Diff of the two buildlogs: -- --- b1/build.log 2025-03-09 01:01:03.510889878 +0000 +++ b2/build.log 2025-03-09 01:09:25.420266246 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Apr 10 19:16:30 -12 2026 -I: pbuilder-time-stamp: 1775891790 +I: Current time: Sun Mar 9 15:01:06 +14 2025 +I: pbuilder-time-stamp: 1741482066 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/374784/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/817158/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Mar 9 01:01 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/817158/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/817158/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='f8fdf4f7bd4845d8a16b55d7faf7c8a5' - 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='374784' - PS1='# ' - PS2='> ' + INVOCATION_ID=a697d3395c8a4020bb69d8d9b8efebfd + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=817158 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.HHfEzPHc/pbuilderrc_zZHD --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.HHfEzPHc/b1 --logfile b1/build.log subread_2.0.8+dfsg-1.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.HHfEzPHc/pbuilderrc_NkWC --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.HHfEzPHc/b2 --logfile b2/build.log subread_2.0.8+dfsg-1.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/374784/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/817158/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -164,7 +196,7 @@ Get: 45 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 28.1 MB in 0s (140 MB/s) +Fetched 28.1 MB in 0s (63.0 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19800 files and directories currently installed.) @@ -334,8 +366,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Apr 11 07:17:01 UTC 2026. -Universal Time is now: Sat Apr 11 07:17:01 UTC 2026. +Local time is now: Sun Mar 9 01:02:00 UTC 2025. +Universal Time is now: Sun Mar 9 01:02:00 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/817158/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/817158/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 @@ -395,7 +431,7 @@ rm -rf bin src/longread-one/make.version find . -name "*.o" -delete dh_auto_clean --sourcedirectory=src -- -f Makefile.Linux - cd src && make -j42 clean -f Makefile.Linux + cd src && make -j20 clean -f Makefile.Linux make[2]: Entering directory '/build/reproducible-path/subread-2.0.8+dfsg/src' rm -f core featureCounts exactSNP removeDup subread-buildindex core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o make[2]: Leaving directory '/build/reproducible-path/subread-2.0.8+dfsg/src' @@ -423,7 +459,7 @@ make[1]: Entering directory '/build/reproducible-path/subread-2.0.8+dfsg' dh_auto_build --sourcedirectory=src -- -f Makefile.Linux CC=x86_64-linux-gnu-gcc ; \ - cd src && make -j42 "INSTALL=install --strip-program=true" -f Makefile.Linux CC=x86_64-linux-gnu-gcc + cd src && make -j20 "INSTALL=install --strip-program=true" -f Makefile.Linux CC=x86_64-linux-gnu-gcc make[2]: Entering directory '/build/reproducible-path/subread-2.0.8+dfsg/src' x86_64-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 -fcf-protection -mtune=generic -msse3 -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.o core.c x86_64-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 -fcf-protection -mtune=generic -msse3 -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-junction.o core-junction.c @@ -454,17 +490,25 @@ gene-value-index.c:87:41: note: in expansion of macro 'SUBREADprintf' 87 | SUBREADprintf("INCHRO:%d ; POS:%d\n", ret, pos); | ^~~~~~~~~~~~~ -input-blc.c: In function 'iCache_continuous_read_lanes': -input-blc.c:580:59: warning: unused variable 'npos' [-Wunused-variable] - 580 | long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET); - | ^~~~ +input-files.c: In function 'reduce_SAM_to_BAM': core-junction.c: In function 'find_donor_receptor': +input-files.c:3240:13: warning: unused variable 'seq_len' [-Wunused-variable] + 3240 | int seq_len = qual - seq - 1; + | ^~~~~~~ core-junction.c:2099:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 2099 | if(0&& FIXLENstrcmp("V0112_0155:7:1101:12618:2466#ACTTGA", rname) == 0) | ^~ core-junction.c:2103:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 2103 | if( (end_site_mismatches + start_site_mismatches) * 500 + insertion_in_between_i < best_testing_score ){ | ^~ +input-blc.c: In function 'iCache_continuous_read_lanes': +input-blc.c:580:59: warning: unused variable 'npos' [-Wunused-variable] + 580 | long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET); + | ^~~~ +input-files.c: In function 'SAM_pairer_fix_format': +input-files.c:4830:50: warning: variable 'readname' set but not used [-Wunused-but-set-variable] + 4830 | char tmpfname [MAX_FILE_NAME_LENGTH+14], readname[256]; + | ^~~~~~~~ gene-algorithms.c: In function 'miltime': gene-algorithms.c:1395:17: warning: 'ftime' is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 1395 | ftime(&trp); @@ -473,14 +517,6 @@ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ -input-files.c: In function 'reduce_SAM_to_BAM': -input-files.c:3240:13: warning: unused variable 'seq_len' [-Wunused-variable] - 3240 | int seq_len = qual - seq - 1; - | ^~~~~~~ -input-files.c: In function 'SAM_pairer_fix_format': -input-files.c:4830:50: warning: variable 'readname' set but not used [-Wunused-but-set-variable] - 4830 | char tmpfname [MAX_FILE_NAME_LENGTH+14], readname[256]; - | ^~~~~~~~ sambam-file.c: In function 'PBam_chunk_headers': sambam-file.c:564:41: warning: '__builtin___strcpy_chk' writing 256 bytes into a region of size 200 [-Wstringop-overflow=] 564 | strcpy(new_event->chro_name, chro_name); @@ -513,28 +549,26 @@ x86_64-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 -fcf-protection -mtune=generic -msse3 -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 x86_64-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 -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o repair read-repair.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -rm -f longread-one/*.o x86_64-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 -fcf-protection -mtune=generic -msse3 -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 x86_64-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 -fcf-protection -mtune=generic -msse3 -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 x86_64-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 -fcf-protection -mtune=generic -msse3 -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 -cd longread-one && make x86_64-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 -fcf-protection -mtune=generic -msse3 -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 +rm -f longread-one/*.o x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -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 -make[3]: Entering directory '/build/reproducible-path/subread-2.0.8+dfsg/src/longread-one' x86_64-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 -fcf-protection -mtune=generic -msse3 -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 +cd longread-one && make x86_64-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 -fcf-protection -mtune=generic -msse3 -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 x86_64-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 -fcf-protection -mtune=generic -msse3 -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 -x86_64-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 -fcf-protection -mtune=generic -msse3 -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 x86_64-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 -fcf-protection -mtune=generic -msse3 -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 +make[3]: Entering directory '/build/reproducible-path/subread-2.0.8+dfsg/src/longread-one' +x86_64-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 -fcf-protection -mtune=generic -msse3 -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 x86_64-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 -fcf-protection -mtune=generic -msse3 -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 x86_64-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 -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +x86_64-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 -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o flattenGTF flattenAnnotations.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-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 -fcf-protection -mtune=generic -msse3 -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 x86_64-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 -fcf-protection -mtune=generic -msse3 -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 -x86_64-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 -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o flattenGTF flattenAnnotations.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-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 -fcf-protection -mtune=generic -msse3 -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 x86_64-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 -fcf-protection -mtune=generic -msse3 -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 -x86_64-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 -fcf-protection -mtune=generic -msse3 -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 -x86_64-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 -fcf-protection -mtune=generic -msse3 -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 detection-calls.c: In function 'DTCwrite_annotations': detection-calls.c:155:9: warning: dangling pointer 'gc_2int' to an unnamed temporary may be used [-Wdangling-pointer=] 155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0); @@ -548,22 +582,6 @@ detection-calls.c:154:48: note: unnamed temporary defined here 154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0}; | ^ -In file included from readSummary.c:41: -readSummary.c: In function 'get_RG_tables': -readSummary.c:2505:31: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] - 2505 | SUBREADprintf("cannot allocate memory for %s (%d)\n", rg_name, strlen(rg_name)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~ - | | - | size_t {aka long unsigned int} -subread.h:142:44: note: in definition of macro 'SUBREADprintf' - 142 | #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__) - | ^~~~~~~~~~~ -readSummary.c:2505:64: note: format string is defined here - 2505 | SUBREADprintf("cannot allocate memory for %s (%d)\n", rg_name, strlen(rg_name)); - | ~^ - | | - | int - | %ld SUBindel.c: In function 'load_global_context_forindel': SUBindel.c:66:31: warning: '.reads' directive writing 6 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 66 | sprintf(tmp_fname, "%s.reads", context->config.index_prefix); @@ -622,6 +640,16 @@ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SUBindel.c: In function 'load_global_context_forindel': +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__) + | ^~~~~~~~~~~ SUBindel.c:87:40: warning: '%02d' directive writing between 2 and 11 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 87 | sprintf(tmp_fname, "%s.%02d.%c.tab", context->config.index_prefix, context->index_block_number, context->config.space_type == GENE_SPACE_COLOR?'c':'b'); | ^~~~ @@ -637,7 +665,17 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +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': SUBindel.c: In function 'load_indexes_forindel': +readSummary.c:3819:58: warning: variable 'assignment_target_number' set but not used [-Wunused-but-set-variable] + 3819 | srInt_64 assignment_target_number = tmp_voter_id; + | ^~~~~~~~~~~~~~~~~~~~~~~~ SUBindel.c: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'); | ^~~~ @@ -653,14 +691,12 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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; | ^~~~~~~~ +x86_64-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 -fcf-protection -mtune=generic -msse3 -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 +x86_64-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 -fcf-protection -mtune=generic -msse3 -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 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; @@ -736,7 +772,7 @@ || Repeat threshold : 100 repeats || || Gapped index : no || || || -|| Free / total memory : 70.6GB / 78.5GB || +|| Free / total memory : 70.8GB / 79.0GB || || || || 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=490.2k bps/s || -|| 16%, 0 mins elapsed, rate=901.4k bps/s || -|| 25%, 0 mins elapsed, rate=1238.9k bps/s || -|| 33%, 0 mins elapsed, rate=1531.2k bps/s || -|| 41%, 0 mins elapsed, rate=1791.3k bps/s || -|| 50%, 0 mins elapsed, rate=2012.0k bps/s || -|| 58%, 0 mins elapsed, rate=2206.1k bps/s || -|| 66%, 0 mins elapsed, rate=2378.2k bps/s || -|| 75%, 0 mins elapsed, rate=2531.8k bps/s || -|| 83%, 0 mins elapsed, rate=2669.8k bps/s || -|| 91%, 0 mins elapsed, rate=2794.4k bps/s || +|| 8%, 0 mins elapsed, rate=275.8k bps/s || +|| 16%, 0 mins elapsed, rate=520.7k bps/s || +|| 25%, 0 mins elapsed, rate=744.1k bps/s || +|| 33%, 0 mins elapsed, rate=941.9k bps/s || +|| 41%, 0 mins elapsed, rate=1123.8k bps/s || +|| 50%, 0 mins elapsed, rate=1286.4k bps/s || +|| 58%, 0 mins elapsed, rate=1438.3k bps/s || +|| 66%, 0 mins elapsed, rate=1578.0k bps/s || +|| 75%, 0 mins elapsed, rate=1710.9k bps/s || +|| 83%, 0 mins elapsed, rate=1826.4k bps/s || +|| 91%, 0 mins elapsed, rate=1937.3k bps/s || || 3.0 GB of memory is needed for index building. || || Build the index... || -|| 8%, 0 mins elapsed, rate=46.5k bps/s || -|| 16%, 0 mins elapsed, rate=91.0k bps/s || -|| 25%, 0 mins elapsed, rate=133.5k bps/s || -|| 33%, 0 mins elapsed, rate=174.2k bps/s || -|| 41%, 0 mins elapsed, rate=213.2k bps/s || -|| 50%, 0 mins elapsed, rate=250.6k bps/s || -|| 58%, 0 mins elapsed, rate=286.4k bps/s || -|| 66%, 0 mins elapsed, rate=320.7k bps/s || -|| 75%, 0 mins elapsed, rate=353.9k bps/s || -|| 83%, 0 mins elapsed, rate=385.6k bps/s || -|| 91%, 0 mins elapsed, rate=416.3k bps/s || +|| 8%, 0 mins elapsed, rate=32.0k bps/s || +|| 16%, 0 mins elapsed, rate=63.0k bps/s || +|| 25%, 0 mins elapsed, rate=93.0k bps/s || +|| 33%, 0 mins elapsed, rate=122.1k bps/s || +|| 41%, 0 mins elapsed, rate=150.0k bps/s || +|| 50%, 0 mins elapsed, rate=176.9k bps/s || +|| 58%, 0 mins elapsed, rate=202.9k bps/s || +|| 66%, 0 mins elapsed, rate=228.1k bps/s || +|| 75%, 0 mins elapsed, rate=252.3k bps/s || +|| 83%, 0 mins elapsed, rate=276.0k bps/s || +|| 91%, 0 mins elapsed, rate=298.9k bps/s || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || @@ -789,7 +825,7 @@ || [ 90.0% finished ] || || [ 100.0% finished ] || || || -|| Total running time: 0.3 minutes. || +|| Total running time: 0.5 minutes. || || Index ../small1 was successfully built. || || || \\============================================================================// @@ -822,7 +858,7 @@ || || \\============================================================================// -//================ Running (10-Apr-2026 19:17:50, pid=386116) ================\\ +//================ Running (09-Mar-2025 15:03:15, pid=894586) ================\\ || || || 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, 1.3 mins elapsed, rate=57.5k reads per second || -|| 74% completed, 1.3 mins elapsed, rate=0.2k reads per second || -|| 83% completed, 1.3 mins elapsed, rate=0.2k reads per second || -|| 91% completed, 1.4 mins elapsed, rate=0.2k reads per second || +|| 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 || || || || Completed successfully. || || || @@ -856,7 +892,7 @@ || || || Indels : 0 || || || -|| Running time : 1.4 minutes || +|| Running time : 0.8 minutes || || || \\============================================================================// @@ -888,7 +924,7 @@ || || \\============================================================================// -//================ Running (10-Apr-2026 19:19:12, pid=391589) ================\\ +//================ Running (09-Mar-2025 15:04:01, pid=936681) ================\\ || || || 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, 1.1 mins elapsed, rate=63.5k reads per second || -|| 74% completed, 1.1 mins elapsed, rate=0.2k reads per second || -|| 83% completed, 1.1 mins elapsed, rate=0.3k reads per second || -|| 91% completed, 1.1 mins elapsed, rate=0.3k reads per second || +|| 33% completed, 0.9 mins elapsed, rate=43.9k reads per second || +|| 74% completed, 0.9 mins elapsed, rate=0.3k reads per second || +|| 83% completed, 0.9 mins elapsed, rate=0.3k reads per second || +|| 91% completed, 0.9 mins elapsed, rate=0.4k reads per second || || || || Completed successfully. || || || @@ -922,7 +958,7 @@ || || || Indels : 0 || || || -|| Running time : 1.1 minutes || +|| Running time : 0.9 minutes || || || \\============================================================================// @@ -959,7 +995,7 @@ || || \\============================================================================// -//================ Running (10-Apr-2026 19:20:16, pid=402126) ================\\ +//================ Running (09-Mar-2025 15:04:53, pid=982512) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -973,7 +1009,7 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.9 mins elapsed, rate=28.7k fragments per second || +|| 33% completed, 0.9 mins elapsed, rate=21.0k 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 || @@ -1002,7 +1038,7 @@ || || || Indels : 0 || || || -|| Running time : 1.0 minutes || +|| Running time : 0.9 minutes || || || \\============================================================================// @@ -1039,7 +1075,7 @@ || || \\============================================================================// -//================ Running (10-Apr-2026 19:21:13, pid=406494) ================\\ +//================ Running (09-Mar-2025 15:05:47, pid=997513) ================\\ || || || 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, 0.9 mins elapsed, rate=30.6k fragments per second || +|| 33% completed, 0.8 mins elapsed, rate=19.9k 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 || +|| 91% completed, 0.9 mins elapsed, rate=0.4k fragments per second || || || || Completed successfully. || || || @@ -1119,7 +1155,7 @@ || || \\============================================================================// -//================ Running (10-Apr-2026 19:22:10, pid=408010) ================\\ +//=============== Running (09-Mar-2025 15:06:39, pid=1027422) ================\\ || || || 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, 0.9 mins elapsed, rate=33.0k fragments per second || +|| 33% completed, 1.3 mins elapsed, rate=19.3k fragments per second || || Estimated fragment length : 497 bp || -|| 74% completed, 0.9 mins elapsed, rate=0.3k fragments per second || -|| 83% completed, 1.0 mins elapsed, rate=0.3k fragments per second || -|| 91% completed, 1.0 mins elapsed, rate=0.3k fragments per second || +|| 74% completed, 1.4 mins elapsed, rate=0.2k fragments per second || +|| 83% completed, 1.4 mins elapsed, rate=0.2k fragments per second || +|| 91% completed, 1.4 mins elapsed, rate=0.2k fragments per second || || || || Completed successfully. || || || @@ -1162,7 +1198,7 @@ || || || Indels : 15 || || || -|| Running time : 1.0 minutes || +|| Running time : 1.4 minutes || || || \\============================================================================// @@ -1200,7 +1236,7 @@ || || \\============================================================================// -//================ Running (10-Apr-2026 19:23:07, pid=412987) ================\\ +//=============== Running (09-Mar-2025 15:08:02, pid=1044723) ================\\ || || 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 : 74.4GB / 78.5GB || +|| Free / total memory : 70.7GB / 79.0GB || || || || 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=3644.9k bps/s || -|| 16%, 0 mins elapsed, rate=5988.0k bps/s || -|| 25%, 0 mins elapsed, rate=7859.2k bps/s || -|| 33%, 0 mins elapsed, rate=9062.9k bps/s || -|| 41%, 0 mins elapsed, rate=9980.0k bps/s || -|| 50%, 0 mins elapsed, rate=10934.6k bps/s || -|| 58%, 0 mins elapsed, rate=11506.4k bps/s || -|| 66%, 0 mins elapsed, rate=12193.7k bps/s || -|| 75%, 0 mins elapsed, rate=12574.8k bps/s || -|| 83%, 0 mins elapsed, rate=13098.8k bps/s || -|| 91%, 0 mins elapsed, rate=13561.0k bps/s || +|| 8%, 0 mins elapsed, rate=2704.2k bps/s || +|| 16%, 0 mins elapsed, rate=4299.1k bps/s || +|| 25%, 0 mins elapsed, rate=5239.5k bps/s || +|| 33%, 0 mins elapsed, rate=5988.0k bps/s || +|| 41%, 0 mins elapsed, rate=6448.6k bps/s || +|| 50%, 0 mins elapsed, rate=6797.2k bps/s || +|| 58%, 0 mins elapsed, rate=7156.4k bps/s || +|| 66%, 0 mins elapsed, rate=7369.8k bps/s || +|| 75%, 0 mins elapsed, rate=7621.1k bps/s || +|| 83%, 0 mins elapsed, rate=7762.2k bps/s || +|| 91%, 0 mins elapsed, rate=7949.6k bps/s || || 0.8 GB of memory is needed for index building. || || Build the index... || -|| 8%, 0 mins elapsed, rate=438.9k bps/s || -|| 16%, 0 mins elapsed, rate=842.5k bps/s || -|| 25%, 0 mins elapsed, rate=1215.0k bps/s || -|| 33%, 0 mins elapsed, rate=1567.0k bps/s || -|| 41%, 0 mins elapsed, rate=1888.1k bps/s || -|| 50%, 0 mins elapsed, rate=2196.5k bps/s || -|| 58%, 0 mins elapsed, rate=2476.1k bps/s || -|| 66%, 0 mins elapsed, rate=2748.6k bps/s || -|| 75%, 0 mins elapsed, rate=3005.9k bps/s || -|| 83%, 0 mins elapsed, rate=3236.8k bps/s || -|| 91%, 0 mins elapsed, rate=3466.7k bps/s || +|| 8%, 0 mins elapsed, rate=262.0k bps/s || +|| 16%, 0 mins elapsed, rate=500.5k bps/s || +|| 25%, 0 mins elapsed, rate=718.6k bps/s || +|| 33%, 0 mins elapsed, rate=918.7k bps/s || +|| 41%, 0 mins elapsed, rate=1103.1k bps/s || +|| 50%, 0 mins elapsed, rate=1273.4k bps/s || +|| 58%, 0 mins elapsed, rate=1431.3k bps/s || +|| 66%, 0 mins elapsed, rate=1578.0k bps/s || +|| 75%, 0 mins elapsed, rate=1714.7k bps/s || +|| 83%, 0 mins elapsed, rate=1842.5k bps/s || +|| 91%, 0 mins elapsed, rate=1957.9k bps/s || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || @@ -1323,7 +1359,7 @@ || [ 90.0% finished ] || || [ 100.0% finished ] || || || -|| Total running time: 0.0 minutes. || +|| Total running time: 0.1 minutes. || || Index ../small1 was successfully built. || || || \\============================================================================// @@ -1361,7 +1397,7 @@ || || \\============================================================================// -//================ Running (10-Apr-2026 19:23:10, pid=412994) ================\\ +//=============== Running (09-Mar-2025 15:08:07, pid=1045488) ================\\ || || || 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=19.9k fragments per second || +|| 41% completed, 0.1 mins elapsed, rate=11.0k fragments per second || || Estimated fragment length : 173 bp || -|| 77% completed, 0.1 mins elapsed, rate=1.6k fragments per second || -|| 87% completed, 0.1 mins elapsed, rate=1.8k fragments per second || -|| 97% completed, 0.1 mins elapsed, rate=1.9k fragments per second || +|| 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=2.0k fragments per second || || || || Completed successfully. || || || @@ -1442,7 +1478,7 @@ || || \\============================================================================// -//================ Running (10-Apr-2026 19:23:18, pid=413103) ================\\ +//=============== Running (09-Mar-2025 15:08:14, pid=1046357) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1456,10 +1492,10 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 41% completed, 0.1 mins elapsed, rate=11.9k fragments per second || +|| 41% completed, 0.1 mins elapsed, rate=5.7k fragments per second || || Estimated fragment length : 174 bp || || 77% completed, 0.1 mins elapsed, rate=1.5k fragments per second || -|| 87% completed, 0.1 mins elapsed, rate=1.6k fragments per second || +|| 87% completed, 0.1 mins elapsed, rate=1.7k fragments per second || || 97% completed, 0.1 mins elapsed, rate=1.8k fragments per second || || || || Completed successfully. || @@ -1661,9 +1697,9 @@ || || \\============================================================================// -//====================== Running (10-Apr-2026 19:23:28) ======================\\ +//====================== Running (09-Mar-2025 15:08:25) ======================\\ || || -|| Split BAM file into result/temp-snps-413705-47B5F4B701E8-* ... || +|| Split BAM file into result/temp-snps-1047801-67DECA8CFE9F-* ... || || processed block chr901@999950 by thread 1/1 [block number=1/1] || || || || Completed successfully. || @@ -1727,10 +1763,10 @@ install -m0755 -d debian/subread-data/usr/share/doc/subread-data install -p -m0644 debian/copyright debian/subread-data/usr/share/doc/subread-data/copyright dh_installchangelogs -O--buildsystem=makefile - install -m0755 -d debian/subread/usr/share/doc/subread - install -p -m0644 debian/.debhelper/generated/subread/dh_installchangelogs.dch.trimmed debian/subread/usr/share/doc/subread/changelog.Debian install -m0755 -d debian/subread-data/usr/share/doc/subread-data install -p -m0644 debian/.debhelper/generated/subread-data/dh_installchangelogs.dch.trimmed debian/subread-data/usr/share/doc/subread-data/changelog.Debian + install -m0755 -d debian/subread/usr/share/doc/subread + install -p -m0644 debian/.debhelper/generated/subread/dh_installchangelogs.dch.trimmed debian/subread/usr/share/doc/subread/changelog.Debian rm -f debian/subread-data.debhelper.log debian/subread.debhelper.log debian/rules override_dh_installexamples-indep make[1]: Entering directory '/build/reproducible-path/subread-2.0.8+dfsg' @@ -1783,28 +1819,28 @@ man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-align.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 man-recode --to-code UTF-8 --suffix .dh-new 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 + chmod 0644 -- debian/subread/usr/share/man/man1/propmapped.1 mv debian/subread/usr/share/man/man1/exactSNP.1.dh-new debian/subread/usr/share/man/man1/exactSNP.1 chmod 0644 -- debian/subread/usr/share/man/man1/exactSNP.1 - mv debian/subread/usr/share/man/man1/featureCounts.1.dh-new debian/subread/usr/share/man/man1/featureCounts.1 - chmod 0644 -- debian/subread/usr/share/man/man1/featureCounts.1 - mv debian/subread/usr/share/man/man1/flattenGTF.1.dh-new debian/subread/usr/share/man/man1/flattenGTF.1 - chmod 0644 -- debian/subread/usr/share/man/man1/flattenGTF.1 mv debian/subread/usr/share/man/man1/genRandomReads.1.dh-new debian/subread/usr/share/man/man1/genRandomReads.1 chmod 0644 -- debian/subread/usr/share/man/man1/genRandomReads.1 - mv debian/subread/usr/share/man/man1/propmapped.1.dh-new debian/subread/usr/share/man/man1/propmapped.1 - chmod 0644 -- debian/subread/usr/share/man/man1/propmapped.1 - mv debian/subread/usr/share/man/man1/subindel.1.dh-new debian/subread/usr/share/man/man1/subindel.1 - chmod 0644 -- debian/subread/usr/share/man/man1/subindel.1 + mv debian/subread/usr/share/man/man1/flattenGTF.1.dh-new debian/subread/usr/share/man/man1/flattenGTF.1 + chmod 0644 -- debian/subread/usr/share/man/man1/flattenGTF.1 + mv debian/subread/usr/share/man/man1/featureCounts.1.dh-new debian/subread/usr/share/man/man1/featureCounts.1 + chmod 0644 -- debian/subread/usr/share/man/man1/featureCounts.1 + mv debian/subread/usr/share/man/man1/qualityScores.1.dh-new debian/subread/usr/share/man/man1/qualityScores.1 + chmod 0644 -- debian/subread/usr/share/man/man1/qualityScores.1 mv debian/subread/usr/share/man/man1/removeDup.1.dh-new debian/subread/usr/share/man/man1/removeDup.1 chmod 0644 -- debian/subread/usr/share/man/man1/removeDup.1 + mv debian/subread/usr/share/man/man1/subjunc.1.dh-new debian/subread/usr/share/man/man1/subjunc.1 + chmod 0644 -- debian/subread/usr/share/man/man1/subjunc.1 + mv debian/subread/usr/share/man/man1/subindel.1.dh-new debian/subread/usr/share/man/man1/subindel.1 + chmod 0644 -- debian/subread/usr/share/man/man1/subindel.1 mv debian/subread/usr/share/man/man1/repair.1.dh-new debian/subread/usr/share/man/man1/repair.1 chmod 0644 -- debian/subread/usr/share/man/man1/repair.1 - mv debian/subread/usr/share/man/man1/qualityScores.1.dh-new debian/subread/usr/share/man/man1/qualityScores.1 - chmod 0644 -- debian/subread/usr/share/man/man1/qualityScores.1 mv debian/subread/usr/share/man/man1/sublong.1.dh-new debian/subread/usr/share/man/man1/sublong.1 chmod 0644 -- debian/subread/usr/share/man/man1/sublong.1 - mv debian/subread/usr/share/man/man1/subjunc.1.dh-new debian/subread/usr/share/man/man1/subjunc.1 - chmod 0644 -- debian/subread/usr/share/man/man1/subjunc.1 mv debian/subread/usr/share/man/man1/subread-align.1.dh-new debian/subread/usr/share/man/man1/subread-align.1 chmod 0644 -- debian/subread/usr/share/man/man1/subread-align.1 mv debian/subread/usr/share/man/man1/subread-buildindex.1.dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 @@ -1829,10 +1865,10 @@ 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/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 + find debian/subread/usr/share/doc -type f -a -true -a ! -regex 'debian/subread/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread-data/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 + find debian/subread/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/subread/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread-data -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 @@ -1845,71 +1881,26 @@ objcopy --compress-debug-sections debian/subread/usr/lib/debug/.dwz/x86_64-linux-gnu/subread.debug chmod 0644 -- debian/subread/usr/lib/debug/.dwz/x86_64-linux-gnu/subread.debug dh_strip -a -O--buildsystem=makefile - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/af - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/af/86d5cd40ab2f6896c069f377df687ca07899b9.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/af/86d5cd40ab2f6896c069f377df687ca07899b9.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/af/86d5cd40ab2f6896c069f377df687ca07899b9.debug debian/subread/usr/bin/subread-align - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ba - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/featureCounts debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ba/9ec00a5feb854ebea072a71ceacce4f16c807b.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ba/9ec00a5feb854ebea072a71ceacce4f16c807b.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/ba/9ec00a5feb854ebea072a71ceacce4f16c807b.debug debian/subread/usr/bin/featureCounts - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c6 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c6/7e563bfbceae3df89a2e763a3e16830fc7d6f1.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c6/7e563bfbceae3df89a2e763a3e16830fc7d6f1.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/c6/7e563bfbceae3df89a2e763a3e16830fc7d6f1.debug debian/subread/usr/bin/subindel - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/df - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/df/b79cf83e2e4eefa739c7bd1e0286c2330badf2.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/df/b79cf83e2e4eefa739c7bd1e0286c2330badf2.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/sublong - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/df/b79cf83e2e4eefa739c7bd1e0286c2330badf2.debug debian/subread/usr/bin/sublong - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/17 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/17/e5fb9733a4e27115ae9f50e30a23cb8216c140.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/17/e5fb9733a4e27115ae9f50e30a23cb8216c140.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/17/e5fb9733a4e27115ae9f50e30a23cb8216c140.debug debian/subread/usr/bin/subjunc - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/eb - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-buildindex debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/eb/95f93c14404e614a9e99d8c4473e0b9a34c944.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/eb/95f93c14404e614a9e99d8c4473e0b9a34c944.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/eb/95f93c14404e614a9e99d8c4473e0b9a34c944.debug debian/subread/usr/bin/subread-buildindex - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26/3e3a7d353f54ef9e013eefea0ed9ab3772bf9a.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26/3e3a7d353f54ef9e013eefea0ed9ab3772bf9a.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/26/3e3a7d353f54ef9e013eefea0ed9ab3772bf9a.debug debian/subread/usr/bin/exactSNP - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/40 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/genRandomReads debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/40/d17561a4178aa2e7d5b32f4022b788c942fe94.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/40/d17561a4178aa2e7d5b32f4022b788c942fe94.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/40/d17561a4178aa2e7d5b32f4022b788c942fe94.debug debian/subread/usr/lib/subread/genRandomReads - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c3 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c3/2378f625c13e8486fbc4a67b031e53166dfd0a.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c3/2378f625c13e8486fbc4a67b031e53166dfd0a.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/c3/2378f625c13e8486fbc4a67b031e53166dfd0a.debug debian/subread/usr/lib/subread/qualityScores install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c1 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/txUnique debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c1/54f615f002a43fd730f93851192eb3ea3733a4.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c1/54f615f002a43fd730f93851192eb3ea3733a4.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/c1/54f615f002a43fd730f93851192eb3ea3733a4.debug debian/subread/usr/lib/subread/txUnique - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/54 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/54/d892b37e74c7629769bf9e36cec2f9f75ac9b4.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/54/d892b37e74c7629769bf9e36cec2f9f75ac9b4.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/54/d892b37e74c7629769bf9e36cec2f9f75ac9b4.debug debian/subread/usr/lib/subread/propmapped - 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/flattenGTF debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ac/d1db8bda83b3cc336baa0449ccfab407c81e35.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ac/d1db8bda83b3cc336baa0449ccfab407c81e35.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/ac/d1db8bda83b3cc336baa0449ccfab407c81e35.debug debian/subread/usr/lib/subread/flattenGTF install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9e objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9e/684bba40f22a949afcb671a10194407d3be7ea.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9e/684bba40f22a949afcb671a10194407d3be7ea.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/9e/684bba40f22a949afcb671a10194407d3be7ea.debug debian/subread/usr/lib/subread/removeDup + 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/flattenGTF debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ac/d1db8bda83b3cc336baa0449ccfab407c81e35.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ac/d1db8bda83b3cc336baa0449ccfab407c81e35.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/ac/d1db8bda83b3cc336baa0449ccfab407c81e35.debug debian/subread/usr/lib/subread/flattenGTF + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/40 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/genRandomReads debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/40/d17561a4178aa2e7d5b32f4022b788c942fe94.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/40/d17561a4178aa2e7d5b32f4022b788c942fe94.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/40/d17561a4178aa2e7d5b32f4022b788c942fe94.debug debian/subread/usr/lib/subread/genRandomReads install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/82 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/subread-fullscan debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/82/c0db4b6065c61dc9c3bdae61dfa5919bc6e881.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/82/c0db4b6065c61dc9c3bdae61dfa5919bc6e881.debug @@ -1920,6 +1911,51 @@ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/82/03931b059e770bf1e7b95ef249c79652776d76.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/82/03931b059e770bf1e7b95ef249c79652776d76.debug debian/subread/usr/lib/subread/repair + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/54 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/54/d892b37e74c7629769bf9e36cec2f9f75ac9b4.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/54/d892b37e74c7629769bf9e36cec2f9f75ac9b4.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/54/d892b37e74c7629769bf9e36cec2f9f75ac9b4.debug debian/subread/usr/lib/subread/propmapped + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c3 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c3/2378f625c13e8486fbc4a67b031e53166dfd0a.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c3/2378f625c13e8486fbc4a67b031e53166dfd0a.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/c3/2378f625c13e8486fbc4a67b031e53166dfd0a.debug debian/subread/usr/lib/subread/qualityScores + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/eb + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-buildindex debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/eb/95f93c14404e614a9e99d8c4473e0b9a34c944.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/eb/95f93c14404e614a9e99d8c4473e0b9a34c944.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/eb/95f93c14404e614a9e99d8c4473e0b9a34c944.debug debian/subread/usr/bin/subread-buildindex + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/17 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/17/e5fb9733a4e27115ae9f50e30a23cb8216c140.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/17/e5fb9733a4e27115ae9f50e30a23cb8216c140.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/17/e5fb9733a4e27115ae9f50e30a23cb8216c140.debug debian/subread/usr/bin/subjunc + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c6 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c6/7e563bfbceae3df89a2e763a3e16830fc7d6f1.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c6/7e563bfbceae3df89a2e763a3e16830fc7d6f1.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/c6/7e563bfbceae3df89a2e763a3e16830fc7d6f1.debug debian/subread/usr/bin/subindel + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ba + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/featureCounts debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ba/9ec00a5feb854ebea072a71ceacce4f16c807b.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ba/9ec00a5feb854ebea072a71ceacce4f16c807b.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/ba/9ec00a5feb854ebea072a71ceacce4f16c807b.debug debian/subread/usr/bin/featureCounts + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/df + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/df/b79cf83e2e4eefa739c7bd1e0286c2330badf2.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/df/b79cf83e2e4eefa739c7bd1e0286c2330badf2.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/sublong + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/df/b79cf83e2e4eefa739c7bd1e0286c2330badf2.debug debian/subread/usr/bin/sublong + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26/3e3a7d353f54ef9e013eefea0ed9ab3772bf9a.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26/3e3a7d353f54ef9e013eefea0ed9ab3772bf9a.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/26/3e3a7d353f54ef9e013eefea0ed9ab3772bf9a.debug debian/subread/usr/bin/exactSNP + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/af + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/af/86d5cd40ab2f6896c069f377df687ca07899b9.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/af/86d5cd40ab2f6896c069f377df687ca07899b9.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/af/86d5cd40ab2f6896c069f377df687ca07899b9.debug debian/subread/usr/bin/subread-align install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/subread/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/subread/usr/lib/debug/.dwz @@ -1931,7 +1967,7 @@ 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/bin/subread-align debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subindel debian/subread/usr/bin/sublong debian/subread/usr/bin/subjunc debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/exactSNP debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/txUnique debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/repair + dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/lib/subread/txUnique debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/qualityScores debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/subjunc debian/subread/usr/bin/subindel debian/subread/usr/bin/featureCounts debian/subread/usr/bin/sublong debian/subread/usr/bin/exactSNP debian/subread/usr/bin/subread-align dh_installdeb -O--buildsystem=makefile install -m0755 -d debian/subread/DEBIAN install -m0755 -d debian/subread-data/DEBIAN @@ -1946,15 +1982,15 @@ 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=17e5fb9733a4e27115ae9f50e30a23cb8216c140 263e3a7d353f54ef9e013eefea0ed9ab3772bf9a 40d17561a4178aa2e7d5b32f4022b788c942fe94 54d892b37e74c7629769bf9e36cec2f9f75ac9b4 8203931b059e770bf1e7b95ef249c79652776d76 82c0db4b6065c61dc9c3bdae61dfa5919bc6e881 9e684bba40f22a949afcb671a10194407d3be7ea acd1db8bda83b3cc336baa0449ccfab407c81e35 af86d5cd40ab2f6896c069f377df687ca07899b9 ba9ec00a5feb854ebea072a71ceacce4f16c807b c154f615f002a43fd730f93851192eb3ea3733a4 c32378f625c13e8486fbc4a67b031e53166dfd0a c67e563bfbceae3df89a2e763a3e16830fc7d6f1 dfb79cf83e2e4eefa739c7bd1e0286c2330badf2 eb95f93c14404e614a9e99d8c4473e0b9a34c944" -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 - chmod 0644 -- debian/subread-data/DEBIAN/control chmod 0644 -- debian/subread/DEBIAN/control dh_md5sums -O--buildsystem=makefile install -m0755 -d debian/subread/DEBIAN install -m0755 -d debian/subread-data/DEBIAN - cd debian/subread >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/subread-data >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums + cd debian/subread >/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 @@ -1974,12 +2010,14 @@ 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/817158/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/817158/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/374784 and its subdirectories -I: Current time: Fri Apr 10 19:24:01 -12 2026 -I: pbuilder-time-stamp: 1775892241 +I: removing directory /srv/workspace/pbuilder/817158 and its subdirectories +I: Current time: Sun Mar 9 15:09:23 +14 2025 +I: pbuilder-time-stamp: 1741482563