Diff of the two buildlogs: -- --- b1/build.log 2025-08-27 08:42:00.099429297 +0000 +++ b2/build.log 2025-08-27 08:46:42.419763533 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Aug 26 20:34:55 -12 2025 -I: pbuilder-time-stamp: 1756283695 +I: Current time: Wed Sep 30 05:05:20 +14 2026 +I: pbuilder-time-stamp: 1790694320 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/1081883/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2845583/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Sep 29 15:05 /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/2845583/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2845583/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='0e083cd7542549288902150bb9df261b' - 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='1081883' - PS1='# ' - PS2='> ' + INVOCATION_ID=148279661f1f44c1ba1af521b52970ff + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2845583 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.z64xAVyy/pbuilderrc_trsh --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.z64xAVyy/b1 --logfile b1/build.log subread_2.0.8+dfsg-1.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.z64xAVyy/pbuilderrc_KfZk --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.z64xAVyy/b2 --logfile b2/build.log subread_2.0.8+dfsg-1.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1081883/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2845583/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 arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian forky/main arm64 debhelper all 13.25 [937 kB] Get: 46 http://deb.debian.org/debian forky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] -Fetched 18.2 MB in 1s (18.9 MB/s) +Fetched 18.2 MB in 0s (142 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19969 files and directories currently installed.) @@ -331,8 +363,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Aug 27 08:35:28 UTC 2025. -Universal Time is now: Wed Aug 27 08:35:28 UTC 2025. +Local time is now: Tue Sep 29 15:05:35 UTC 2026. +Universal Time is now: Tue Sep 29 15:05:35 UTC 2026. 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/2845583/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/2845583/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 @@ -435,14 +471,6 @@ aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HelperFunctions.o HelperFunctions.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o interval_merge.o interval_merge.c gene-value-index.c: In function 'is_offset_in_chro': -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); - | ^~~~~ -In file included from gene-algorithms.c:33: -/usr/include/aarch64-linux-gnu/sys/timeb.h:29:12: note: declared here - 29 | extern int ftime (struct timeb *__timebuf) - | ^~~~~ gene-value-index.c:85:33: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 85 | if( pos < chros -> padding || pos >= ( chros->read_offsets[n] - chros->read_offsets[n-1] - chros -> padding )) | ^~ @@ -454,25 +482,31 @@ gene-value-index.c:87:41: note: in expansion of macro 'SUBREADprintf' 87 | SUBREADprintf("INCHRO:%d ; POS:%d\n", ret, pos); | ^~~~~~~~~~~~~ +input-files.c: In function 'reduce_SAM_to_BAM': +input-files.c:3240:13: warning: unused variable 'seq_len' [-Wunused-variable] + 3240 | int seq_len = qual - seq - 1; + | ^~~~~~~ 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) | ^~ +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o long-hashtable.o long-hashtable.c core-junction.c:2103:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 2103 | if( (end_site_mismatches + start_site_mismatches) * 500 + insertion_in_between_i < best_testing_score ){ | ^~ -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o long-hashtable.o long-hashtable.c -input-files.c: In function 'reduce_SAM_to_BAM': -input-files.c:3240:13: warning: unused variable 'seq_len' [-Wunused-variable] - 3240 | int seq_len = qual - seq - 1; - | ^~~~~~~ -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.c input-files.c: In function 'SAM_pairer_fix_format': input-files.c:4830:50: warning: variable 'readname' set but not used [-Wunused-but-set-variable] 4830 | char tmpfname [MAX_FILE_NAME_LENGTH+14], readname[256]; | ^~~~~~~~ -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seek-zlib.o seek-zlib.c -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-blc.o input-blc.c +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.c +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); + | ^~~~~ +In file included from gene-algorithms.c:33: +/usr/include/aarch64-linux-gnu/sys/timeb.h:29:12: note: declared here + 29 | extern int ftime (struct timeb *__timebuf) + | ^~~~~ 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); @@ -481,6 +515,7 @@ subread.h:571:14: note: destination object 'chro_name' of size 200 571 | char chro_name[MAX_CHROMOSOME_NAME_LEN]; | ^~~~~~~~~ +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seek-zlib.o seek-zlib.c In file included from /usr/include/string.h:548, from sambam-file.c:30: In function 'strcpy', @@ -488,6 +523,7 @@ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: warning: '__builtin___memcpy_chk' writing 256 bytes into a region of size 200 overflows the destination [-Wstringop-overflow=] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-blc.o input-blc.c input-blc.c: In function 'iCache_continuous_read_lanes': input-blc.c:580:59: warning: unused variable 'npos' [-Wunused-variable] 580 | long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET); @@ -511,16 +547,16 @@ aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o repair read-repair.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o txUnique tx-unique.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm rm -f longread-one/*.o +cd longread-one && make aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o removeDup removeDupReads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +make[3]: Entering directory '/build/reproducible-path/subread-2.0.8+dfsg/src/longread-one' aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o 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 -cd longread-one && make aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o 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' aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMsorted-hashtable.o -c LRMsorted-hashtable.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subindel SUBindel.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMbase-index.o -c LRMbase-index.c +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMchro-event.o -c LRMchro-event.c detection-calls.c: In function 'DTCwrite_annotations': detection-calls.c:155:109: warning: dangling pointer 'gc_2int' to an unnamed temporary may be used [-Wdangling-pointer=] 155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0); @@ -607,22 +643,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -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'); - | ^~~~ -SUBindel.c:110:36: note: directive argument in the range [0, 2147483646] - 110 | sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, block_no, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b'); - | ^~~~~~~~~~~~~~~~~~ -In function 'sprintf', - inlined from 'load_indexes_forindel' at SUBindel.c:110:3: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 12 and 1019 bytes into a destination of size 1000 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 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=] @@ -639,6 +659,22 @@ | | | int | %ld +SUBindel.c: In function 'load_indexes_forindel': +SUBindel.c:110:40: warning: '%02d' directive writing between 2 and 10 bytes into a region of size between 0 and 999 [-Wformat-overflow=] + 110 | sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, block_no, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b'); + | ^~~~ +SUBindel.c:110:36: note: directive argument in the range [0, 2147483646] + 110 | sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, block_no, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b'); + | ^~~~~~~~~~~~~~~~~~ +In function 'sprintf', + inlined from 'load_indexes_forindel' at SUBindel.c:110:3: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 12 and 1019 bytes into a destination of size 1000 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 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; @@ -647,19 +683,19 @@ readSummary.c:3889:32: warning: unused variable 'sample_i' [-Wunused-variable] 3889 | int xk1, xk2, ret = 0, sample_i; | ^~~~~~~~ -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm readSummary.c: In function 'readSummary': readSummary.c: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; | ^~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-fullscan fullscan.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o flattenGTF flattenAnnotations.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMbase-index.o -c LRMbase-index.c -aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMchro-event.o -c LRMchro-event.c +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhelper.o -c LRMhelper.c +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-fullscan fullscan.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMseek-zlib.o -c LRMseek-zlib.c +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMfile-io.o -c LRMfile-io.c +aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o flattenGTF flattenAnnotations.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhashtable.o -c LRMhashtable.c aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRM longread-mapping.c LRMsorted-hashtable.o LRMbase-index.o LRMchro-event.o LRMhelper.o LRMseek-zlib.o LRMfile-io.o LRMhashtable.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE longread-mapping.c: In function 'LRMmiltime': @@ -670,6 +706,7 @@ /usr/include/aarch64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ +make[3]: Leaving directory '/build/reproducible-path/subread-2.0.8+dfsg/src/longread-one' readSummary.c: In function 'vote_and_add_count': readSummary.c:3752:66: warning: 'longest_overlap_score' may be used uninitialized [-Wmaybe-uninitialized] 3752 | if(longest_overlap_score > scoring_numbers[score_x1]) scoring_numbers[score_x1] = 0; @@ -677,7 +714,6 @@ readSummary.c:3521:51: note: 'longest_overlap_score' was declared here 3521 | int scoring_count = 0, score_x1, longest_overlap_score; | ^~~~~~~~~~~~~~~~~~~~~ -make[3]: Leaving directory '/build/reproducible-path/subread-2.0.8+dfsg/src/longread-one' mkdir -p ../bin/utilities mv longread-one/LRM longread-one/sublong mv longread-one/sublong subread-align subjunc featureCounts subindel exactSNP subread-buildindex ../bin/ @@ -732,7 +768,7 @@ || Repeat threshold : 100 repeats || || Gapped index : no || || || -|| Free / total memory : 8.8GB / 31.3GB || +|| Free / total memory : 28.3GB / 31.3GB || || || || 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=161.2k bps/s || -|| 16%, 0 mins elapsed, rate=298.3k bps/s || -|| 25%, 0 mins elapsed, rate=411.6k bps/s || -|| 33%, 0 mins elapsed, rate=516.7k bps/s || -|| 41%, 0 mins elapsed, rate=601.4k bps/s || -|| 50%, 0 mins elapsed, rate=681.6k bps/s || -|| 58%, 0 mins elapsed, rate=747.5k bps/s || -|| 66%, 0 mins elapsed, rate=816.9k bps/s || -|| 75%, 0 mins elapsed, rate=885.5k bps/s || -|| 83%, 0 mins elapsed, rate=948.3k bps/s || -|| 91%, 0 mins elapsed, rate=1008.9k bps/s || +|| 8%, 0 mins elapsed, rate=1905.3k bps/s || +|| 16%, 0 mins elapsed, rate=3163.5k bps/s || +|| 25%, 0 mins elapsed, rate=3992.0k bps/s || +|| 33%, 0 mins elapsed, rate=4593.5k bps/s || +|| 41%, 0 mins elapsed, rate=5111.7k bps/s || +|| 50%, 0 mins elapsed, rate=5467.3k bps/s || +|| 58%, 0 mins elapsed, rate=5753.2k bps/s || +|| 66%, 0 mins elapsed, rate=5988.0k bps/s || +|| 75%, 0 mins elapsed, rate=6235.4k bps/s || +|| 83%, 0 mins elapsed, rate=6399.4k bps/s || +|| 91%, 0 mins elapsed, rate=6540.1k bps/s || || 3.0 GB of memory is needed for index building. || || Build the index... || -|| 8%, 0 mins elapsed, rate=24.0k bps/s || -|| 16%, 0 mins elapsed, rate=47.2k bps/s || -|| 25%, 0 mins elapsed, rate=69.4k bps/s || -|| 33%, 0 mins elapsed, rate=90.7k bps/s || -|| 41%, 0 mins elapsed, rate=111.7k bps/s || -|| 50%, 0 mins elapsed, rate=132.3k bps/s || -|| 58%, 0 mins elapsed, rate=152.4k bps/s || -|| 66%, 0 mins elapsed, rate=172.3k bps/s || -|| 75%, 0 mins elapsed, rate=190.3k bps/s || -|| 83%, 0 mins elapsed, rate=207.9k bps/s || -|| 91%, 0 mins elapsed, rate=224.3k bps/s || +|| 8%, 0 mins elapsed, rate=63.0k bps/s || +|| 16%, 0 mins elapsed, rate=123.9k bps/s || +|| 25%, 0 mins elapsed, rate=182.9k bps/s || +|| 33%, 0 mins elapsed, rate=240.0k bps/s || +|| 41%, 0 mins elapsed, rate=295.4k bps/s || +|| 50%, 0 mins elapsed, rate=348.8k bps/s || +|| 58%, 0 mins elapsed, rate=400.6k bps/s || +|| 66%, 0 mins elapsed, rate=451.0k bps/s || +|| 75%, 0 mins elapsed, rate=499.7k bps/s || +|| 83%, 0 mins elapsed, rate=547.2k bps/s || +|| 91%, 0 mins elapsed, rate=593.0k 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: 0.4 minutes. || +|| Total running time: 0.1 minutes. || || Index ../small1 was successfully built. || || || \\============================================================================// @@ -818,7 +854,7 @@ || || \\============================================================================// -//=============== Running (26-Aug-2025 20:36:43, pid=1087386) ================\\ +//=============== Running (30-Sep-2026 05:06:13, pid=2872058) ================\\ || || || 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, 1.1 mins elapsed, rate=24.7k 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, 0.4 mins elapsed, rate=64.7k reads per second || +|| 74% completed, 0.4 mins elapsed, rate=0.6k reads per second || +|| 83% completed, 0.4 mins elapsed, rate=0.7k reads per second || +|| 91% completed, 0.4 mins elapsed, rate=0.7k reads per second || || || || Completed successfully. || || || @@ -852,7 +888,7 @@ || || || Indels : 0 || || || -|| Running time : 1.1 minutes || +|| Running time : 0.4 minutes || || || \\============================================================================// @@ -884,7 +920,7 @@ || || \\============================================================================// -//=============== Running (26-Aug-2025 20:37:48, pid=1096283) ================\\ +//=============== Running (30-Sep-2026 05:06:38, pid=2877132) ================\\ || || || 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, 0.8 mins elapsed, rate=57.5k 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 || +|| 33% completed, 0.4 mins elapsed, rate=62.3k reads per second || +|| 74% completed, 0.4 mins elapsed, rate=0.6k reads per second || +|| 83% completed, 0.4 mins elapsed, rate=0.7k reads per second || +|| 91% completed, 0.4 mins elapsed, rate=0.7k reads per second || || || || Completed successfully. || || || @@ -918,7 +954,7 @@ || || || Indels : 0 || || || -|| Running time : 0.9 minutes || +|| Running time : 0.4 minutes || || || \\============================================================================// @@ -955,7 +991,7 @@ || || \\============================================================================// -//=============== Running (26-Aug-2025 20:38:40, pid=1107677) ================\\ +//=============== Running (30-Sep-2026 05:07:04, pid=2886089) ================\\ || || || 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, 0.9 mins elapsed, rate=16.0k fragments per second || +|| 33% completed, 0.4 mins elapsed, rate=31.4k fragments per second || || Estimated fragment length : 495 bp || -|| 74% completed, 1.0 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, 0.4 mins elapsed, rate=0.6k fragments per second || +|| 83% completed, 0.4 mins elapsed, rate=0.6k fragments per second || +|| 91% completed, 0.4 mins elapsed, rate=0.7k fragments per second || || || || Completed successfully. || || || @@ -998,7 +1034,7 @@ || || || Indels : 0 || || || -|| Running time : 1.0 minutes || +|| Running time : 0.4 minutes || || || \\============================================================================// @@ -1035,7 +1071,7 @@ || || \\============================================================================// -//=============== Running (26-Aug-2025 20:39:37, pid=1112778) ================\\ +//=============== Running (30-Sep-2026 05:07:30, pid=2895997) ================\\ || || || 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, 0.7 mins elapsed, rate=26.5k fragments per second || +|| 33% completed, 0.4 mins elapsed, rate=27.3k fragments per second || || Estimated fragment length : 495 bp || -|| 74% completed, 0.8 mins elapsed, rate=0.3k fragments per second || -|| 83% completed, 0.8 mins elapsed, rate=0.4k fragments per second || -|| 91% completed, 0.8 mins elapsed, rate=0.4k fragments per second || +|| 74% completed, 0.4 mins elapsed, rate=0.6k fragments per second || +|| 83% completed, 0.4 mins elapsed, rate=0.6k fragments per second || +|| 91% completed, 0.4 mins elapsed, rate=0.7k fragments per second || || || || Completed successfully. || || || @@ -1078,7 +1114,7 @@ || || || Indels : 0 || || || -|| Running time : 0.8 minutes || +|| Running time : 0.5 minutes || || || \\============================================================================// @@ -1115,7 +1151,7 @@ || || \\============================================================================// -//=============== Running (26-Aug-2025 20:40:23, pid=1115765) ================\\ +//=============== Running (30-Sep-2026 05:07:57, pid=2903225) ================\\ || || || 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, 0.5 mins elapsed, rate=28.7k fragments per second || +|| 33% completed, 0.4 mins elapsed, rate=33.3k fragments per second || || Estimated fragment length : 497 bp || || 74% completed, 0.5 mins elapsed, rate=0.5k fragments per second || -|| 83% completed, 0.5 mins elapsed, rate=0.5k fragments per second || -|| 91% completed, 0.5 mins elapsed, rate=0.6k fragments per second || +|| 83% completed, 0.5 mins elapsed, rate=0.6k fragments per second || +|| 91% completed, 0.5 mins elapsed, rate=0.7k fragments per second || || || || Completed successfully. || || || @@ -1196,7 +1232,7 @@ || || \\============================================================================// -//=============== Running (26-Aug-2025 20:40:56, pid=1117477) ================\\ +//=============== Running (30-Sep-2026 05:08:25, pid=2915117) ================\\ || || 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 : 22.2GB / 31.3GB || +|| Free / total memory : 28.7GB / 31.3GB || || || || 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=4191.6k bps/s || -|| 16%, 0 mins elapsed, rate=6706.6k bps/s || -|| 25%, 0 mins elapsed, rate=8383.2k bps/s || -|| 33%, 0 mins elapsed, rate=9580.8k bps/s || -|| 41%, 0 mins elapsed, rate=10479.0k bps/s || -|| 50%, 0 mins elapsed, rate=11177.6k bps/s || -|| 58%, 0 mins elapsed, rate=11736.5k bps/s || -|| 66%, 0 mins elapsed, rate=12419.6k bps/s || -|| 75%, 0 mins elapsed, rate=12787.9k bps/s || -|| 83%, 0 mins elapsed, rate=13098.8k bps/s || -|| 91%, 0 mins elapsed, rate=13364.5k bps/s || +|| 8%, 0 mins elapsed, rate=8383.2k bps/s || +|| 16%, 0 mins elapsed, rate=11975.8k bps/s || +|| 25%, 0 mins elapsed, rate=13236.6k bps/s || +|| 33%, 0 mins elapsed, rate=13971.9k bps/s || +|| 41%, 0 mins elapsed, rate=14969.9k bps/s || +|| 50%, 0 mins elapsed, rate=15718.5k bps/s || +|| 58%, 0 mins elapsed, rate=15860.0k bps/s || +|| 66%, 0 mins elapsed, rate=16357.4k bps/s || +|| 75%, 0 mins elapsed, rate=16766.4k bps/s || +|| 83%, 0 mins elapsed, rate=16766.3k bps/s || +|| 91%, 0 mins elapsed, rate=17076.8k bps/s || || 0.8 GB of memory is needed for index building. || || Build the index... || -|| 8%, 0 mins elapsed, rate=347.9k bps/s || -|| 16%, 0 mins elapsed, rate=662.7k bps/s || -|| 25%, 0 mins elapsed, rate=938.4k bps/s || -|| 33%, 0 mins elapsed, rate=1180.7k bps/s || -|| 41%, 0 mins elapsed, rate=1392.6k bps/s || -|| 50%, 0 mins elapsed, rate=1607.0k bps/s || -|| 58%, 0 mins elapsed, rate=1767.5k bps/s || -|| 66%, 0 mins elapsed, rate=1943.9k bps/s || -|| 75%, 0 mins elapsed, rate=2084.2k bps/s || -|| 83%, 0 mins elapsed, rate=2241.5k bps/s || -|| 91%, 0 mins elapsed, rate=2352.4k bps/s || +|| 8%, 0 mins elapsed, rate=687.1k bps/s || +|| 16%, 0 mins elapsed, rate=1309.9k bps/s || +|| 25%, 0 mins elapsed, rate=1876.8k bps/s || +|| 33%, 0 mins elapsed, rate=2378.2k bps/s || +|| 41%, 0 mins elapsed, rate=2851.4k bps/s || +|| 50%, 0 mins elapsed, rate=3287.5k bps/s || +|| 58%, 0 mins elapsed, rate=3690.7k bps/s || +|| 66%, 0 mins elapsed, rate=4040.1k bps/s || +|| 75%, 0 mins elapsed, rate=4386.6k bps/s || +|| 83%, 0 mins elapsed, rate=4709.7k bps/s || +|| 91%, 0 mins elapsed, rate=4984.6k bps/s || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || @@ -1357,7 +1393,7 @@ || || \\============================================================================// -//=============== Running (26-Aug-2025 20:40:58, pid=1117517) ================\\ +//=============== Running (30-Sep-2026 05:08:27, pid=2915583) ================\\ || || || 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, 0.1 mins elapsed, rate=21.7k fragments per second || +|| 41% completed, 0.1 mins elapsed, rate=20.5k fragments per second || || Estimated fragment length : 173 bp || -|| 77% completed, 0.1 mins elapsed, rate=2.6k fragments per second || -|| 87% completed, 0.1 mins elapsed, rate=2.9k fragments per second || -|| 97% completed, 0.1 mins elapsed, rate=3.2k fragments per second || +|| 77% completed, 0.1 mins elapsed, rate=3.1k fragments per second || +|| 87% completed, 0.1 mins elapsed, rate=3.4k fragments per second || +|| 97% completed, 0.1 mins elapsed, rate=3.7k fragments per second || || || || Completed successfully. || || || @@ -1438,7 +1474,7 @@ || || \\============================================================================// -//=============== Running (26-Aug-2025 20:41:03, pid=1117579) ================\\ +//=============== Running (30-Sep-2026 05:08:32, pid=2917816) ================\\ || || || 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, 0.1 mins elapsed, rate=10.9k fragments per second || +|| 41% completed, 0.1 mins elapsed, rate=11.6k fragments per second || || Estimated fragment length : 174 bp || -|| 77% completed, 0.1 mins elapsed, rate=2.6k fragments per second || -|| 87% completed, 0.1 mins elapsed, rate=2.8k fragments per second || -|| 97% completed, 0.1 mins elapsed, rate=3.1k fragments per second || +|| 77% completed, 0.1 mins elapsed, rate=2.8k fragments per second || +|| 87% completed, 0.1 mins elapsed, rate=3.1k fragments per second || +|| 97% completed, 0.1 mins elapsed, rate=3.4k fragments per second || || || || Completed successfully. || || || @@ -1657,9 +1693,9 @@ || || \\============================================================================// -//====================== Running (26-Aug-2025 20:41:10) ======================\\ +//====================== Running (30-Sep-2026 05:08:37) ======================\\ || || -|| Split BAM file into result/temp-snps-1118253-CFFAA4BB00CD-* ... || +|| Split BAM file into result/temp-snps-2920987-3BD4FFFC1107-* ... || || processed block chr901@999950 by thread 1/1 [block number=1/1] || || || || Completed successfully. || @@ -1765,16 +1801,16 @@ install -p -m0644 ./debian/subread-buildindex.1 debian/subread/usr/share/man/man1/subread-buildindex.1 install -m0755 -d debian/subread/usr/share/man/man1/ install -p -m0644 ./debian/subread-fullscan.1 debian/subread/usr/share/man/man1/subread-fullscan.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/removeDup.1 debian/subread/usr/share/man/man1/repair.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/sublong.1 debian/subread/usr/share/man/man1/subread-align.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/flattenGTF.1 debian/subread/usr/share/man/man1/genRandomReads.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/exactSNP.1 debian/subread/usr/share/man/man1/featureCounts.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subindel.1 debian/subread/usr/share/man/man1/subjunc.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/propmapped.1 debian/subread/usr/share/man/man1/qualityScores.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 debian/subread/usr/share/man/man1/subread-fullscan.1 - mv debian/subread/usr/share/man/man1/flattenGTF.1.dh-new debian/subread/usr/share/man/man1/flattenGTF.1 - mv debian/subread/usr/share/man/man1/genRandomReads.1.dh-new debian/subread/usr/share/man/man1/genRandomReads.1 - chmod 0644 -- debian/subread/usr/share/man/man1/flattenGTF.1 debian/subread/usr/share/man/man1/genRandomReads.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/exactSNP.1 debian/subread/usr/share/man/man1/featureCounts.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/flattenGTF.1 debian/subread/usr/share/man/man1/genRandomReads.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/sublong.1 debian/subread/usr/share/man/man1/subread-align.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subindel.1 debian/subread/usr/share/man/man1/subjunc.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/removeDup.1 debian/subread/usr/share/man/man1/repair.1 + mv debian/subread/usr/share/man/man1/propmapped.1.dh-new debian/subread/usr/share/man/man1/propmapped.1 + mv debian/subread/usr/share/man/man1/qualityScores.1.dh-new debian/subread/usr/share/man/man1/qualityScores.1 + chmod 0644 -- debian/subread/usr/share/man/man1/propmapped.1 debian/subread/usr/share/man/man1/qualityScores.1 mv debian/subread/usr/share/man/man1/subindel.1.dh-new debian/subread/usr/share/man/man1/subindel.1 mv debian/subread/usr/share/man/man1/subjunc.1.dh-new debian/subread/usr/share/man/man1/subjunc.1 chmod 0644 -- debian/subread/usr/share/man/man1/subindel.1 debian/subread/usr/share/man/man1/subjunc.1 @@ -1784,15 +1820,15 @@ mv debian/subread/usr/share/man/man1/sublong.1.dh-new debian/subread/usr/share/man/man1/sublong.1 mv debian/subread/usr/share/man/man1/subread-align.1.dh-new debian/subread/usr/share/man/man1/subread-align.1 chmod 0644 -- debian/subread/usr/share/man/man1/sublong.1 debian/subread/usr/share/man/man1/subread-align.1 + mv debian/subread/usr/share/man/man1/flattenGTF.1.dh-new debian/subread/usr/share/man/man1/flattenGTF.1 + mv debian/subread/usr/share/man/man1/genRandomReads.1.dh-new debian/subread/usr/share/man/man1/genRandomReads.1 + chmod 0644 -- debian/subread/usr/share/man/man1/flattenGTF.1 debian/subread/usr/share/man/man1/genRandomReads.1 mv debian/subread/usr/share/man/man1/exactSNP.1.dh-new debian/subread/usr/share/man/man1/exactSNP.1 mv debian/subread/usr/share/man/man1/featureCounts.1.dh-new debian/subread/usr/share/man/man1/featureCounts.1 chmod 0644 -- debian/subread/usr/share/man/man1/exactSNP.1 debian/subread/usr/share/man/man1/featureCounts.1 mv debian/subread/usr/share/man/man1/subread-buildindex.1.dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 mv debian/subread/usr/share/man/man1/subread-fullscan.1.dh-new debian/subread/usr/share/man/man1/subread-fullscan.1 chmod 0644 -- debian/subread/usr/share/man/man1/subread-buildindex.1 debian/subread/usr/share/man/man1/subread-fullscan.1 - mv debian/subread/usr/share/man/man1/propmapped.1.dh-new debian/subread/usr/share/man/man1/propmapped.1 - mv debian/subread/usr/share/man/man1/qualityScores.1.dh-new debian/subread/usr/share/man/man1/qualityScores.1 - chmod 0644 -- debian/subread/usr/share/man/man1/propmapped.1 debian/subread/usr/share/man/man1/qualityScores.1 dh_installsystemduser -O--buildsystem=makefile dh_perl -O--buildsystem=makefile dh_link -O--buildsystem=makefile @@ -1800,23 +1836,23 @@ 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 cd debian/subread-data + cd debian/subread chmod a-x usr/share/doc/subread/changelog.Debian usr/share/man/man1/exactSNP.1 usr/share/man/man1/featureCounts.1 usr/share/man/man1/flattenGTF.1 usr/share/man/man1/genRandomReads.1 usr/share/man/man1/propmapped.1 usr/share/man/man1/qualityScores.1 usr/share/man/man1/removeDup.1 usr/share/man/man1/repair.1 usr/share/man/man1/subindel.1 usr/share/man/man1/subjunc.1 usr/share/man/man1/sublong.1 usr/share/man/man1/subread-align.1 usr/share/man/man1/subread-buildindex.1 usr/share/man/man1/subread-fullscan.1 gzip -9nf usr/share/doc/subread/changelog.Debian usr/share/man/man1/exactSNP.1 usr/share/man/man1/featureCounts.1 usr/share/man/man1/flattenGTF.1 usr/share/man/man1/genRandomReads.1 usr/share/man/man1/propmapped.1 usr/share/man/man1/qualityScores.1 usr/share/man/man1/removeDup.1 usr/share/man/man1/repair.1 usr/share/man/man1/subindel.1 usr/share/man/man1/subjunc.1 usr/share/man/man1/sublong.1 usr/share/man/man1/subread-align.1 usr/share/man/man1/subread-buildindex.1 usr/share/man/man1/subread-fullscan.1 - cd '/build/reproducible-path/subread-2.0.8+dfsg' 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 f -a -true -a ! -regex 'debian/subread/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/subread-data/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/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 @@ -1837,16 +1873,6 @@ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/06/16b65463838a92c7a24036df1ee6fc5d8380d6.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/06/16b65463838a92c7a24036df1ee6fc5d8380d6.debug debian/subread/usr/lib/subread/subread-fullscan - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/91 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/repair debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/91/de3b1ed9550b4b873f19125e14f79029b9e526.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/91/de3b1ed9550b4b873f19125e14f79029b9e526.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/91/de3b1ed9550b4b873f19125e14f79029b9e526.debug debian/subread/usr/lib/subread/repair - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/8b - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/8b/cb0e2b9fbc3543c9e926ffd4307e59f2126d2c.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/8b/cb0e2b9fbc3543c9e926ffd4307e59f2126d2c.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/8b/cb0e2b9fbc3543c9e926ffd4307e59f2126d2c.debug debian/subread/usr/lib/subread/removeDup install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1a objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/genRandomReads debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1a/5873c8b805cb133e5da851619a40032c48228f.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1a/5873c8b805cb133e5da851619a40032c48228f.debug @@ -1857,46 +1883,56 @@ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d7/322d685282cecc96f1aaaf55f067508267fa3c.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/d7/322d685282cecc96f1aaaf55f067508267fa3c.debug debian/subread/usr/lib/subread/flattenGTF - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e0 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e0/5a03f5c41379926f78185433e1b623f3cc26bf.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e0/5a03f5c41379926f78185433e1b623f3cc26bf.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/e0/5a03f5c41379926f78185433e1b623f3cc26bf.debug debian/subread/usr/lib/subread/qualityScores + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/8b + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/8b/cb0e2b9fbc3543c9e926ffd4307e59f2126d2c.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/8b/cb0e2b9fbc3543c9e926ffd4307e59f2126d2c.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/8b/cb0e2b9fbc3543c9e926ffd4307e59f2126d2c.debug debian/subread/usr/lib/subread/removeDup + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/91 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/repair debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/91/de3b1ed9550b4b873f19125e14f79029b9e526.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/91/de3b1ed9550b4b873f19125e14f79029b9e526.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/91/de3b1ed9550b4b873f19125e14f79029b9e526.debug debian/subread/usr/lib/subread/repair install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e9 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e9/4e3a07b226a72442d5d297d5aeb46cf9a5b9e7.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e9/4e3a07b226a72442d5d297d5aeb46cf9a5b9e7.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/e9/4e3a07b226a72442d5d297d5aeb46cf9a5b9e7.debug debian/subread/usr/lib/subread/propmapped - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ec - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/featureCounts debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ec/bc4542acbf01229c8bab2db1f5c2d662efa224.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ec/bc4542acbf01229c8bab2db1f5c2d662efa224.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/ec/bc4542acbf01229c8bab2db1f5c2d662efa224.debug debian/subread/usr/bin/featureCounts + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e0 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e0/5a03f5c41379926f78185433e1b623f3cc26bf.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e0/5a03f5c41379926f78185433e1b623f3cc26bf.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/e0/5a03f5c41379926f78185433e1b623f3cc26bf.debug debian/subread/usr/lib/subread/qualityScores install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d3 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-buildindex debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d3/e4bc4c2b6c3b3c8fe3784bbf0ae207000dd904.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d3/e4bc4c2b6c3b3c8fe3784bbf0ae207000dd904.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/d3/e4bc4c2b6c3b3c8fe3784bbf0ae207000dd904.debug debian/subread/usr/bin/subread-buildindex + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ec + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/featureCounts debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ec/bc4542acbf01229c8bab2db1f5c2d662efa224.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ec/bc4542acbf01229c8bab2db1f5c2d662efa224.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/ec/bc4542acbf01229c8bab2db1f5c2d662efa224.debug debian/subread/usr/bin/featureCounts + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/41 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/41/e815d885cfec59f18741def24d87fb77e529c0.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/41/e815d885cfec59f18741def24d87fb77e529c0.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/41/e815d885cfec59f18741def24d87fb77e529c0.debug debian/subread/usr/bin/exactSNP install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e6 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e6/9e5dc6d37a64c6cca118d1cc9de5dd6ca76db2.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e6/9e5dc6d37a64c6cca118d1cc9de5dd6ca76db2.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/e6/9e5dc6d37a64c6cca118d1cc9de5dd6ca76db2.debug debian/subread/usr/bin/subread-align - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ed - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ed/5716aa58f094ffe91144df7b0d9926ae798035.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ed/5716aa58f094ffe91144df7b0d9926ae798035.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/ed/5716aa58f094ffe91144df7b0d9926ae798035.debug debian/subread/usr/bin/subindel install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d9 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d9/7f42e6dd628cee709acc12775b79ec1f8be1ea.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d9/7f42e6dd628cee709acc12775b79ec1f8be1ea.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/d9/7f42e6dd628cee709acc12775b79ec1f8be1ea.debug debian/subread/usr/bin/subjunc - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/41 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/41/e815d885cfec59f18741def24d87fb77e529c0.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/41/e815d885cfec59f18741def24d87fb77e529c0.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/41/e815d885cfec59f18741def24d87fb77e529c0.debug debian/subread/usr/bin/exactSNP + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ed + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ed/5716aa58f094ffe91144df7b0d9926ae798035.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ed/5716aa58f094ffe91144df7b0d9926ae798035.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/ed/5716aa58f094ffe91144df7b0d9926ae798035.debug debian/subread/usr/bin/subindel install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a1 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a1/a670d87c89fda3073df8654469ddeb7ee48a90.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a1/a670d87c89fda3073df8654469ddeb7ee48a90.debug @@ -1913,7 +1949,7 @@ rm -f debian/subread/DEBIAN/shlibs dh_shlibdeps -a -O--buildsystem=makefile install -m0755 -d debian/subread/DEBIAN - dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/lib/subread/txUnique debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/propmapped debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/subread-align debian/subread/usr/bin/subindel debian/subread/usr/bin/subjunc debian/subread/usr/bin/exactSNP debian/subread/usr/bin/sublong + dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/lib/subread/txUnique debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/removeDup 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/featureCounts debian/subread/usr/bin/exactSNP debian/subread/usr/bin/subread-align debian/subread/usr/bin/subjunc debian/subread/usr/bin/subindel debian/subread/usr/bin/sublong dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect @@ -1931,27 +1967,27 @@ 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 +dpkg-gencontrol: warning: Depends field of package subread-data: substitution variable ${shlibs:Depends} used, but is not defined + chmod 0644 -- debian/subread-data/DEBIAN/control chmod 0644 -- debian/subread/DEBIAN/control dh_md5sums -O--buildsystem=makefile install -m0755 -d debian/subread/DEBIAN 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 + cd debian/subread-data >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/subread/DEBIAN/md5sums install -m0755 -d debian/.debhelper/subread/dbgsym-root/DEBIAN cd debian/.debhelper/subread/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/subread-data/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/md5sums dh_builddeb -O--buildsystem=makefile - dpkg-deb --root-owner-group --build debian/subread .. dpkg-deb --root-owner-group --build debian/.debhelper/subread/dbgsym-root .. + dpkg-deb --root-owner-group --build debian/subread .. dpkg-deb --root-owner-group --build debian/subread-data .. -dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_2.0.8+dfsg-1_arm64.deb'. dpkg-deb: building package 'subread' in '../subread_2.0.8+dfsg-1_arm64.deb'. +dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_2.0.8+dfsg-1_arm64.deb'. dpkg-deb: building package 'subread-data' in '../subread-data_2.0.8+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../subread_2.0.8+dfsg-1_arm64.buildinfo dpkg-genchanges --build=binary -O../subread_2.0.8+dfsg-1_arm64.changes @@ -1960,12 +1996,14 @@ 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/2845583/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2845583/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/1081883 and its subdirectories -I: Current time: Tue Aug 26 20:41:59 -12 2025 -I: pbuilder-time-stamp: 1756284119 +I: removing directory /srv/workspace/pbuilder/2845583 and its subdirectories +I: Current time: Wed Sep 30 05:09:41 +14 2026 +I: pbuilder-time-stamp: 1790694581