Diff of the two buildlogs: -- --- b1/build.log 2023-04-15 04:34:54.880516042 +0000 +++ b2/build.log 2023-04-15 04:44:31.674894485 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu May 16 22:52:30 -12 2024 -I: pbuilder-time-stamp: 1715943150 +I: Current time: Sat Apr 15 18:35:03 +14 2023 +I: pbuilder-time-stamp: 1681533303 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./subread_2.0.3+dfsg.orig.tar.xz] I: copying [./subread_2.0.3+dfsg-1.debian.tar.xz] I: Extracting source -gpgv: Signature made Sun Aug 15 00:32:00 2021 -12 +gpgv: Signature made Mon Aug 16 02:32:00 2021 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key @@ -32,11 +32,20 @@ dpkg-source: info: applying cross.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/20149/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/14521/tmp/hooks/D01_modify_environment starting +debug: Running on codethink16-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 +lrwxrwxrwx 1 root root 4 Jan 6 03:20 /bin/sh -> dash +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/14521/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/14521/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' + 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=8' @@ -46,38 +55,38 @@ IFS=' ' LANG='C' - LANGUAGE='en_US:en' + LANGUAGE='nl_BE:nl' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' + 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' - PPID='20149' + PPID='14521' PS1='# ' PS2='> ' 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.D94F7bvr/pbuilderrc_W18z --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.D94F7bvr/b1 --logfile b1/build.log subread_2.0.3+dfsg-1.dsc' + 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.D94F7bvr/pbuilderrc_cEUq --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.D94F7bvr/b2 --logfile b2/build.log --extrapackages usrmerge subread_2.0.3+dfsg-1.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' + TZ='/usr/share/zoneinfo/Etc/GMT-14' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a - Linux codethink13-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 16 07:10 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/20149/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 15 02:48 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/14521/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -162,7 +171,7 @@ Get: 41 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 43 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] -Fetched 24.7 MB in 1s (40.3 MB/s) +Fetched 24.7 MB in 2s (16.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19616 files and directories currently installed.) @@ -350,8 +359,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/subread-2.0.3+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_2.0.3+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/14521/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/14521/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/subread-2.0.3+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_2.0.3+dfsg-1_source.changes dpkg-buildpackage: info: source package subread dpkg-buildpackage: info: source version 2.0.3+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -405,17 +423,17 @@ aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-algorithms.o gene-algorithms.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-files.o input-files.c +sambam-file.c: In function 'SamBam_writer_sort_bins_to_BAM': core-junction.c: In function 'find_donor_receptor': +sambam-file.c:2381:31: warning: variable 'last_written_BAI_chro' set but not used [-Wunused-but-set-variable] + 2381 | int old_chro_no = -1, last_written_BAI_chro = -1;; + | ^~~~~~~~~~~~~~~~~~~~~ core-junction.c:2096:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 2096 | if(0&& FIXLENstrcmp("V0112_0155:7:1101:12618:2466#ACTTGA", rname) == 0) | ^~ core-junction.c:2100:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 2100 | if( (end_site_mismatches + start_site_mismatches) * 500 + insertion_in_between_i < best_testing_score ){ | ^~ -sambam-file.c: In function 'SamBam_writer_sort_bins_to_BAM': -sambam-file.c:2381:31: warning: variable 'last_written_BAI_chro' set but not used [-Wunused-but-set-variable] - 2381 | int old_chro_no = -1, last_written_BAI_chro = -1;; - | ^~~~~~~~~~~~~~~~~~~~~ gene-algorithms.c: In function 'miltime': gene-algorithms.c:1585:17: warning: 'ftime' is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 1585 | ftime(&trp); @@ -455,13 +473,13 @@ aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o genRandomReads gen_rand_reads.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 -ffile-prefix-map=/build/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o detectionCall detection-calls.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm echo " " > longread-one/make.version +rm -f longread-one/*.o aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -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 -ffile-prefix-map=/build/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -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 aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -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 +cd longread-one && make aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o removeDup removeDupReads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -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 make[3]: Entering directory '/build/subread-2.0.3+dfsg/src/longread-one' aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.3"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMsorted-hashtable.o -c LRMsorted-hashtable.c detection-calls.c: In function 'DTCwrite_annotations': @@ -507,6 +525,7 @@ readSummary.c:6243:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 6243 | fread(tofill -> inbin + tofill -> inbin_len, 1, binlen, notmapped_fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm SUBindel.c: In function 'load_global_context_forindel': SUBindel.c:66:31: warning: '.reads' directive writing 6 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 66 | sprintf(tmp_fname, "%s.reads", context->config.index_prefix); @@ -580,7 +599,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -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 -ffile-prefix-map=/build/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -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 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'); @@ -597,7 +616,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -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 -ffile-prefix-map=/build/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.3"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMbase-index.o -c LRMbase-index.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -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 -ffile-prefix-map=/build/subread-2.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.3"\" -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 @@ -672,7 +690,7 @@ || Repeat threshold : 100 repeats || || Gapped index : no || || || -|| Free / total memory : 62.0GB / 62.9GB || +|| Free / total memory : 52.2GB / 62.9GB || || || || Input files : 1 file in total || || o chr901.fa || @@ -688,30 +706,30 @@ || 52 uninformative subreads were found. || || These subreads were excluded from index building. || || Estimate the index size... || -|| 8%, 0 mins elapsed, rate=1197.6k bps/s || -|| 16%, 0 mins elapsed, rate=1842.5k bps/s || -|| 25%, 0 mins elapsed, rate=2265.7k bps/s || -|| 33%, 0 mins elapsed, rate=2540.4k bps/s || -|| 41%, 0 mins elapsed, rate=2757.6k bps/s || -|| 50%, 0 mins elapsed, rate=2907.5k bps/s || -|| 58%, 0 mins elapsed, rate=3040.5k bps/s || -|| 66%, 0 mins elapsed, rate=3148.6k bps/s || -|| 75%, 0 mins elapsed, rate=3252.1k bps/s || -|| 83%, 0 mins elapsed, rate=3313.5k bps/s || -|| 91%, 0 mins elapsed, rate=3402.8k bps/s || +|| 8%, 0 mins elapsed, rate=1035.0k bps/s || +|| 16%, 0 mins elapsed, rate=1552.4k bps/s || +|| 25%, 0 mins elapsed, rate=1862.9k bps/s || +|| 33%, 0 mins elapsed, rate=2069.9k bps/s || +|| 41%, 0 mins elapsed, rate=2217.8k bps/s || +|| 50%, 0 mins elapsed, rate=2328.7k bps/s || +|| 58%, 0 mins elapsed, rate=2405.0k bps/s || +|| 66%, 0 mins elapsed, rate=2465.6k bps/s || +|| 75%, 0 mins elapsed, rate=2523.4k bps/s || +|| 83%, 0 mins elapsed, rate=2571.5k bps/s || +|| 91%, 0 mins elapsed, rate=2605.0k bps/s || || 1.3 GB of memory is needed for index building. || || Build the index... || -|| 8%, 0 mins elapsed, rate=101.2k bps/s || -|| 16%, 0 mins elapsed, rate=193.6k bps/s || -|| 25%, 0 mins elapsed, rate=278.8k bps/s || -|| 33%, 0 mins elapsed, rate=357.1k bps/s || -|| 41%, 0 mins elapsed, rate=429.5k bps/s || -|| 50%, 0 mins elapsed, rate=496.5k bps/s || -|| 58%, 0 mins elapsed, rate=558.3k bps/s || -|| 66%, 0 mins elapsed, rate=616.4k bps/s || -|| 75%, 0 mins elapsed, rate=671.3k bps/s || -|| 83%, 0 mins elapsed, rate=722.1k bps/s || -|| 91%, 0 mins elapsed, rate=770.4k bps/s || +|| 8%, 0 mins elapsed, rate=93.6k bps/s || +|| 16%, 0 mins elapsed, rate=177.6k bps/s || +|| 25%, 0 mins elapsed, rate=254.0k bps/s || +|| 33%, 0 mins elapsed, rate=323.1k bps/s || +|| 41%, 0 mins elapsed, rate=386.0k bps/s || +|| 50%, 0 mins elapsed, rate=443.6k bps/s || +|| 58%, 0 mins elapsed, rate=496.5k bps/s || +|| 66%, 0 mins elapsed, rate=545.2k bps/s || +|| 75%, 0 mins elapsed, rate=589.9k bps/s || +|| 83%, 0 mins elapsed, rate=631.3k bps/s || +|| 91%, 0 mins elapsed, rate=669.7k bps/s || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || @@ -725,7 +743,7 @@ || [ 90.0% finished ] || || [ 100.0% finished ] || || || -|| Total running time: 0.1 minutes. || +|| Total running time: 0.2 minutes. || || Index ../small1 was successfully built. || || || \\============================================================================// @@ -758,7 +776,7 @@ || || \\============================================================================// -//================ Running (16-May-2024 22:53:55, pid=21623) =================\\ +//================ Running (15-Apr-2023 18:39:07, pid=20709) =================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -772,10 +790,10 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.4 mins elapsed, rate=38.1k reads per second || +|| 33% completed, 0.4 mins elapsed, rate=30.3k 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 || +|| 83% completed, 0.5 mins elapsed, rate=0.6k reads per second || +|| 91% completed, 0.5 mins elapsed, rate=0.7k reads per second || || || || Completed successfully. || || || @@ -792,7 +810,7 @@ || || || Indels : 0 || || || -|| Running time : 0.4 minutes || +|| Running time : 0.5 minutes || || || \\============================================================================// @@ -824,7 +842,7 @@ || || \\============================================================================// -//================ Running (16-May-2024 22:54:21, pid=21629) =================\\ +//================ Running (15-Apr-2023 18:39:35, pid=21259) =================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -838,10 +856,10 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.4 mins elapsed, rate=38.3k reads per second || -|| 74% completed, 0.4 mins elapsed, rate=0.6k reads per second || -|| 83% completed, 0.4 mins elapsed, rate=0.7k reads per second || -|| 91% completed, 0.4 mins elapsed, rate=0.7k reads per second || +|| 33% completed, 0.4 mins elapsed, rate=30.6k reads per second || +|| 74% completed, 0.5 mins elapsed, rate=0.6k reads per second || +|| 83% completed, 0.5 mins elapsed, rate=0.6k reads per second || +|| 91% completed, 0.5 mins elapsed, rate=0.7k reads per second || || || || Completed successfully. || || || @@ -858,7 +876,7 @@ || || || Indels : 0 || || || -|| Running time : 0.4 minutes || +|| Running time : 0.5 minutes || || || \\============================================================================// @@ -895,7 +913,7 @@ || || \\============================================================================// -//================ Running (16-May-2024 22:54:47, pid=21633) =================\\ +//================ Running (15-Apr-2023 18:40:03, pid=21817) =================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -909,11 +927,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.4 mins elapsed, rate=18.4k fragments per second || +|| 33% completed, 0.5 mins elapsed, rate=14.6k fragments per second || || Estimated fragment length : 495 bp || -|| 74% completed, 0.4 mins elapsed, rate=0.6k fragments per second || -|| 83% completed, 0.4 mins elapsed, rate=0.6k fragments per second || -|| 91% completed, 0.4 mins elapsed, rate=0.7k fragments per second || +|| 74% completed, 0.5 mins elapsed, rate=0.5k fragments per second || +|| 83% completed, 0.5 mins elapsed, rate=0.6k fragments per second || +|| 91% completed, 0.5 mins elapsed, rate=0.6k fragments per second || || || || Completed successfully. || || || @@ -975,7 +993,7 @@ || || \\============================================================================// -//================ Running (16-May-2024 22:55:15, pid=21650) =================\\ +//================ Running (15-Apr-2023 18:40:34, pid=22962) =================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -989,11 +1007,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.4 mins elapsed, rate=18.3k fragments per second || +|| 33% completed, 0.4 mins elapsed, rate=14.8k fragments per second || || Estimated fragment length : 495 bp || -|| 74% completed, 0.4 mins elapsed, rate=0.6k fragments per second || -|| 83% completed, 0.4 mins elapsed, rate=0.6k fragments per second || -|| 91% completed, 0.4 mins elapsed, rate=0.7k fragments per second || +|| 74% completed, 0.5 mins elapsed, rate=0.5k fragments per second || +|| 83% completed, 0.5 mins elapsed, rate=0.6k fragments per second || +|| 91% completed, 0.5 mins elapsed, rate=0.7k fragments per second || || || || Completed successfully. || || || @@ -1055,7 +1073,7 @@ || || \\============================================================================// -//================ Running (16-May-2024 22:55:43, pid=21656) =================\\ +//================ Running (15-Apr-2023 18:41:03, pid=23929) =================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1069,11 +1087,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 0.4 mins elapsed, rate=19.6k fragments per second || +|| 33% completed, 0.4 mins elapsed, rate=15.6k fragments per second || || Estimated fragment length : 497 bp || -|| 74% completed, 0.4 mins elapsed, rate=0.6k fragments per second || -|| 83% completed, 0.4 mins elapsed, rate=0.6k fragments per second || -|| 91% completed, 0.4 mins elapsed, rate=0.7k fragments per second || +|| 74% 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. || || || @@ -1098,7 +1116,7 @@ || || || Indels : 15 || || || -|| Running time : 0.4 minutes || +|| Running time : 0.5 minutes || || || \\============================================================================// @@ -1136,7 +1154,7 @@ || || \\============================================================================// -//================ Running (16-May-2024 22:56:10, pid=21664) =================\\ +//================ Running (15-Apr-2023 18:41:31, pid=24522) =================\\ || || 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. @@ -1206,7 +1224,7 @@ || Repeat threshold : 100 repeats || || Gapped index : yes || || || -|| Free / total memory : 62.0GB / 62.9GB || +|| Free / total memory : 52.9GB / 62.9GB || || || || Input files : 1 file in total || || o chr901.fa || @@ -1222,30 +1240,30 @@ || 2 uninformative subreads were found. || || These subreads were excluded from index building. || || Estimate the index size... || -|| 8%, 0 mins elapsed, rate=5239.5k bps/s || -|| 16%, 0 mins elapsed, rate=6986.0k bps/s || -|| 25%, 0 mins elapsed, rate=7621.1k bps/s || -|| 33%, 0 mins elapsed, rate=8178.7k bps/s || -|| 41%, 0 mins elapsed, rate=8554.3k bps/s || -|| 50%, 0 mins elapsed, rate=8824.4k bps/s || -|| 58%, 0 mins elapsed, rate=8891.3k bps/s || -|| 66%, 0 mins elapsed, rate=9062.9k bps/s || -|| 75%, 0 mins elapsed, rate=9201.1k bps/s || -|| 83%, 0 mins elapsed, rate=9314.7k bps/s || -|| 91%, 0 mins elapsed, rate=9409.7k bps/s || +|| 8%, 0 mins elapsed, rate=4657.4k bps/s || +|| 16%, 0 mins elapsed, rate=5781.6k bps/s || +|| 25%, 0 mins elapsed, rate=6134.1k bps/s || +|| 33%, 0 mins elapsed, rate=6448.6k bps/s || +|| 41%, 0 mins elapsed, rate=6653.3k bps/s || +|| 50%, 0 mins elapsed, rate=6797.2k bps/s || +|| 58%, 0 mins elapsed, rate=6903.8k bps/s || +|| 66%, 0 mins elapsed, rate=6986.0k bps/s || +|| 75%, 0 mins elapsed, rate=7051.3k bps/s || +|| 83%, 0 mins elapsed, rate=7104.4k bps/s || +|| 91%, 0 mins elapsed, rate=7148.5k bps/s || || 0.6 GB of memory is needed for index building. || || Build the index... || -|| 8%, 0 mins elapsed, rate=735.4k bps/s || -|| 16%, 0 mins elapsed, rate=1309.9k bps/s || -|| 25%, 0 mins elapsed, rate=1758.7k bps/s || -|| 33%, 0 mins elapsed, rate=2135.8k bps/s || -|| 41%, 0 mins elapsed, rate=2451.2k bps/s || -|| 50%, 0 mins elapsed, rate=2704.3k bps/s || -|| 58%, 0 mins elapsed, rate=2934.1k bps/s || -|| 66%, 0 mins elapsed, rate=3133.9k bps/s || -|| 75%, 0 mins elapsed, rate=3294.7k bps/s || -|| 83%, 0 mins elapsed, rate=3449.9k bps/s || -|| 91%, 0 mins elapsed, rate=3588.1k bps/s || +|| 8%, 0 mins elapsed, rate=676.1k bps/s || +|| 16%, 0 mins elapsed, rate=1180.7k bps/s || +|| 25%, 0 mins elapsed, rate=1581.7k bps/s || +|| 33%, 0 mins elapsed, rate=1894.5k bps/s || +|| 41%, 0 mins elapsed, rate=2149.5k bps/s || +|| 50%, 0 mins elapsed, rate=2372.6k bps/s || +|| 58%, 0 mins elapsed, rate=2551.4k bps/s || +|| 66%, 0 mins elapsed, rate=2715.2k bps/s || +|| 75%, 0 mins elapsed, rate=2847.1k bps/s || +|| 83%, 0 mins elapsed, rate=2962.3k bps/s || +|| 91%, 0 mins elapsed, rate=3023.4k bps/s || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || @@ -1297,7 +1315,7 @@ || || \\============================================================================// -//================ Running (16-May-2024 22:56:12, pid=21671) =================\\ +//================ Running (15-Apr-2023 18:41:34, pid=24573) =================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1311,11 +1329,11 @@ || 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=8.0k fragments per second || || Estimated fragment length : 173 bp || -|| 77% completed, 0.1 mins elapsed, rate=2.5k fragments per second || -|| 87% completed, 0.1 mins elapsed, rate=2.7k fragments per second || -|| 97% completed, 0.1 mins elapsed, rate=2.9k fragments per second || +|| 77% completed, 0.1 mins elapsed, rate=2.2k fragments per second || +|| 87% completed, 0.1 mins elapsed, rate=2.4k fragments per second || +|| 97% completed, 0.1 mins elapsed, rate=2.5k fragments per second || || || || Completed successfully. || || || @@ -1378,7 +1396,7 @@ || || \\============================================================================// -//================ Running (16-May-2024 22:56:18, pid=21673) =================\\ +//================ Running (15-Apr-2023 18:41:41, pid=24719) =================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1392,11 +1410,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 41% completed, 0.1 mins elapsed, rate=6.1k fragments per second || +|| 41% completed, 0.1 mins elapsed, rate=4.1k fragments per second || || Estimated fragment length : 174 bp || -|| 77% completed, 0.1 mins elapsed, rate=2.2k fragments per second || -|| 87% completed, 0.1 mins elapsed, rate=2.3k fragments per second || -|| 97% completed, 0.1 mins elapsed, rate=2.4k fragments per second || +|| 77% completed, 0.1 mins elapsed, rate=1.8k fragments per second || +|| 87% completed, 0.1 mins elapsed, rate=1.9k fragments per second || +|| 97% completed, 0.1 mins elapsed, rate=2.0k fragments per second || || || || Completed successfully. || || || @@ -1596,9 +1614,9 @@ || || \\============================================================================// -//====================== Running (16-May-2024 22:56:25) ======================\\ +//====================== Running (15-Apr-2023 18:41:52) ======================\\ || || -|| Split BAM file into result/temp-snps-022214-5F98ECA8FD8F-* ... || +|| Split BAM file into result/temp-snps-025503-022705A1FE6E-* ... || || processed block chr901@999950 by thread 1/1 [block number=1/1] || || || || Completed successfully. || @@ -1660,10 +1678,10 @@ install -m0755 -d debian/subread-data/usr/share/doc/subread-data install -p -m0644 debian/copyright debian/subread-data/usr/share/doc/subread-data/copyright dh_installchangelogs -O--buildsystem=makefile - install -m0755 -d debian/subread/usr/share/doc/subread - install -p -m0644 debian/.debhelper/generated/subread/dh_installchangelogs.dch.trimmed debian/subread/usr/share/doc/subread/changelog.Debian install -m0755 -d debian/subread-data/usr/share/doc/subread-data install -p -m0644 debian/.debhelper/generated/subread-data/dh_installchangelogs.dch.trimmed debian/subread-data/usr/share/doc/subread-data/changelog.Debian + install -m0755 -d debian/subread/usr/share/doc/subread + install -p -m0644 debian/.debhelper/generated/subread/dh_installchangelogs.dch.trimmed debian/subread/usr/share/doc/subread/changelog.Debian rm -f debian/subread-data.debhelper.log debian/subread.debhelper.log debian/rules override_dh_installexamples-indep make[1]: Entering directory '/build/subread-2.0.3+dfsg' @@ -1703,57 +1721,57 @@ 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 debian/subread/usr/share/man/man1/featureCounts.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/flattenGTF.1 debian/subread/usr/share/man/man1/genRandomReads.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/propmapped.1 debian/subread/usr/share/man/man1/qualityScores.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/removeDup.1 debian/subread/usr/share/man/man1/repair.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subindel.1 debian/subread/usr/share/man/man1/subjunc.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/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/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 - 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/removeDup.1.dh-new debian/subread/usr/share/man/man1/removeDup.1 - mv debian/subread/usr/share/man/man1/repair.1.dh-new debian/subread/usr/share/man/man1/repair.1 - chmod 0644 -- debian/subread/usr/share/man/man1/removeDup.1 debian/subread/usr/share/man/man1/repair.1 - mv debian/subread/usr/share/man/man1/sublong.1.dh-new debian/subread/usr/share/man/man1/sublong.1 - mv debian/subread/usr/share/man/man1/subread-align.1.dh-new debian/subread/usr/share/man/man1/subread-align.1 - chmod 0644 -- debian/subread/usr/share/man/man1/sublong.1 debian/subread/usr/share/man/man1/subread-align.1 mv debian/subread/usr/share/man/man1/subindel.1.dh-new debian/subread/usr/share/man/man1/subindel.1 mv debian/subread/usr/share/man/man1/subjunc.1.dh-new debian/subread/usr/share/man/man1/subjunc.1 chmod 0644 -- debian/subread/usr/share/man/man1/subindel.1 debian/subread/usr/share/man/man1/subjunc.1 + mv debian/subread/usr/share/man/man1/propmapped.1.dh-new debian/subread/usr/share/man/man1/propmapped.1 + mv debian/subread/usr/share/man/man1/qualityScores.1.dh-new debian/subread/usr/share/man/man1/qualityScores.1 + chmod 0644 -- debian/subread/usr/share/man/man1/propmapped.1 debian/subread/usr/share/man/man1/qualityScores.1 mv debian/subread/usr/share/man/man1/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/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/removeDup.1.dh-new debian/subread/usr/share/man/man1/removeDup.1 + mv debian/subread/usr/share/man/man1/repair.1.dh-new debian/subread/usr/share/man/man1/repair.1 + chmod 0644 -- debian/subread/usr/share/man/man1/removeDup.1 debian/subread/usr/share/man/man1/repair.1 + mv debian/subread/usr/share/man/man1/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 dh_installinit -O--buildsystem=makefile dh_installsystemduser -O--buildsystem=makefile dh_perl -O--buildsystem=makefile dh_link -O--buildsystem=makefile dh_strip_nondeterminism -O--buildsystem=makefile dh_compress -O--buildsystem=makefile - cd debian/subread cd debian/subread-data + cd debian/subread 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 + 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/subread-2.0.3+dfsg' cd '/build/subread-2.0.3+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-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 ! -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/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-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/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-data/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 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-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/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 dh_missing -O--buildsystem=makefile @@ -1818,16 +1836,16 @@ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/48/e7419fd7f90ec1d879648b7a43d996f5b96326.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/48/e7419fd7f90ec1d879648b7a43d996f5b96326.debug debian/subread/usr/bin/featureCounts - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6e - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6e/85d93a664c0d46db01b58050876103306c1a01.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6e/85d93a664c0d46db01b58050876103306c1a01.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/6e/85d93a664c0d46db01b58050876103306c1a01.debug debian/subread/usr/bin/sublong install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e3 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e3/f9add37ab74922099e43d712b0d3563497ad9e.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e3/f9add37ab74922099e43d712b0d3563497ad9e.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/e3/f9add37ab74922099e43d712b0d3563497ad9e.debug debian/subread/usr/bin/exactSNP + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6e + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6e/85d93a664c0d46db01b58050876103306c1a01.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6e/85d93a664c0d46db01b58050876103306c1a01.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/6e/85d93a664c0d46db01b58050876103306c1a01.debug debian/subread/usr/bin/sublong install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/08 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/08/266e6674015f9ff8a1e55619d6ea1d92834390.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/08/266e6674015f9ff8a1e55619d6ea1d92834390.debug @@ -1850,20 +1868,20 @@ rm -f debian/subread-data/DEBIAN/shlibs dh_shlibdeps -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/qualityScores debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/subread-align debian/subread/usr/bin/featureCounts debian/subread/usr/bin/sublong debian/subread/usr/bin/exactSNP debian/subread/usr/bin/subindel debian/subread/usr/bin/subjunc + dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/lib/subread/txUnique debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/subread-align debian/subread/usr/bin/featureCounts debian/subread/usr/bin/exactSNP debian/subread/usr/bin/sublong debian/subread/usr/bin/subindel debian/subread/usr/bin/subjunc dh_installdeb -O--buildsystem=makefile install -m0755 -d debian/subread/DEBIAN install -m0755 -d debian/subread-data/DEBIAN dh_gencontrol -O--buildsystem=makefile - install -m0755 -d debian/subread-data/DEBIAN - echo misc:Depends= >> debian/subread-data.substvars - echo misc:Pre-Depends= >> debian/subread-data.substvars - dpkg-gencontrol -psubread-data -ldebian/changelog -Tdebian/subread-data.substvars -Pdebian/subread-data install -m0755 -d debian/subread/DEBIAN echo misc:Depends= >> debian/subread.substvars echo misc:Pre-Depends= >> debian/subread.substvars install -m0755 -d debian/.debhelper/subread/dbgsym-root/DEBIAN dpkg-gencontrol -psubread -ldebian/changelog -Tdebian/subread.substvars -Pdebian/.debhelper/subread/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=subread-dbgsym "-DDepends=subread (= \${binary:Version})" "-DDescription=debug symbols for subread" "-DBuild-Ids=08266e6674015f9ff8a1e55619d6ea1d92834390 183e4aa0f2b1c48f17d285402deb3441b2e843e2 27fdf123682350b173ab945cf38b2df8adc5eb74 2901a70a58f9011f732a93eb80550568846b480e 2c2e32ad64b03c1fc6978808471afa4e1ab2b5a4 3c9597f2fdf3ae610505b42c27a9ae5f34f2fd40 437bdbf031b7727451919edf1eb395b9c2e16a7c 48e7419fd7f90ec1d879648b7a43d996f5b96326 6e85d93a664c0d46db01b58050876103306c1a01 75c4098ac8ed92cc924285a74b384a522b567aae 9744afec8dedb137e6ed6e24304abfe589443c13 b530e78178464d6e8143b4fa4ff3b7396e6f7daf d07cf366ed72b401cbd26ad90630bf4d7acaf77b e3f9add37ab74922099e43d712b0d3563497ad9e f0efacca307986c17a19caa0b4e6cba4600ca2e7" -DSection=debug -UMulti-Arch -UReplaces -UBreaks + install -m0755 -d debian/subread-data/DEBIAN + echo misc:Depends= >> debian/subread-data.substvars + echo misc:Pre-Depends= >> debian/subread-data.substvars + dpkg-gencontrol -psubread-data -ldebian/changelog -Tdebian/subread-data.substvars -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 @@ -1871,21 +1889,21 @@ chmod 0644 -- debian/subread/DEBIAN/control dh_md5sums -O--buildsystem=makefile install -m0755 -d debian/subread-data/DEBIAN - install -m0755 -d debian/subread/DEBIAN cd debian/subread-data >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums + install -m0755 -d debian/subread/DEBIAN cd debian/subread >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums + chmod 0644 -- debian/subread-data/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-data .. + dpkg-deb --root-owner-group --build debian/.debhelper/subread/dbgsym-root .. +dpkg-deb: building package 'subread-data' in '../subread-data_2.0.3+dfsg-1_all.deb'. dpkg-deb: building package 'subread' in '../subread_2.0.3+dfsg-1_arm64.deb'. dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_2.0.3+dfsg-1_arm64.deb'. -dpkg-deb: building package 'subread-data' in '../subread-data_2.0.3+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../subread_2.0.3+dfsg-1_arm64.buildinfo dpkg-genchanges --build=binary -O../subread_2.0.3+dfsg-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1893,12 +1911,14 @@ 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/14521/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/14521/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/20149 and its subdirectories -I: Current time: Thu May 16 22:57:53 -12 2024 -I: pbuilder-time-stamp: 1715943473 +I: removing directory /srv/workspace/pbuilder/14521 and its subdirectories +I: Current time: Sat Apr 15 18:44:30 +14 2023 +I: pbuilder-time-stamp: 1681533870