Diff of the two buildlogs: -- --- b1/build.log 2025-08-29 18:19:42.385340545 +0000 +++ b2/build.log 2025-08-29 18:31:44.734205299 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Oct 1 12:24:06 -12 2026 -I: pbuilder-time-stamp: 1790900646 +I: Current time: Sat Aug 30 08:19:48 +14 2025 +I: pbuilder-time-stamp: 1756491589 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -28,53 +28,85 @@ 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/2667482/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2459406/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-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 Aug 29 18:21 /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/2459406/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2459406/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='forky' - 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=40 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='029ac7b4ee164c86a1e7152cc30dbeba' - 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='2667482' - PS1='# ' - PS2='> ' + INVOCATION_ID=8ee9dc3685d948ad9092470a51ee924d + 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=2459406 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.hEoUjKMG/pbuilderrc_Tjj3 --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hEoUjKMG/b1 --logfile b1/build.log subread_2.0.8+dfsg-1.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - 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.hEoUjKMG/pbuilderrc_CrSw --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hEoUjKMG/b2 --logfile b2/build.log subread_2.0.8+dfsg-1.dsc' + SUDO_GID=110 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=105 + 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 6.12.41+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.41-1 (2025-08-12) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.41+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.41-1 (2025-08-12) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2667482/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2459406/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: 44 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Get: 46 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 18.8 MB in 8s (2308 kB/s) +Fetched 18.8 MB in 0s (99.2 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1: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 ... 19855 files and directories currently installed.) @@ -331,8 +363,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Oct 2 00:27:17 UTC 2026. -Universal Time is now: Fri Oct 2 00:27:17 UTC 2026. +Local time is now: Fri Aug 29 18:24:16 UTC 2025. +Universal Time is now: Fri Aug 29 18:24:16 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... @@ -375,7 +407,11 @@ 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/2459406/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/2459406/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 @@ -391,7 +427,7 @@ 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 -j40 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' @@ -419,7 +455,7 @@ 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 -j40 "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 @@ -454,6 +490,13 @@ 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); | ^~~~ +core-junction.c: In function 'find_donor_receptor': +core-junction.c:2099:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 2099 | if(0&& FIXLENstrcmp("V0112_0155:7:1101:12618:2466#ACTTGA", rname) == 0) + | ^~ +core-junction.c:2103:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 2103 | if( (end_site_mismatches + start_site_mismatches) * 500 + insertion_in_between_i < best_testing_score ){ + | ^~ gene-algorithms.c: In function 'miltime': gene-algorithms.c:1395:17: warning: 'ftime' is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 1395 | ftime(&trp); @@ -462,13 +505,6 @@ /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ -core-junction.c: In function 'find_donor_receptor': -core-junction.c:2099:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 2099 | if(0&& FIXLENstrcmp("V0112_0155:7:1101:12618:2466#ACTTGA", rname) == 0) - | ^~ -core-junction.c:2103:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 2103 | if( (end_site_mismatches + start_site_mismatches) * 500 + insertion_in_between_i < best_testing_score ){ - | ^~ 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; @@ -510,27 +546,43 @@ 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 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 -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 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 +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 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 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 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 -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 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 +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 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 -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 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 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 +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 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 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 +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 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); @@ -617,6 +669,14 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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; + | ^~~~~~~~ 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'); @@ -633,30 +693,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -In file included from readSummary.c:41: -readSummary.c: In function 'get_RG_tables': -readSummary.c:2505:31: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] - 2505 | SUBREADprintf("cannot allocate memory for %s (%d)\n", rg_name, strlen(rg_name)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~ - | | - | size_t {aka long unsigned int} -subread.h:142:44: note: in definition of macro 'SUBREADprintf' - 142 | #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__) - | ^~~~~~~~~~~ -readSummary.c:2505:64: note: format string is defined here - 2505 | SUBREADprintf("cannot allocate memory for %s (%d)\n", rg_name, strlen(rg_name)); - | ~^ - | | - | int - | %ld -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; - | ^~~~~~~~ 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; @@ -732,7 +768,7 @@ || Repeat threshold : 100 repeats || || Gapped index : no || || || -|| Free / total memory : 35.4GB / 78.5GB || +|| Free / total memory : 5.3GB / 78.5GB || || || || Input files : 1 file in total || || o chr901.fa || @@ -748,30 +784,30 @@ || 52 uninformative subreads were found. || || These subreads were excluded from index building. || || Estimate the index size... || -|| 8%, 0 mins elapsed, rate=122.6k bps/s || -|| 16%, 0 mins elapsed, rate=232.5k bps/s || -|| 25%, 0 mins elapsed, rate=336.2k bps/s || -|| 33%, 0 mins elapsed, rate=432.7k bps/s || -|| 41%, 0 mins elapsed, rate=522.0k bps/s || -|| 50%, 0 mins elapsed, rate=605.3k bps/s || -|| 58%, 0 mins elapsed, rate=683.1k bps/s || -|| 66%, 0 mins elapsed, rate=746.0k bps/s || -|| 75%, 0 mins elapsed, rate=785.1k bps/s || -|| 83%, 0 mins elapsed, rate=822.7k bps/s || -|| 91%, 0 mins elapsed, rate=880.8k bps/s || +|| 8%, 0 mins elapsed, rate=280.4k bps/s || +|| 16%, 0 mins elapsed, rate=530.6k bps/s || +|| 25%, 0 mins elapsed, rate=755.2k bps/s || +|| 33%, 0 mins elapsed, rate=955.4k bps/s || +|| 41%, 0 mins elapsed, rate=1135.9k bps/s || +|| 50%, 0 mins elapsed, rate=1303.1k bps/s || +|| 58%, 0 mins elapsed, rate=1452.5k bps/s || +|| 66%, 0 mins elapsed, rate=1596.8k bps/s || +|| 75%, 0 mins elapsed, rate=1726.5k bps/s || +|| 83%, 0 mins elapsed, rate=1846.5k bps/s || +|| 91%, 0 mins elapsed, rate=1957.9k bps/s || || 3.0 GB of memory is needed for index building. || || Build the index... || -|| 8%, 0 mins elapsed, rate=19.8k bps/s || -|| 16%, 0 mins elapsed, rate=39.0k bps/s || -|| 25%, 0 mins elapsed, rate=57.8k bps/s || -|| 33%, 0 mins elapsed, rate=76.1k bps/s || -|| 41%, 0 mins elapsed, rate=63.6k bps/s || -|| 50%, 0 mins elapsed, rate=75.0k bps/s || -|| 58%, 0 mins elapsed, rate=86.3k bps/s || -|| 66%, 0 mins elapsed, rate=97.8k bps/s || -|| 75%, 0 mins elapsed, rate=109.2k bps/s || -|| 83%, 0 mins elapsed, rate=120.4k bps/s || -|| 91%, 0 mins elapsed, rate=131.4k bps/s || +|| 8%, 0 mins elapsed, rate=23.7k bps/s || +|| 16%, 0 mins elapsed, rate=46.9k bps/s || +|| 25%, 0 mins elapsed, rate=69.7k bps/s || +|| 33%, 0 mins elapsed, rate=92.0k bps/s || +|| 41%, 0 mins elapsed, rate=113.8k bps/s || +|| 50%, 0 mins elapsed, rate=135.2k bps/s || +|| 58%, 0 mins elapsed, rate=156.2k bps/s || +|| 66%, 0 mins elapsed, rate=176.7k bps/s || +|| 75%, 0 mins elapsed, rate=196.9k bps/s || +|| 83%, 0 mins elapsed, rate=216.6k bps/s || +|| 91%, 0 mins elapsed, rate=236.0k bps/s || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || @@ -785,7 +821,7 @@ || [ 90.0% finished ] || || [ 100.0% finished ] || || || -|| Total running time: 0.8 minutes. || +|| Total running time: 0.2 minutes. || || Index ../small1 was successfully built. || || || \\============================================================================// @@ -818,7 +854,7 @@ || || \\============================================================================// -//=============== Running (01-Oct-2026 12:29:24, pid=2743443) ================\\ +//=============== Running (30-Aug-2025 08:25:00, pid=2474555) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -832,10 +868,10 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 2.0 mins elapsed, rate=22.4k reads per second || -|| 74% completed, 2.0 mins elapsed, rate=0.1k reads per second || -|| 83% completed, 2.0 mins elapsed, rate=0.1k reads per second || -|| 91% completed, 2.0 mins elapsed, rate=0.2k reads per second || +|| 33% completed, 1.0 mins elapsed, rate=31.2k reads per second || +|| 74% completed, 1.0 mins elapsed, rate=0.3k reads per second || +|| 83% completed, 1.0 mins elapsed, rate=0.3k reads per second || +|| 91% completed, 1.0 mins elapsed, rate=0.3k reads per second || || || || Completed successfully. || || || @@ -852,7 +888,7 @@ || || || Indels : 0 || || || -|| Running time : 2.0 minutes || +|| Running time : 1.0 minutes || || || \\============================================================================// @@ -884,7 +920,7 @@ || || \\============================================================================// -//=============== Running (01-Oct-2026 12:31:26, pid=2770006) ================\\ +//=============== Running (30-Aug-2025 08:26:00, pid=2478612) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -898,10 +934,10 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 1.9 mins elapsed, rate=33.8k reads per second || -|| 74% completed, 2.0 mins elapsed, rate=0.1k reads per second || -|| 83% completed, 2.0 mins elapsed, rate=0.1k reads per second || -|| 91% completed, 2.0 mins elapsed, rate=0.2k reads per second || +|| 33% completed, 1.0 mins elapsed, rate=47.3k reads per second || +|| 74% completed, 1.0 mins elapsed, rate=0.2k reads per second || +|| 83% completed, 1.0 mins elapsed, rate=0.3k reads per second || +|| 91% completed, 1.0 mins elapsed, rate=0.3k reads per second || || || || Completed successfully. || || || @@ -918,7 +954,7 @@ || || || Indels : 0 || || || -|| Running time : 2.0 minutes || +|| Running time : 1.0 minutes || || || \\============================================================================// @@ -955,7 +991,7 @@ || || \\============================================================================// -//=============== Running (01-Oct-2026 12:33:24, pid=2773604) ================\\ +//=============== Running (30-Aug-2025 08:27:02, pid=2479022) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -969,11 +1005,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 2.1 mins elapsed, rate=10.3k fragments per second || +|| 33% completed, 1.2 mins elapsed, rate=15.0k fragments per second || || Estimated fragment length : 495 bp || -|| 74% completed, 2.2 mins elapsed, rate=0.1k fragments per second || -|| 83% completed, 2.2 mins elapsed, rate=0.1k fragments per second || -|| 91% completed, 2.2 mins elapsed, rate=0.1k fragments per second || +|| 74% completed, 1.2 mins elapsed, rate=0.2k fragments per second || +|| 83% completed, 1.2 mins elapsed, rate=0.2k fragments per second || +|| 91% completed, 1.2 mins elapsed, rate=0.3k fragments per second || || || || Completed successfully. || || || @@ -998,7 +1034,7 @@ || || || Indels : 0 || || || -|| Running time : 2.2 minutes || +|| Running time : 1.2 minutes || || || \\============================================================================// @@ -1035,7 +1071,7 @@ || || \\============================================================================// -//=============== Running (01-Oct-2026 12:35:35, pid=2776352) ================\\ +//=============== Running (30-Aug-2025 08:28:15, pid=2479237) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1049,11 +1085,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 2.0 mins elapsed, rate=9.4k fragments per second || +|| 33% completed, 1.1 mins elapsed, rate=20.4k fragments per second || || Estimated fragment length : 495 bp || -|| 74% completed, 2.0 mins elapsed, rate=0.1k fragments per second || -|| 83% completed, 2.0 mins elapsed, rate=0.1k fragments per second || -|| 91% completed, 2.0 mins elapsed, rate=0.2k fragments per second || +|| 74% completed, 1.1 mins elapsed, rate=0.2k fragments per second || +|| 83% completed, 1.1 mins elapsed, rate=0.2k fragments per second || +|| 91% completed, 1.1 mins elapsed, rate=0.3k fragments per second || || || || Completed successfully. || || || @@ -1078,7 +1114,7 @@ || || || Indels : 0 || || || -|| Running time : 2.0 minutes || +|| Running time : 1.1 minutes || || || \\============================================================================// @@ -1115,7 +1151,7 @@ || || \\============================================================================// -//=============== Running (01-Oct-2026 12:37:36, pid=2778428) ================\\ +//=============== Running (30-Aug-2025 08:29:24, pid=2479397) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1129,11 +1165,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 2.2 mins elapsed, rate=16.7k fragments per second || +|| 33% completed, 1.2 mins elapsed, rate=16.3k fragments per second || || Estimated fragment length : 497 bp || -|| 74% completed, 2.2 mins elapsed, rate=0.1k fragments per second || -|| 83% completed, 2.2 mins elapsed, rate=0.1k fragments per second || -|| 91% completed, 2.2 mins elapsed, rate=0.1k fragments per second || +|| 74% completed, 1.2 mins elapsed, rate=0.2k fragments per second || +|| 83% completed, 1.2 mins elapsed, rate=0.2k fragments per second || +|| 91% completed, 1.2 mins elapsed, rate=0.3k fragments per second || || || || Completed successfully. || || || @@ -1158,7 +1194,7 @@ || || || Indels : 15 || || || -|| Running time : 2.2 minutes || +|| Running time : 1.2 minutes || || || \\============================================================================// @@ -1196,7 +1232,7 @@ || || \\============================================================================// -//=============== Running (01-Oct-2026 12:39:48, pid=2781103) ================\\ +//=============== Running (30-Aug-2025 08:30:36, pid=2479583) ================\\ || || 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. @@ -1266,7 +1302,7 @@ || Repeat threshold : 100 repeats || || Gapped index : yes || || || -|| Free / total memory : 36.0GB / 78.5GB || +|| Free / total memory : 4.3GB / 78.5GB || || || || Input files : 1 file in total || || o chr901.fa || @@ -1282,30 +1318,30 @@ || 2 uninformative subreads were found. || || These subreads were excluded from index building. || || Estimate the index size... || -|| 8%, 0 mins elapsed, rate=1581.7k bps/s || -|| 16%, 0 mins elapsed, rate=2748.6k bps/s || -|| 25%, 0 mins elapsed, rate=3353.3k bps/s || -|| 33%, 0 mins elapsed, rate=4040.1k bps/s || -|| 41%, 0 mins elapsed, rate=4606.1k bps/s || -|| 50%, 0 mins elapsed, rate=5080.7k bps/s || -|| 58%, 0 mins elapsed, rate=5433.6k bps/s || -|| 66%, 0 mins elapsed, rate=5781.5k bps/s || -|| 75%, 0 mins elapsed, rate=6084.6k bps/s || -|| 83%, 0 mins elapsed, rate=6350.9k bps/s || -|| 91%, 0 mins elapsed, rate=6586.8k bps/s || +|| 8%, 0 mins elapsed, rate=1996.0k bps/s || +|| 16%, 0 mins elapsed, rate=3493.0k bps/s || +|| 25%, 0 mins elapsed, rate=4657.3k bps/s || +|| 33%, 0 mins elapsed, rate=5588.8k bps/s || +|| 41%, 0 mins elapsed, rate=6350.9k bps/s || +|| 50%, 0 mins elapsed, rate=6890.3k bps/s || +|| 58%, 0 mins elapsed, rate=7428.2k bps/s || +|| 66%, 0 mins elapsed, rate=7890.1k bps/s || +|| 75%, 0 mins elapsed, rate=8291.1k bps/s || +|| 83%, 0 mins elapsed, rate=8642.5k bps/s || +|| 91%, 0 mins elapsed, rate=9040.7k bps/s || || 0.8 GB of memory is needed for index building. || || Build the index... || -|| 8%, 0 mins elapsed, rate=168.3k bps/s || -|| 16%, 0 mins elapsed, rate=324.3k bps/s || -|| 25%, 0 mins elapsed, rate=470.1k bps/s || -|| 33%, 0 mins elapsed, rate=605.3k bps/s || -|| 41%, 0 mins elapsed, rate=731.5k bps/s || -|| 50%, 0 mins elapsed, rate=849.6k bps/s || -|| 58%, 0 mins elapsed, rate=960.4k bps/s || -|| 66%, 0 mins elapsed, rate=1064.5k bps/s || -|| 75%, 0 mins elapsed, rate=1162.5k bps/s || -|| 83%, 0 mins elapsed, rate=1255.0k bps/s || -|| 91%, 0 mins elapsed, rate=1340.3k bps/s || +|| 8%, 0 mins elapsed, rate=271.3k bps/s || +|| 16%, 0 mins elapsed, rate=522.3k bps/s || +|| 25%, 0 mins elapsed, rate=757.5k bps/s || +|| 33%, 0 mins elapsed, rate=974.8k bps/s || +|| 41%, 0 mins elapsed, rate=1180.7k bps/s || +|| 50%, 0 mins elapsed, rate=1370.6k bps/s || +|| 58%, 0 mins elapsed, rate=1548.3k bps/s || +|| 66%, 0 mins elapsed, rate=1715.2k bps/s || +|| 75%, 0 mins elapsed, rate=1876.8k bps/s || +|| 83%, 0 mins elapsed, rate=2024.9k bps/s || +|| 91%, 0 mins elapsed, rate=2164.7k bps/s || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || @@ -1357,7 +1393,7 @@ || || \\============================================================================// -//=============== Running (01-Oct-2026 12:39:55, pid=2781425) ================\\ +//=============== Running (30-Aug-2025 08:30:39, pid=2479593) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1371,11 +1407,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 41% completed, 0.2 mins elapsed, rate=6.9k fragments per second || +|| 41% completed, 0.1 mins elapsed, rate=16.3k fragments per second || || Estimated fragment length : 173 bp || -|| 77% completed, 0.2 mins elapsed, rate=0.9k fragments per second || -|| 87% completed, 0.2 mins elapsed, rate=1.0k fragments per second || -|| 97% completed, 0.2 mins elapsed, rate=1.1k fragments per second || +|| 77% completed, 0.2 mins elapsed, rate=1.3k fragments per second || +|| 87% completed, 0.2 mins elapsed, rate=1.5k fragments per second || +|| 97% completed, 0.2 mins elapsed, rate=1.6k fragments per second || || || || Completed successfully. || || || @@ -1438,7 +1474,7 @@ || || \\============================================================================// -//=============== Running (01-Oct-2026 12:40:09, pid=2782735) ================\\ +//=============== Running (30-Aug-2025 08:30:49, pid=2479605) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1452,11 +1488,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 41% completed, 0.3 mins elapsed, rate=3.8k fragments per second || +|| 41% completed, 0.1 mins elapsed, rate=7.1k fragments per second || || Estimated fragment length : 174 bp || -|| 77% completed, 0.4 mins elapsed, rate=0.5k fragments per second || -|| 87% completed, 0.4 mins elapsed, rate=0.6k fragments per second || -|| 97% completed, 0.4 mins elapsed, rate=0.7k fragments per second || +|| 77% completed, 0.2 mins elapsed, rate=1.3k fragments per second || +|| 87% completed, 0.2 mins elapsed, rate=1.4k fragments per second || +|| 97% completed, 0.2 mins elapsed, rate=1.6k fragments per second || || || || Completed successfully. || || || @@ -1483,7 +1519,7 @@ || Fusions : 33 || || Indels : 180 || || || -|| Running time : 0.4 minutes || +|| Running time : 0.2 minutes || || || \\============================================================================// @@ -1657,9 +1693,9 @@ || || \\============================================================================// -//====================== Running (01-Oct-2026 12:40:38) ======================\\ +//====================== Running (30-Aug-2025 08:31:00) ======================\\ || || -|| Split BAM file into result/temp-snps-2785581-765AC4D62741-* ... || +|| Split BAM file into result/temp-snps-2480198-E12FDCC9F56D-* ... || || processed block chr901@999950 by thread 1/1 [block number=1/1] || || || || Completed successfully. || @@ -1672,7 +1708,7 @@ || Reported SNPs : 416 || || Reported indels : 22 || || || -|| Running time : 0.1 minutes || +|| Running time : 0.0 minutes || || || \\============================================================================// @@ -1723,10 +1759,10 @@ 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-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 + 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 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' @@ -1766,47 +1802,47 @@ 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/exactSNP.1 + man-recode --to-code UTF-8 --suffix .dh-new 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 + man-recode --to-code UTF-8 --suffix .dh-new 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 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/removeDup.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/qualityScores.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/genRandomReads.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/featureCounts.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/removeDup.1 man-recode --to-code UTF-8 --suffix .dh-new 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 man-recode --to-code UTF-8 --suffix .dh-new 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 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-fullscan.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 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/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/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/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/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/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/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/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/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/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/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/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/subread-fullscan.1.dh-new debian/subread/usr/share/man/man1/subread-fullscan.1 - chmod 0644 -- debian/subread/usr/share/man/man1/subread-fullscan.1 - mv debian/subread/usr/share/man/man1/subread-buildindex.1.dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 - chmod 0644 -- debian/subread/usr/share/man/man1/subread-buildindex.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/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/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/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 + chmod 0644 -- debian/subread/usr/share/man/man1/subread-buildindex.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-fullscan.1.dh-new debian/subread/usr/share/man/man1/subread-fullscan.1 + chmod 0644 -- debian/subread/usr/share/man/man1/subread-fullscan.1 dh_installsystemduser -O--buildsystem=makefile dh_perl -O--buildsystem=makefile dh_link -O--buildsystem=makefile @@ -1814,23 +1850,23 @@ 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 gzip -9nf usr/share/doc/subread/changelog.Debian usr/share/man/man1/exactSNP.1 usr/share/man/man1/featureCounts.1 usr/share/man/man1/flattenGTF.1 usr/share/man/man1/genRandomReads.1 usr/share/man/man1/propmapped.1 usr/share/man/man1/qualityScores.1 usr/share/man/man1/removeDup.1 usr/share/man/man1/repair.1 usr/share/man/man1/subindel.1 usr/share/man/man1/subjunc.1 usr/share/man/man1/sublong.1 usr/share/man/man1/subread-align.1 usr/share/man/man1/subread-buildindex.1 usr/share/man/man1/subread-fullscan.1 - chmod a-x usr/share/doc/subread-data/changelog.Debian usr/share/doc/subread/examples/annotation/hg19_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/hg38_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm10_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm9_RefSeq_exon.txt cd '/build/reproducible-path/subread-2.0.8+dfsg' - gzip -9nf usr/share/doc/subread-data/changelog.Debian usr/share/doc/subread/examples/annotation/hg19_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/hg38_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm10_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm9_RefSeq_exon.txt cd '/build/reproducible-path/subread-2.0.8+dfsg' dh_fixperms -O--buildsystem=makefile find debian/subread ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/subread-data ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s - find debian/subread/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/man -type f -a -true -a -true -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/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/subread/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w @@ -1841,81 +1877,81 @@ 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/d8 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d8/66450fd8ac26953fe6b7676e684a9d7d7d303b.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d8/66450fd8ac26953fe6b7676e684a9d7d7d303b.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/d8/66450fd8ac26953fe6b7676e684a9d7d7d303b.debug debian/subread/usr/bin/subread-align - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/78 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/featureCounts debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/78/81bb6668b2f6c8ab26f3fb13c645a417763243.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/78/81bb6668b2f6c8ab26f3fb13c645a417763243.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/78/81bb6668b2f6c8ab26f3fb13c645a417763243.debug debian/subread/usr/bin/featureCounts install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e1 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e1/1011813f0b58151a8dccb98cfd8124cc4fd098.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e1/1011813f0b58151a8dccb98cfd8124cc4fd098.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/e1/1011813f0b58151a8dccb98cfd8124cc4fd098.debug debian/subread/usr/bin/subindel - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/30 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/30/39e3873cb0161677730b6bca71efe7c0bf28e8.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/30/39e3873cb0161677730b6bca71efe7c0bf28e8.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/30/39e3873cb0161677730b6bca71efe7c0bf28e8.debug debian/subread/usr/bin/sublong - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6f - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6f/9ce5c48cb98d2502e6f30a096215358c871e3f.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6f/9ce5c48cb98d2502e6f30a096215358c871e3f.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/6f/9ce5c48cb98d2502e6f30a096215358c871e3f.debug debian/subread/usr/bin/subjunc - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/89 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-buildindex debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/89/f3773ba930ac825cd7f69eb9f54a1f27d9ee8c.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/89/f3773ba930ac825cd7f69eb9f54a1f27d9ee8c.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/89/f3773ba930ac825cd7f69eb9f54a1f27d9ee8c.debug debian/subread/usr/bin/subread-buildindex install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d6 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d6/8932e28da9cb6f5ebe95c537cc34bce82d671a.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d6/8932e28da9cb6f5ebe95c537cc34bce82d671a.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/d6/8932e28da9cb6f5ebe95c537cc34bce82d671a.debug debian/subread/usr/bin/exactSNP - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2c - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/genRandomReads debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2c/273e83fa8db3cf912d54b3ecd0a0405b4b3102.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2c/273e83fa8db3cf912d54b3ecd0a0405b4b3102.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/2c/273e83fa8db3cf912d54b3ecd0a0405b4b3102.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/c3/3c1a190951fc30533073e2a9e5aab2b95e209a.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c3/3c1a190951fc30533073e2a9e5aab2b95e209a.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/c3/3c1a190951fc30533073e2a9e5aab2b95e209a.debug debian/subread/usr/lib/subread/qualityScores - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b6 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/txUnique debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b6/07dcf8450b0078a373d9bcd846c38fdb9bedd2.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b6/07dcf8450b0078a373d9bcd846c38fdb9bedd2.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/b6/07dcf8450b0078a373d9bcd846c38fdb9bedd2.debug debian/subread/usr/lib/subread/txUnique + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/89 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-buildindex debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/89/f3773ba930ac825cd7f69eb9f54a1f27d9ee8c.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/89/f3773ba930ac825cd7f69eb9f54a1f27d9ee8c.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/89/f3773ba930ac825cd7f69eb9f54a1f27d9ee8c.debug debian/subread/usr/bin/subread-buildindex + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6f + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6f/9ce5c48cb98d2502e6f30a096215358c871e3f.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6f/9ce5c48cb98d2502e6f30a096215358c871e3f.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/6f/9ce5c48cb98d2502e6f30a096215358c871e3f.debug debian/subread/usr/bin/subjunc + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d8 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d8/66450fd8ac26953fe6b7676e684a9d7d7d303b.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d8/66450fd8ac26953fe6b7676e684a9d7d7d303b.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/d8/66450fd8ac26953fe6b7676e684a9d7d7d303b.debug debian/subread/usr/bin/subread-align + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/30 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/30/39e3873cb0161677730b6bca71efe7c0bf28e8.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/30/39e3873cb0161677730b6bca71efe7c0bf28e8.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/30/39e3873cb0161677730b6bca71efe7c0bf28e8.debug debian/subread/usr/bin/sublong + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/78 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/featureCounts debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/78/81bb6668b2f6c8ab26f3fb13c645a417763243.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/78/81bb6668b2f6c8ab26f3fb13c645a417763243.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/78/81bb6668b2f6c8ab26f3fb13c645a417763243.debug debian/subread/usr/bin/featureCounts install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/fb objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/fb/ab041802ff8af0e66853ad2f1156b7afd6b88e.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/fb/ab041802ff8af0e66853ad2f1156b7afd6b88e.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/fb/ab041802ff8af0e66853ad2f1156b7afd6b88e.debug debian/subread/usr/lib/subread/propmapped - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6e - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/flattenGTF debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6e/8010252d4c9bdc74d8e1aebea71a1217b15743.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6e/8010252d4c9bdc74d8e1aebea71a1217b15743.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/6e/8010252d4c9bdc74d8e1aebea71a1217b15743.debug debian/subread/usr/lib/subread/flattenGTF - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b3 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b3/e4e7784211b164f99b0828a6417c4e3598ae0e.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b3/e4e7784211b164f99b0828a6417c4e3598ae0e.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/b3/e4e7784211b164f99b0828a6417c4e3598ae0e.debug debian/subread/usr/lib/subread/removeDup + 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/c3/3c1a190951fc30533073e2a9e5aab2b95e209a.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c3/3c1a190951fc30533073e2a9e5aab2b95e209a.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/c3/3c1a190951fc30533073e2a9e5aab2b95e209a.debug debian/subread/usr/lib/subread/qualityScores install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7a objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/subread-fullscan debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7a/19bbb5c1013d916ed16bef5aeee9d12e019f26.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7a/19bbb5c1013d916ed16bef5aeee9d12e019f26.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/subread-fullscan objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7a/19bbb5c1013d916ed16bef5aeee9d12e019f26.debug debian/subread/usr/lib/subread/subread-fullscan + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6e + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/flattenGTF debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6e/8010252d4c9bdc74d8e1aebea71a1217b15743.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6e/8010252d4c9bdc74d8e1aebea71a1217b15743.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/6e/8010252d4c9bdc74d8e1aebea71a1217b15743.debug debian/subread/usr/lib/subread/flattenGTF install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e6 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/repair debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e6/4cc0003e57920a62a2065b16419878f10d9757.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e6/4cc0003e57920a62a2065b16419878f10d9757.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/e6/4cc0003e57920a62a2065b16419878f10d9757.debug debian/subread/usr/lib/subread/repair + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b6 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/txUnique debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b6/07dcf8450b0078a373d9bcd846c38fdb9bedd2.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b6/07dcf8450b0078a373d9bcd846c38fdb9bedd2.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/b6/07dcf8450b0078a373d9bcd846c38fdb9bedd2.debug debian/subread/usr/lib/subread/txUnique + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b3 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b3/e4e7784211b164f99b0828a6417c4e3598ae0e.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b3/e4e7784211b164f99b0828a6417c4e3598ae0e.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/b3/e4e7784211b164f99b0828a6417c4e3598ae0e.debug debian/subread/usr/lib/subread/removeDup + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2c + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/genRandomReads debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2c/273e83fa8db3cf912d54b3ecd0a0405b4b3102.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2c/273e83fa8db3cf912d54b3ecd0a0405b4b3102.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/2c/273e83fa8db3cf912d54b3ecd0a0405b4b3102.debug debian/subread/usr/lib/subread/genRandomReads 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 @@ -1927,7 +1963,7 @@ 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/bin/subindel debian/subread/usr/bin/exactSNP debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/subjunc debian/subread/usr/bin/subread-align debian/subread/usr/bin/sublong debian/subread/usr/bin/featureCounts debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/txUnique debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/genRandomReads dh_installdeb -O--buildsystem=makefile install -m0755 -d debian/subread/DEBIAN install -m0755 -d debian/subread-data/DEBIAN @@ -1941,28 +1977,28 @@ echo misc:Depends= >> debian/subread-data.substvars echo misc:Pre-Depends= >> debian/subread-data.substvars dpkg-gencontrol -psubread-data -ldebian/changelog -Tdebian/subread-data.substvars -cdebian/control -Pdebian/subread-data +dpkg-gencontrol: warning: Depends field of package subread-data: substitution variable ${shlibs:Depends} used, but is not defined + chmod 0644 -- debian/subread-data/DEBIAN/control chmod 0644 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/control dpkg-gencontrol -psubread -ldebian/changelog -Tdebian/subread.substvars -cdebian/control -Pdebian/subread chmod 0644 -- debian/subread/DEBIAN/control -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 dh_md5sums -O--buildsystem=makefile install -m0755 -d debian/subread/DEBIAN - cd debian/subread >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums install -m0755 -d debian/subread-data/DEBIAN cd debian/subread-data >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums + 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 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-data .. dpkg-deb --root-owner-group --build debian/subread .. dpkg-deb --root-owner-group --build debian/.debhelper/subread/dbgsym-root .. -dpkg-deb: building package 'subread' in '../subread_2.0.8+dfsg-1_amd64.deb'. -dpkg-deb: building package 'subread-data' in '../subread-data_2.0.8+dfsg-1_all.deb'. + dpkg-deb --root-owner-group --build debian/subread-data .. dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_2.0.8+dfsg-1_amd64.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_amd64.deb'. dpkg-genbuildinfo --build=binary -O../subread_2.0.8+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../subread_2.0.8+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1970,12 +2006,14 @@ 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/2459406/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2459406/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/2667482 and its subdirectories -I: Current time: Thu Oct 1 12:42:39 -12 2026 -I: pbuilder-time-stamp: 1790901759 +I: removing directory /srv/workspace/pbuilder/2459406 and its subdirectories +I: Current time: Sat Aug 30 08:31:43 +14 2025 +I: pbuilder-time-stamp: 1756492303