64-linux-gnu/subread.debug chmod 0644 -- debian/subread/usr/lib/debug/.dwz/aarch64-linux-gnu/subread.debug dh_strip -a -O--buildsystem=makefile - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/8d - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/subread-fullscan debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/8d/801c76350969fb93e3e1d41860156a37bfb61e.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/8d/801c76350969fb93e3e1d41860156a37bfb61e.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/8d/801c76350969fb93e3e1d41860156a37bfb61e.debug debian/subread/usr/lib/subread/subread-fullscan install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/41 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/txUnique debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/41/6412898f6c3dcd0e042207d0903355bd604d69.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/41/6412898f6c3dcd0e042207d0903355bd604d69.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/41/6412898f6c3dcd0e042207d0903355bd604d69.debug debian/subread/usr/lib/subread/txUnique + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/8d + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/subread-fullscan debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/8d/801c76350969fb93e3e1d41860156a37bfb61e.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/8d/801c76350969fb93e3e1d41860156a37bfb61e.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/8d/801c76350969fb93e3e1d41860156a37bfb61e.debug debian/subread/usr/lib/subread/subread-fullscan install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6f objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/repair debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6f/018bbd9200bed3974f9135ce480fbe7b3ff6dd.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6f/018bbd9200bed3974f9135ce480fbe7b3ff6dd.debug @@ -1851,6 +1887,16 @@ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/37/7f41a4b58ab574648ecf365f687047ca629cc6.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/37/7f41a4b58ab574648ecf365f687047ca629cc6.debug debian/subread/usr/lib/subread/removeDup + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/43 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/43/4b9fb04a8a2dbd1fa7e7987fe4efadba78ee74.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/43/4b9fb04a8a2dbd1fa7e7987fe4efadba78ee74.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/43/4b9fb04a8a2dbd1fa7e7987fe4efadba78ee74.debug debian/subread/usr/lib/subread/qualityScores + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ac + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ac/2e18f5d084e0b4c688c8e5da7c32c002b54fa6.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ac/2e18f5d084e0b4c688c8e5da7c32c002b54fa6.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/ac/2e18f5d084e0b4c688c8e5da7c32c002b54fa6.debug debian/subread/usr/lib/subread/propmapped install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bd objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/genRandomReads debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bd/5fa1a69f757447eb64b4de01d6e0dd3b12fcc1.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bd/5fa1a69f757447eb64b4de01d6e0dd3b12fcc1.debug @@ -1861,16 +1907,6 @@ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9f/f55c96886a27aa309b45a81d04e61b09547333.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/9f/f55c96886a27aa309b45a81d04e61b09547333.debug debian/subread/usr/lib/subread/flattenGTF - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ac - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ac/2e18f5d084e0b4c688c8e5da7c32c002b54fa6.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ac/2e18f5d084e0b4c688c8e5da7c32c002b54fa6.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/ac/2e18f5d084e0b4c688c8e5da7c32c002b54fa6.debug debian/subread/usr/lib/subread/propmapped - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/43 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/43/4b9fb04a8a2dbd1fa7e7987fe4efadba78ee74.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/43/4b9fb04a8a2dbd1fa7e7987fe4efadba78ee74.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/43/4b9fb04a8a2dbd1fa7e7987fe4efadba78ee74.debug debian/subread/usr/lib/subread/qualityScores install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e7 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-buildindex debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e7/5170fee8db79c5fbc1a3fbd55d7b3aafdfb7e1.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e7/5170fee8db79c5fbc1a3fbd55d7b3aafdfb7e1.debug @@ -1881,26 +1917,26 @@ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/32/b35bb01fdd45d734b02ca8942e4f88aae519b6.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/32/b35bb01fdd45d734b02ca8942e4f88aae519b6.debug debian/subread/usr/bin/featureCounts - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/24 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/24/1d5648a78871d27d906f4d7110907a7a96be17.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/24/1d5648a78871d27d906f4d7110907a7a96be17.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/24/1d5648a78871d27d906f4d7110907a7a96be17.debug debian/subread/usr/bin/subread-align install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a4 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a4/126c8f0ef07ea579a2511433343032ba5eb1a0.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a4/126c8f0ef07ea579a2511433343032ba5eb1a0.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/a4/126c8f0ef07ea579a2511433343032ba5eb1a0.debug debian/subread/usr/bin/exactSNP - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d5 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d5/e396d3758548648599b635c9b8ac79b6cdcd73.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d5/e396d3758548648599b635c9b8ac79b6cdcd73.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subjunc - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d5/e396d3758548648599b635c9b8ac79b6cdcd73.debug debian/subread/usr/bin/subjunc + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/24 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/24/1d5648a78871d27d906f4d7110907a7a96be17.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/24/1d5648a78871d27d906f4d7110907a7a96be17.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/24/1d5648a78871d27d906f4d7110907a7a96be17.debug debian/subread/usr/bin/subread-align install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/03 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/03/acf66d4a9cc5e0e45a5ff9f08f38439425edf2.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/03/acf66d4a9cc5e0e45a5ff9f08f38439425edf2.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/03/acf66d4a9cc5e0e45a5ff9f08f38439425edf2.debug debian/subread/usr/bin/subindel + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d5 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d5/e396d3758548648599b635c9b8ac79b6cdcd73.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d5/e396d3758548648599b635c9b8ac79b6cdcd73.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subjunc + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d5/e396d3758548648599b635c9b8ac79b6cdcd73.debug debian/subread/usr/bin/subjunc install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b0 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b0/6f24ff3642d62804f9afbc1368864bfaad0182.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b0/6f24ff3642d62804f9afbc1368864bfaad0182.debug @@ -1917,7 +1953,7 @@ rm -f debian/subread/DEBIAN/shlibs dh_shlibdeps -a -O--buildsystem=makefile install -m0755 -d debian/subread/DEBIAN - dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/txUnique debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/qualityScores debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subread-align debian/subread/usr/bin/exactSNP debian/subread/usr/bin/subjunc debian/subread/usr/bin/subindel debian/subread/usr/bin/sublong + dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/lib/subread/txUnique debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/featureCounts debian/subread/usr/bin/exactSNP debian/subread/usr/bin/subread-align debian/subread/usr/bin/subindel debian/subread/usr/bin/subjunc debian/subread/usr/bin/sublong dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect @@ -1935,10 +1971,10 @@ 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=03acf66d4a9cc5e0e45a5ff9f08f38439425edf2 241d5648a78871d27d906f4d7110907a7a96be17 32b35bb01fdd45d734b02ca8942e4f88aae519b6 377f41a4b58ab574648ecf365f687047ca629cc6 416412898f6c3dcd0e042207d0903355bd604d69 434b9fb04a8a2dbd1fa7e7987fe4efadba78ee74 6f018bbd9200bed3974f9135ce480fbe7b3ff6dd 8d801c76350969fb93e3e1d41860156a37bfb61e 9ff55c96886a27aa309b45a81d04e61b09547333 a4126c8f0ef07ea579a2511433343032ba5eb1a0 ac2e18f5d084e0b4c688c8e5da7c32c002b54fa6 b06f24ff3642d62804f9afbc1368864bfaad0182 bd5fa1a69f757447eb64b4de01d6e0dd3b12fcc1 d5e396d3758548648599b635c9b8ac79b6cdcd73 e75170fee8db79c5fbc1a3fbd55d7b3aafdfb7e1" -DSection=debug -UMulti-Arch -UReplaces -UBreaks -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 +dpkg-gencontrol: warning: Depends field of package subread-data: substitution variable ${shlibs:Depends} used, but is not defined + chmod 0644 -- debian/subread-data/DEBIAN/control chmod 0644 -- debian/subread/DEBIAN/control dh_md5sums -O--buildsystem=makefile install -m0755 -d debian/subread-data/DEBIAN @@ -1951,12 +1987,12 @@ chmod 0644 -- debian/subread-data/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/md5sums dh_builddeb -O--buildsystem=makefile + dpkg-deb --root-owner-group --build debian/subread .. dpkg-deb --root-owner-group --build debian/.debhelper/subread/dbgsym-root .. dpkg-deb --root-owner-group --build debian/subread-data .. - dpkg-deb --root-owner-group --build debian/subread .. +dpkg-deb: building package 'subread' in '../subread_2.0.8+dfsg-1_arm64.deb'. dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_2.0.8+dfsg-1_arm64.deb'. dpkg-deb: building package 'subread-data' in '../subread-data_2.0.8+dfsg-1_all.deb'. -dpkg-deb: building package 'subread' in '../subread_2.0.8+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../subread_2.0.8+dfsg-1_arm64.buildinfo dpkg-genchanges --build=binary -O../subread_2.0.8+dfsg-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1964,12 +2000,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1362745/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1362745/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/3921293 and its subdirectories -I: Current time: Wed Apr 8 00:06:41 -12 2026 -I: pbuilder-time-stamp: 1775650001 +I: removing directory /srv/workspace/pbuilder/1362745 and its subdirectories +I: Current time: Thu Mar 6 19:50:18 +14 2025 +I: pbuilder-time-stamp: 1741240218