Diff of the two buildlogs: -- --- b1/build.log 2024-05-15 14:05:14.660876020 +0000 +++ b2/build.log 2024-05-15 14:35:44.315017807 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jun 17 08:21:03 -12 2025 -I: pbuilder-time-stamp: 1750191663 +I: Current time: Thu May 16 04:05:19 +14 2024 +I: pbuilder-time-stamp: 1715781919 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying 0001-src-Makefile.Linux-Do-not-set-CFLAGS-and-CXXFLAGS-to.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/4030515/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/828607/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 15 14:05 /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/828607/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/828607/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='4e1e4ca5f6dd4757ab843b4ed18af450' - 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='4030515' - PS1='# ' - PS2='> ' + INVOCATION_ID=00a5e22eb0c8412da5175ac2afd79e5d + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=828607 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.lbv7B9T5/pbuilderrc_T07O --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.lbv7B9T5/b1 --logfile b1/build.log subread_2.0.6+dfsg-3.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.lbv7B9T5/pbuilderrc_KwW9 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.lbv7B9T5/b2 --logfile b2/build.log subread_2.0.6+dfsg-3.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 16 17:46 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4030515/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 14 11:24 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/828607/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -166,7 +198,7 @@ Get: 44 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] -Fetched 25.9 MB in 0s (107 MB/s) +Fetched 25.9 MB in 2s (13.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19699 files and directories currently installed.) @@ -333,8 +365,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Jun 17 20:21:33 UTC 2025. -Universal Time is now: Tue Jun 17 20:21:33 UTC 2025. +Local time is now: Wed May 15 14:07:40 UTC 2024. +Universal Time is now: Wed May 15 14:07:40 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -377,7 +409,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/subread-2.0.6+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_2.0.6+dfsg-3_source.changes +I: user script /srv/workspace/pbuilder/828607/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/828607/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/subread-2.0.6+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_2.0.6+dfsg-3_source.changes dpkg-buildpackage: info: source package subread dpkg-buildpackage: info: source version 2.0.6+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -393,7 +429,7 @@ rm -rf bin src/longread-one/make.version find . -name "*.o" -delete dh_auto_clean --sourcedirectory=src -- -f Makefile.Linux - cd src && make -j42 clean -f Makefile.Linux + cd src && make -j20 clean -f Makefile.Linux make[2]: Entering directory '/build/reproducible-path/subread-2.0.6+dfsg/src' rm -f core featureCounts exactSNP removeDup subread-buildindex core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o make[2]: Leaving directory '/build/reproducible-path/subread-2.0.6+dfsg/src' @@ -421,7 +457,7 @@ make[1]: Entering directory '/build/reproducible-path/subread-2.0.6+dfsg' dh_auto_build --sourcedirectory=src -- -f Makefile.Linux CC=x86_64-linux-gnu-gcc ; \ - cd src && make -j42 "INSTALL=install --strip-program=true" -f Makefile.Linux CC=x86_64-linux-gnu-gcc + cd src && make -j20 "INSTALL=install --strip-program=true" -f Makefile.Linux CC=x86_64-linux-gnu-gcc make[2]: Entering directory '/build/reproducible-path/subread-2.0.6+dfsg/src' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core.o core.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-junction.o core-junction.c @@ -440,18 +476,6 @@ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seek-zlib.o seek-zlib.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-blc.o input-blc.c -gene-value-index.c: In function 'is_offset_in_chro': -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 )) - | ^~ -In file included from gene-value-index.h:24, - from gene-value-index.c:25: -subread.h:143:28: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 143 | #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__) - | ^~~~~~~ -gene-value-index.c:87:41: note: in expansion of macro 'SUBREADprintf' - 87 | SUBREADprintf("INCHRO:%d ; POS:%d\n", ret, pos); - | ^~~~~~~~~~~~~ input-blc.c: In function 'iCache_continuous_read_lanes': input-blc.c:579:59: warning: unused variable 'npos' [-Wunused-variable] 579 | long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET); @@ -486,20 +510,12 @@ input-blc.c:498:49: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 498 | read(tfp -> cbcl_bin_fd,&btmp,4);// Number of bins | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gene-algorithms.c: In function 'miltime': input-blc.c:501:57: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 501 | read(tfp -> cbcl_bin_fd,&fromv,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ input-blc.c:502:57: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 502 | read(tfp -> cbcl_bin_fd,&tov,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here - 29 | extern int ftime (struct timeb *__timebuf) - | ^~~~~ input-blc.c:511:49: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 511 | read(tfp -> cbcl_bin_fd,&btmp,4);// Number of tiles (gzipped blocks) in this file | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -518,32 +534,50 @@ input-blc.c:524:49: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 524 | read(tfp -> cbcl_bin_fd,&btmp,1); // excluding non-FP? | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gene-value-index.c: In function 'is_offset_in_chro': +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 )) + | ^~ +In file included from gene-value-index.h:24, + from gene-value-index.c:25: +subread.h:143:28: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 143 | #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__) + | ^~~~~~~ +gene-value-index.c:87:41: note: in expansion of macro 'SUBREADprintf' + 87 | SUBREADprintf("INCHRO:%d ; POS:%d\n", ret, pos); + | ^~~~~~~~~~~~~ +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/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here + 29 | extern int ftime (struct timeb *__timebuf) + | ^~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o detectionCall detection-calls.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm echo " " > longread-one/make.version x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o repair read-repair.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o txUnique tx-unique.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm rm -f longread-one/*.o -x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -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 -x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o exactSNP SNPCalling.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-buildindex index-builder.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -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 -x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm cd longread-one && make -x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-fullscan fullscan.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o flattenGTF flattenAnnotations.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -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 make[3]: Entering directory '/build/reproducible-path/subread-2.0.6+dfsg/src/longread-one' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMsorted-hashtable.o -c LRMsorted-hashtable.c +x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMbase-index.o -c LRMbase-index.c +x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o exactSNP SNPCalling.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMchro-event.o -c LRMchro-event.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhelper.o -c LRMhelper.c +x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-buildindex index-builder.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMseek-zlib.o -c LRMseek-zlib.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMfile-io.o -c LRMfile-io.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhashtable.o -c LRMhashtable.c +x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -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 detection-calls.c: In function 'DTCwrite_annotations': detection-calls.c:155:9: warning: dangling pointer 'gc_2int' to an unnamed temporary may be used [-Wdangling-pointer=] 155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0); @@ -662,6 +696,8 @@ | | | int | %ld +x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o flattenGTF flattenAnnotations.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -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': longread-mapping.c:234:9: warning: 'ftime' is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] @@ -733,7 +769,7 @@ || Repeat threshold : 100 repeats || || Gapped index : no || || || -|| Free / total memory : 65.7GB / 78.5GB || +|| Free / total memory : 52.5GB / 78.8GB || || || || Input files : 1 file in total || || o chr901.fa || @@ -749,30 +785,30 @@ || 52 uninformative subreads were found. || || These subreads were excluded from index building. || || Estimate the index size... || -|| 8%, 0 mins elapsed, rate=598.8k bps/s || -|| 16%, 0 mins elapsed, rate=1110.4k bps/s || -|| 25%, 0 mins elapsed, rate=1552.4k bps/s || -|| 33%, 0 mins elapsed, rate=1949.6k bps/s || -|| 41%, 0 mins elapsed, rate=2290.5k bps/s || -|| 50%, 0 mins elapsed, rate=2592.7k bps/s || -|| 58%, 0 mins elapsed, rate=2862.6k bps/s || -|| 66%, 0 mins elapsed, rate=3133.9k bps/s || -|| 75%, 0 mins elapsed, rate=3368.3k bps/s || -|| 83%, 0 mins elapsed, rate=3582.6k bps/s || -|| 91%, 0 mins elapsed, rate=3810.5k bps/s || +|| 8%, 0 mins elapsed, rate=254.8k bps/s || +|| 16%, 0 mins elapsed, rate=479.0k bps/s || +|| 25%, 0 mins elapsed, rate=679.7k bps/s || +|| 33%, 0 mins elapsed, rate=857.6k bps/s || +|| 41%, 0 mins elapsed, rate=1017.4k bps/s || +|| 50%, 0 mins elapsed, rate=1161.6k bps/s || +|| 58%, 0 mins elapsed, rate=1284.1k bps/s || +|| 66%, 0 mins elapsed, rate=1403.0k bps/s || +|| 75%, 0 mins elapsed, rate=1515.0k bps/s || +|| 83%, 0 mins elapsed, rate=1618.4k bps/s || +|| 91%, 0 mins elapsed, rate=1714.0k bps/s || || 3.0 GB of memory is needed for index building. || || Build the index... || -|| 8%, 0 mins elapsed, rate=53.4k bps/s || -|| 16%, 0 mins elapsed, rate=105.0k bps/s || -|| 25%, 0 mins elapsed, rate=155.1k bps/s || -|| 33%, 0 mins elapsed, rate=203.7k bps/s || -|| 41%, 0 mins elapsed, rate=250.8k bps/s || -|| 50%, 0 mins elapsed, rate=296.8k bps/s || -|| 58%, 0 mins elapsed, rate=341.4k bps/s || -|| 66%, 0 mins elapsed, rate=385.0k bps/s || -|| 75%, 0 mins elapsed, rate=427.5k bps/s || -|| 83%, 0 mins elapsed, rate=468.6k bps/s || -|| 91%, 0 mins elapsed, rate=509.8k bps/s || +|| 8%, 0 mins elapsed, rate=7.6k bps/s || +|| 16%, 0 mins elapsed, rate=14.9k bps/s || +|| 25%, 0 mins elapsed, rate=21.7k bps/s || +|| 33%, 0 mins elapsed, rate=28.3k bps/s || +|| 41%, 0 mins elapsed, rate=34.6k bps/s || +|| 50%, 0 mins elapsed, rate=40.6k bps/s || +|| 58%, 0 mins elapsed, rate=46.3k bps/s || +|| 66%, 0 mins elapsed, rate=51.6k bps/s || +|| 75%, 0 mins elapsed, rate=57.0k bps/s || +|| 83%, 0 mins elapsed, rate=62.2k bps/s || +|| 91%, 0 mins elapsed, rate=67.4k bps/s || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || @@ -786,7 +822,7 @@ || [ 90.0% finished ] || || [ 100.0% finished ] || || || -|| Total running time: 0.1 minutes. || +|| Total running time: 1.6 minutes. || || Index ../small1 was successfully built. || || || \\============================================================================// @@ -819,7 +855,7 @@ || || \\============================================================================// -//=============== Running (17-Jun-2025 08:22:07, pid=4041434) ================\\ +//================ Running (16-May-2024 04:12:25, pid=869842) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -833,10 +869,10 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 1.0 mins elapsed, rate=61.7k reads per second || -|| 74% completed, 1.0 mins elapsed, rate=0.3k reads per second || -|| 83% completed, 1.0 mins elapsed, rate=0.3k reads per second || -|| 91% completed, 1.0 mins elapsed, rate=0.3k reads per second || +|| 33% completed, 2.7 mins elapsed, rate=8.1k reads per second || +|| 74% completed, 2.7 mins elapsed, rate=0.1k reads per second || +|| 83% completed, 2.8 mins elapsed, rate=0.1k reads per second || +|| 91% completed, 2.8 mins elapsed, rate=0.1k reads per second || || || || Completed successfully. || || || @@ -853,7 +889,7 @@ || || || Indels : 0 || || || -|| Running time : 1.0 minutes || +|| Running time : 2.8 minutes || || || \\============================================================================// @@ -885,7 +921,7 @@ || || \\============================================================================// -//=============== Running (17-Jun-2025 08:23:04, pid=4048081) ================\\ +//================ Running (16-May-2024 04:15:12, pid=891763) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -899,10 +935,10 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 1.0 mins elapsed, rate=61.7k reads per second || -|| 74% completed, 1.0 mins elapsed, rate=0.3k reads per second || -|| 83% completed, 1.0 mins elapsed, rate=0.3k reads per second || -|| 91% completed, 1.0 mins elapsed, rate=0.3k reads per second || +|| 33% completed, 2.9 mins elapsed, rate=6.2k reads per second || +|| 74% completed, 2.9 mins elapsed, rate=0.1k reads per second || +|| 83% completed, 2.9 mins elapsed, rate=0.1k reads per second || +|| 91% completed, 2.9 mins elapsed, rate=0.1k reads per second || || || || Completed successfully. || || || @@ -919,7 +955,7 @@ || || || Indels : 0 || || || -|| Running time : 1.0 minutes || +|| Running time : 2.9 minutes || || || \\============================================================================// @@ -956,7 +992,7 @@ || || \\============================================================================// -//=============== Running (17-Jun-2025 08:24:03, pid=4056329) ================\\ +//================ Running (16-May-2024 04:18:09, pid=910478) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -970,11 +1006,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 1.0 mins elapsed, rate=30.2k fragments per second || +|| 33% completed, 3.2 mins elapsed, rate=5.3k fragments per second || || Estimated fragment length : 495 bp || -|| 74% completed, 1.0 mins elapsed, rate=0.2k 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, 3.2 mins elapsed, rate=0.1k fragments per second || +|| 83% completed, 3.3 mins elapsed, rate=0.1k fragments per second || +|| 91% completed, 3.3 mins elapsed, rate=0.1k fragments per second || || || || Completed successfully. || || || @@ -999,7 +1035,7 @@ || || || Indels : 0 || || || -|| Running time : 1.0 minutes || +|| Running time : 3.3 minutes || || || \\============================================================================// @@ -1036,7 +1072,7 @@ || || \\============================================================================// -//=============== Running (17-Jun-2025 08:25:03, pid=4066135) ================\\ +//================ Running (16-May-2024 04:21:29, pid=933619) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1050,11 +1086,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 1.0 mins elapsed, rate=29.2k fragments per second || +|| 33% completed, 3.5 mins elapsed, rate=5.2k fragments per second || || Estimated fragment length : 495 bp || -|| 74% completed, 1.1 mins elapsed, rate=0.2k fragments per second || -|| 83% completed, 1.1 mins elapsed, rate=0.3k fragments per second || -|| 91% completed, 1.1 mins elapsed, rate=0.3k fragments per second || +|| 74% completed, 3.6 mins elapsed, rate=0.1k fragments per second || +|| 83% completed, 3.6 mins elapsed, rate=0.1k fragments per second || +|| 91% completed, 3.6 mins elapsed, rate=0.1k fragments per second || || || || Completed successfully. || || || @@ -1079,7 +1115,7 @@ || || || Indels : 0 || || || -|| Running time : 1.1 minutes || +|| Running time : 3.6 minutes || || || \\============================================================================// @@ -1116,7 +1152,7 @@ || || \\============================================================================// -//=============== Running (17-Jun-2025 08:26:07, pid=4086647) ================\\ +//================ Running (16-May-2024 04:25:07, pid=950296) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1130,11 +1166,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 33% completed, 1.0 mins elapsed, rate=31.6k fragments per second || +|| 33% completed, 3.4 mins elapsed, rate=4.2k fragments per second || || Estimated fragment length : 497 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, 3.4 mins elapsed, rate=0.1k fragments per second || +|| 83% completed, 3.4 mins elapsed, rate=0.1k fragments per second || +|| 91% completed, 3.5 mins elapsed, rate=0.1k fragments per second || || || || Completed successfully. || || || @@ -1159,7 +1195,7 @@ || || || Indels : 15 || || || -|| Running time : 1.0 minutes || +|| Running time : 3.5 minutes || || || \\============================================================================// @@ -1197,7 +1233,7 @@ || || \\============================================================================// -//=============== Running (17-Jun-2025 08:27:06, pid=4088556) ================\\ +//================ Running (16-May-2024 04:28:37, pid=959789) ================\\ || || 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. @@ -1267,7 +1303,7 @@ || Repeat threshold : 100 repeats || || Gapped index : yes || || || -|| Free / total memory : 65.6GB / 78.5GB || +|| Free / total memory : 57.5GB / 78.8GB || || || || Input files : 1 file in total || || o chr901.fa || @@ -1283,30 +1319,30 @@ || 2 uninformative subreads were found. || || These subreads were excluded from index building. || || Estimate the index size... || -|| 8%, 0 mins elapsed, rate=4412.2k bps/s || -|| 16%, 0 mins elapsed, rate=7289.7k bps/s || -|| 25%, 0 mins elapsed, rate=9314.6k bps/s || -|| 33%, 0 mins elapsed, rate=10817.0k bps/s || -|| 41%, 0 mins elapsed, rate=11976.0k bps/s || -|| 50%, 0 mins elapsed, rate=12897.2k bps/s || -|| 58%, 0 mins elapsed, rate=13972.0k bps/s || -|| 66%, 0 mins elapsed, rate=14579.5k bps/s || -|| 75%, 0 mins elapsed, rate=15089.7k bps/s || -|| 83%, 0 mins elapsed, rate=15524.4k bps/s || -|| 91%, 0 mins elapsed, rate=16178.1k bps/s || +|| 8%, 0 mins elapsed, rate=382.8k bps/s || +|| 16%, 0 mins elapsed, rate=649.9k bps/s || +|| 25%, 0 mins elapsed, rate=832.8k bps/s || +|| 33%, 0 mins elapsed, rate=995.0k bps/s || +|| 41%, 0 mins elapsed, rate=1097.3k bps/s || +|| 50%, 0 mins elapsed, rate=1125.3k bps/s || +|| 58%, 0 mins elapsed, rate=1176.0k bps/s || +|| 66%, 0 mins elapsed, rate=1210.6k bps/s || +|| 75%, 0 mins elapsed, rate=1251.2k bps/s || +|| 83%, 0 mins elapsed, rate=1274.0k bps/s || +|| 91%, 0 mins elapsed, rate=1328.7k bps/s || || 0.8 GB of memory is needed for index building. || || Build the index... || -|| 8%, 0 mins elapsed, rate=429.9k bps/s || -|| 16%, 0 mins elapsed, rate=821.9k bps/s || -|| 25%, 0 mins elapsed, rate=1186.3k bps/s || -|| 33%, 0 mins elapsed, rate=1524.2k bps/s || -|| 41%, 0 mins elapsed, rate=1838.4k bps/s || -|| 50%, 0 mins elapsed, rate=2131.3k bps/s || -|| 58%, 0 mins elapsed, rate=2405.0k bps/s || -|| 66%, 0 mins elapsed, rate=2661.3k bps/s || -|| 75%, 0 mins elapsed, rate=2901.9k bps/s || -|| 83%, 0 mins elapsed, rate=3128.1k bps/s || -|| 91%, 0 mins elapsed, rate=3341.1k bps/s || +|| 8%, 0 mins elapsed, rate=36.8k bps/s || +|| 16%, 0 mins elapsed, rate=71.8k bps/s || +|| 25%, 0 mins elapsed, rate=105.0k bps/s || +|| 33%, 0 mins elapsed, rate=137.4k bps/s || +|| 41%, 0 mins elapsed, rate=169.2k bps/s || +|| 50%, 0 mins elapsed, rate=198.7k bps/s || +|| 58%, 0 mins elapsed, rate=226.4k bps/s || +|| 66%, 0 mins elapsed, rate=251.7k bps/s || +|| 75%, 0 mins elapsed, rate=276.1k bps/s || +|| 83%, 0 mins elapsed, rate=300.5k bps/s || +|| 91%, 0 mins elapsed, rate=322.0k bps/s || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || @@ -1320,7 +1356,7 @@ || [ 90.0% finished ] || || [ 100.0% finished ] || || || -|| Total running time: 0.0 minutes. || +|| Total running time: 0.3 minutes. || || Index ../small1 was successfully built. || || || \\============================================================================// @@ -1358,7 +1394,7 @@ || || \\============================================================================// -//=============== Running (17-Jun-2025 08:27:09, pid=4088626) ================\\ +//================ Running (16-May-2024 04:28:56, pid=960642) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1372,11 +1408,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 41% completed, 0.1 mins elapsed, rate=20.8k fragments per second || +|| 41% completed, 0.4 mins elapsed, rate=4.5k fragments per second || || Estimated fragment length : 173 bp || -|| 77% completed, 0.1 mins elapsed, rate=1.5k fragments per second || -|| 87% completed, 0.1 mins elapsed, rate=1.7k fragments per second || -|| 97% completed, 0.1 mins elapsed, rate=1.9k fragments per second || +|| 77% completed, 0.4 mins elapsed, rate=0.5k fragments per second || +|| 87% completed, 0.5 mins elapsed, rate=0.5k fragments per second || +|| 97% completed, 0.5 mins elapsed, rate=0.5k fragments per second || || || || Completed successfully. || || || @@ -1402,7 +1438,7 @@ || Junctions : 419 || || Indels : 177 || || || -|| Running time : 0.1 minutes || +|| Running time : 0.5 minutes || || || \\============================================================================// @@ -1439,7 +1475,7 @@ || || \\============================================================================// -//=============== Running (17-Jun-2025 08:27:17, pid=4090013) ================\\ +//================ Running (16-May-2024 04:29:25, pid=962410) ================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1453,11 +1489,11 @@ || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || -|| 41% completed, 0.1 mins elapsed, rate=11.9k fragments per second || +|| 41% completed, 0.5 mins elapsed, rate=1.3k fragments per second || || Estimated fragment length : 174 bp || -|| 77% completed, 0.1 mins elapsed, rate=1.5k fragments per second || -|| 87% completed, 0.1 mins elapsed, rate=1.6k fragments per second || -|| 97% completed, 0.2 mins elapsed, rate=1.7k fragments per second || +|| 77% completed, 0.5 mins elapsed, rate=0.4k fragments per second || +|| 87% completed, 0.6 mins elapsed, rate=0.4k fragments per second || +|| 97% completed, 0.6 mins elapsed, rate=0.4k fragments per second || || || || Completed successfully. || || || @@ -1484,7 +1520,7 @@ || Fusions : 33 || || Indels : 180 || || || -|| Running time : 0.2 minutes || +|| Running time : 0.6 minutes || || || \\============================================================================// @@ -1657,9 +1693,9 @@ || || \\============================================================================// -//====================== Running (17-Jun-2025 08:27:27) ======================\\ +//====================== Running (16-May-2024 04:30:11) ======================\\ || || -|| Split BAM file into result/temp-snps-4092963-522AC0F4F503-* ... || +|| Split BAM file into result/temp-snps-964796-C55EA8440BE2-* ... || || processed block chr901@999950 by thread 1/1 [block number=1/1] || || || || Completed successfully. || @@ -1672,7 +1708,7 @@ || Reported SNPs : 416 || || Reported indels : 22 || || || -|| Running time : 0.0 minutes || +|| Running time : 0.1 minutes || || || \\============================================================================// @@ -1723,10 +1759,10 @@ install -m0755 -d debian/subread-data/usr/share/doc/subread-data install -p -m0644 debian/copyright debian/subread-data/usr/share/doc/subread-data/copyright dh_installchangelogs -O--buildsystem=makefile - install -m0755 -d debian/subread-data/usr/share/doc/subread-data - install -p -m0644 debian/.debhelper/generated/subread-data/dh_installchangelogs.dch.trimmed debian/subread-data/usr/share/doc/subread-data/changelog.Debian install -m0755 -d debian/subread/usr/share/doc/subread install -p -m0644 debian/.debhelper/generated/subread/dh_installchangelogs.dch.trimmed debian/subread/usr/share/doc/subread/changelog.Debian + install -m0755 -d debian/subread-data/usr/share/doc/subread-data + install -p -m0644 debian/.debhelper/generated/subread-data/dh_installchangelogs.dch.trimmed debian/subread-data/usr/share/doc/subread-data/changelog.Debian rm -f debian/subread-data.debhelper.log debian/subread.debhelper.log debian/rules override_dh_installexamples-indep make[1]: Entering directory '/build/reproducible-path/subread-2.0.6+dfsg' @@ -1765,48 +1801,48 @@ 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/exactSNP.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/featureCounts.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subjunc.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/flattenGTF.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/featureCounts.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/genRandomReads.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/propmapped.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/qualityScores.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/removeDup.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/propmapped.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/exactSNP.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/repair.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subindel.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subjunc.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/sublong.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/qualityScores.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-align.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/sublong.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-fullscan.1 - mv debian/subread/usr/share/man/man1/exactSNP.1.dh-new debian/subread/usr/share/man/man1/exactSNP.1 - chmod 0644 -- debian/subread/usr/share/man/man1/exactSNP.1 - mv debian/subread/usr/share/man/man1/featureCounts.1.dh-new debian/subread/usr/share/man/man1/featureCounts.1 - chmod 0644 -- debian/subread/usr/share/man/man1/featureCounts.1 - mv debian/subread/usr/share/man/man1/genRandomReads.1.dh-new debian/subread/usr/share/man/man1/genRandomReads.1 - chmod 0644 -- debian/subread/usr/share/man/man1/genRandomReads.1 - mv debian/subread/usr/share/man/man1/flattenGTF.1.dh-new debian/subread/usr/share/man/man1/flattenGTF.1 - chmod 0644 -- debian/subread/usr/share/man/man1/flattenGTF.1 - mv debian/subread/usr/share/man/man1/qualityScores.1.dh-new debian/subread/usr/share/man/man1/qualityScores.1 - chmod 0644 -- debian/subread/usr/share/man/man1/qualityScores.1 + mv debian/subread/usr/share/man/man1/subjunc.1.dh-new debian/subread/usr/share/man/man1/subjunc.1 + chmod 0644 -- debian/subread/usr/share/man/man1/subjunc.1 mv debian/subread/usr/share/man/man1/removeDup.1.dh-new debian/subread/usr/share/man/man1/removeDup.1 chmod 0644 -- debian/subread/usr/share/man/man1/removeDup.1 mv debian/subread/usr/share/man/man1/propmapped.1.dh-new debian/subread/usr/share/man/man1/propmapped.1 chmod 0644 -- debian/subread/usr/share/man/man1/propmapped.1 mv debian/subread/usr/share/man/man1/repair.1.dh-new debian/subread/usr/share/man/man1/repair.1 chmod 0644 -- debian/subread/usr/share/man/man1/repair.1 - mv debian/subread/usr/share/man/man1/subindel.1.dh-new debian/subread/usr/share/man/man1/subindel.1 - chmod 0644 -- debian/subread/usr/share/man/man1/subindel.1 mv debian/subread/usr/share/man/man1/sublong.1.dh-new debian/subread/usr/share/man/man1/sublong.1 chmod 0644 -- debian/subread/usr/share/man/man1/sublong.1 - mv debian/subread/usr/share/man/man1/subjunc.1.dh-new debian/subread/usr/share/man/man1/subjunc.1 - chmod 0644 -- debian/subread/usr/share/man/man1/subjunc.1 + mv debian/subread/usr/share/man/man1/exactSNP.1.dh-new debian/subread/usr/share/man/man1/exactSNP.1 + chmod 0644 -- debian/subread/usr/share/man/man1/exactSNP.1 + mv debian/subread/usr/share/man/man1/qualityScores.1.dh-new debian/subread/usr/share/man/man1/qualityScores.1 + chmod 0644 -- debian/subread/usr/share/man/man1/qualityScores.1 mv debian/subread/usr/share/man/man1/subread-buildindex.1.dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 chmod 0644 -- debian/subread/usr/share/man/man1/subread-buildindex.1 - mv debian/subread/usr/share/man/man1/subread-align.1.dh-new debian/subread/usr/share/man/man1/subread-align.1 - chmod 0644 -- debian/subread/usr/share/man/man1/subread-align.1 + mv debian/subread/usr/share/man/man1/flattenGTF.1.dh-new debian/subread/usr/share/man/man1/flattenGTF.1 + chmod 0644 -- debian/subread/usr/share/man/man1/flattenGTF.1 + mv debian/subread/usr/share/man/man1/subindel.1.dh-new debian/subread/usr/share/man/man1/subindel.1 + chmod 0644 -- debian/subread/usr/share/man/man1/subindel.1 mv debian/subread/usr/share/man/man1/subread-fullscan.1.dh-new debian/subread/usr/share/man/man1/subread-fullscan.1 chmod 0644 -- debian/subread/usr/share/man/man1/subread-fullscan.1 + mv debian/subread/usr/share/man/man1/featureCounts.1.dh-new debian/subread/usr/share/man/man1/featureCounts.1 + chmod 0644 -- debian/subread/usr/share/man/man1/featureCounts.1 + mv debian/subread/usr/share/man/man1/genRandomReads.1.dh-new debian/subread/usr/share/man/man1/genRandomReads.1 + chmod 0644 -- debian/subread/usr/share/man/man1/genRandomReads.1 + mv debian/subread/usr/share/man/man1/subread-align.1.dh-new debian/subread/usr/share/man/man1/subread-align.1 + chmod 0644 -- debian/subread/usr/share/man/man1/subread-align.1 dh_installsystemduser -O--buildsystem=makefile dh_perl -O--buildsystem=makefile dh_link -O--buildsystem=makefile @@ -1814,17 +1850,17 @@ Using 1714041519 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 - 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 + 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 - 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 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/reproducible-path/subread-2.0.6+dfsg' cd '/build/reproducible-path/subread-2.0.6+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 ! -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/usr/share/doc -type f -a -true -a ! -regex 'debian/subread/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread-data/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 @@ -1841,81 +1877,81 @@ objcopy --compress-debug-sections debian/subread/usr/lib/debug/.dwz/x86_64-linux-gnu/subread.debug chmod 0644 -- debian/subread/usr/lib/debug/.dwz/x86_64-linux-gnu/subread.debug dh_strip -a -O--buildsystem=makefile - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f7 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f7/56c2b338ccd69e4227f70fc6144aad18a2c706.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f7/56c2b338ccd69e4227f70fc6144aad18a2c706.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/f7/56c2b338ccd69e4227f70fc6144aad18a2c706.debug debian/subread/usr/bin/subread-align - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4b - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/featureCounts debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4b/66a0c855f65034b9c88c2604f64e2d8e24fc4e.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4b/66a0c855f65034b9c88c2604f64e2d8e24fc4e.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/4b/66a0c855f65034b9c88c2604f64e2d8e24fc4e.debug debian/subread/usr/bin/featureCounts install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/25 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/25/4b4052f1e2ebcd9909b0ad8fb72d9fcfab759d.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/25/4b4052f1e2ebcd9909b0ad8fb72d9fcfab759d.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/25/4b4052f1e2ebcd9909b0ad8fb72d9fcfab759d.debug debian/subread/usr/bin/subindel - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0c - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0c/55ef4af20140aaf7fcb3560b08b4ad162fdd90.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0c/55ef4af20140aaf7fcb3560b08b4ad162fdd90.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/0c/55ef4af20140aaf7fcb3560b08b4ad162fdd90.debug debian/subread/usr/bin/sublong - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0b - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0b/d0cf3b544b5735c28db9cc7ad8e1bd5d748246.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0b/d0cf3b544b5735c28db9cc7ad8e1bd5d748246.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/0b/d0cf3b544b5735c28db9cc7ad8e1bd5d748246.debug debian/subread/usr/bin/subjunc - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-buildindex debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5/e2d3345f1d0afc84d44f1381918b1e6e5d9c34.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5/e2d3345f1d0afc84d44f1381918b1e6e5d9c34.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/f5/e2d3345f1d0afc84d44f1381918b1e6e5d9c34.debug debian/subread/usr/bin/subread-buildindex install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2d objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2d/476f0a481c5f537ae2e34f367ddc29edc84203.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2d/476f0a481c5f537ae2e34f367ddc29edc84203.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/2d/476f0a481c5f537ae2e34f367ddc29edc84203.debug debian/subread/usr/bin/exactSNP - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6f - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/genRandomReads debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6f/4fdc7167c4c9b6f1b051e85c3c12f38f1e855a.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6f/4fdc7167c4c9b6f1b051e85c3c12f38f1e855a.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/genRandomReads - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6f/4fdc7167c4c9b6f1b051e85c3c12f38f1e855a.debug debian/subread/usr/lib/subread/genRandomReads - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bc - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bc/86d036954c26bb2a4f5524a23d0b8a450432ff.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bc/86d036954c26bb2a4f5524a23d0b8a450432ff.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/bc/86d036954c26bb2a4f5524a23d0b8a450432ff.debug debian/subread/usr/lib/subread/qualityScores - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bf - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/txUnique debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bf/8d32639f2d323f9de36c7e78821c915931e18c.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bf/8d32639f2d323f9de36c7e78821c915931e18c.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/txUnique - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bf/8d32639f2d323f9de36c7e78821c915931e18c.debug debian/subread/usr/lib/subread/txUnique + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-buildindex debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5/e2d3345f1d0afc84d44f1381918b1e6e5d9c34.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5/e2d3345f1d0afc84d44f1381918b1e6e5d9c34.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/f5/e2d3345f1d0afc84d44f1381918b1e6e5d9c34.debug debian/subread/usr/bin/subread-buildindex + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0b + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0b/d0cf3b544b5735c28db9cc7ad8e1bd5d748246.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0b/d0cf3b544b5735c28db9cc7ad8e1bd5d748246.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/0b/d0cf3b544b5735c28db9cc7ad8e1bd5d748246.debug debian/subread/usr/bin/subjunc + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f7 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f7/56c2b338ccd69e4227f70fc6144aad18a2c706.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f7/56c2b338ccd69e4227f70fc6144aad18a2c706.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/f7/56c2b338ccd69e4227f70fc6144aad18a2c706.debug debian/subread/usr/bin/subread-align + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0c + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0c/55ef4af20140aaf7fcb3560b08b4ad162fdd90.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0c/55ef4af20140aaf7fcb3560b08b4ad162fdd90.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/0c/55ef4af20140aaf7fcb3560b08b4ad162fdd90.debug debian/subread/usr/bin/sublong + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4b + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/featureCounts debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4b/66a0c855f65034b9c88c2604f64e2d8e24fc4e.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4b/66a0c855f65034b9c88c2604f64e2d8e24fc4e.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/4b/66a0c855f65034b9c88c2604f64e2d8e24fc4e.debug debian/subread/usr/bin/featureCounts install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/87 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/87/d4fe4204462f658b032c3b52322c1ed2b4343b.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/87/d4fe4204462f658b032c3b52322c1ed2b4343b.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/87/d4fe4204462f658b032c3b52322c1ed2b4343b.debug debian/subread/usr/lib/subread/propmapped - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/fe - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/flattenGTF debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/fe/a9825a8fe565f69be8210e3f771792b4a6c616.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/fe/a9825a8fe565f69be8210e3f771792b4a6c616.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/fe/a9825a8fe565f69be8210e3f771792b4a6c616.debug debian/subread/usr/lib/subread/flattenGTF - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a3 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a3/e6485c8d3af5cf50b4688a643c3fff3571a395.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a3/e6485c8d3af5cf50b4688a643c3fff3571a395.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/a3/e6485c8d3af5cf50b4688a643c3fff3571a395.debug debian/subread/usr/lib/subread/removeDup + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bc + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bc/86d036954c26bb2a4f5524a23d0b8a450432ff.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bc/86d036954c26bb2a4f5524a23d0b8a450432ff.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/bc/86d036954c26bb2a4f5524a23d0b8a450432ff.debug debian/subread/usr/lib/subread/qualityScores install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/subread-fullscan debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5/35a71c76b73412c7a951bf2ad032f554bb838f.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5/35a71c76b73412c7a951bf2ad032f554bb838f.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/f5/35a71c76b73412c7a951bf2ad032f554bb838f.debug debian/subread/usr/lib/subread/subread-fullscan + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/fe + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/flattenGTF debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/fe/a9825a8fe565f69be8210e3f771792b4a6c616.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/fe/a9825a8fe565f69be8210e3f771792b4a6c616.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/fe/a9825a8fe565f69be8210e3f771792b4a6c616.debug debian/subread/usr/lib/subread/flattenGTF install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/14 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/repair debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/14/8524a3f5d05379d4f5c899fd58b535d6fe7fa7.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/14/8524a3f5d05379d4f5c899fd58b535d6fe7fa7.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/14/8524a3f5d05379d4f5c899fd58b535d6fe7fa7.debug debian/subread/usr/lib/subread/repair + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bf + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/txUnique debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bf/8d32639f2d323f9de36c7e78821c915931e18c.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bf/8d32639f2d323f9de36c7e78821c915931e18c.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/txUnique + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bf/8d32639f2d323f9de36c7e78821c915931e18c.debug debian/subread/usr/lib/subread/txUnique + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a3 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a3/e6485c8d3af5cf50b4688a643c3fff3571a395.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a3/e6485c8d3af5cf50b4688a643c3fff3571a395.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/a3/e6485c8d3af5cf50b4688a643c3fff3571a395.debug debian/subread/usr/lib/subread/removeDup + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6f + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/genRandomReads debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6f/4fdc7167c4c9b6f1b051e85c3c12f38f1e855a.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6f/4fdc7167c4c9b6f1b051e85c3c12f38f1e855a.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/genRandomReads + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6f/4fdc7167c4c9b6f1b051e85c3c12f38f1e855a.debug debian/subread/usr/lib/subread/genRandomReads install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/subread/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/subread/usr/lib/debug/.dwz @@ -1927,42 +1963,42 @@ rm -f debian/subread/DEBIAN/shlibs dh_shlibdeps -a -O--buildsystem=makefile install -m0755 -d debian/subread/DEBIAN - dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/bin/subread-align debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subindel debian/subread/usr/bin/sublong debian/subread/usr/bin/subjunc debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/exactSNP debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/txUnique debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/repair + dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/bin/subindel debian/subread/usr/bin/exactSNP debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/subjunc debian/subread/usr/bin/subread-align debian/subread/usr/bin/sublong debian/subread/usr/bin/featureCounts debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/txUnique debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/genRandomReads dh_installdeb -O--buildsystem=makefile install -m0755 -d debian/subread/DEBIAN install -m0755 -d debian/subread-data/DEBIAN 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 -cdebian/control -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 -cdebian/control -Pdebian/.debhelper/subread/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=subread-dbgsym "-DDepends=subread (= \${binary:Version})" "-DDescription=debug symbols for subread" "-DBuild-Ids=0bd0cf3b544b5735c28db9cc7ad8e1bd5d748246 0c55ef4af20140aaf7fcb3560b08b4ad162fdd90 148524a3f5d05379d4f5c899fd58b535d6fe7fa7 254b4052f1e2ebcd9909b0ad8fb72d9fcfab759d 2d476f0a481c5f537ae2e34f367ddc29edc84203 4b66a0c855f65034b9c88c2604f64e2d8e24fc4e 6f4fdc7167c4c9b6f1b051e85c3c12f38f1e855a 87d4fe4204462f658b032c3b52322c1ed2b4343b a3e6485c8d3af5cf50b4688a643c3fff3571a395 bc86d036954c26bb2a4f5524a23d0b8a450432ff bf8d32639f2d323f9de36c7e78821c915931e18c f535a71c76b73412c7a951bf2ad032f554bb838f f5e2d3345f1d0afc84d44f1381918b1e6e5d9c34 f756c2b338ccd69e4227f70fc6144aad18a2c706 fea9825a8fe565f69be8210e3f771792b4a6c616" -DSection=debug -UMulti-Arch -UReplaces -UBreaks -dpkg-gencontrol: warning: Depends field of package subread-data: substitution variable ${shlibs:Depends} used, but is not defined - chmod 0644 -- debian/subread-data/DEBIAN/control + 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 -cdebian/control -Pdebian/subread-data chmod 0644 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/control dpkg-gencontrol -psubread -ldebian/changelog -Tdebian/subread.substvars -cdebian/control -Pdebian/subread chmod 0644 -- debian/subread/DEBIAN/control +dpkg-gencontrol: warning: Depends field of package subread-data: substitution variable ${shlibs:Depends} used, but is not defined + chmod 0644 -- debian/subread-data/DEBIAN/control dh_md5sums -O--buildsystem=makefile install -m0755 -d debian/subread/DEBIAN + cd debian/subread >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums install -m0755 -d debian/subread-data/DEBIAN cd debian/subread-data >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums - cd debian/subread >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/subread/DEBIAN/md5sums install -m0755 -d debian/.debhelper/subread/dbgsym-root/DEBIAN cd debian/.debhelper/subread/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums - chmod 0644 -- debian/subread-data/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/md5sums + chmod 0644 -- debian/subread-data/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: building package 'subread' in '../subread_2.0.6+dfsg-3_amd64.deb'. -dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_2.0.6+dfsg-3_amd64.deb'. dpkg-deb: building package 'subread-data' in '../subread-data_2.0.6+dfsg-3_all.deb'. + dpkg-deb --root-owner-group --build debian/.debhelper/subread/dbgsym-root .. + dpkg-deb --root-owner-group --build debian/subread .. +dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_2.0.6+dfsg-3_amd64.deb'. +dpkg-deb: building package 'subread' in '../subread_2.0.6+dfsg-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../subread_2.0.6+dfsg-3_amd64.buildinfo dpkg-genchanges --build=binary -O../subread_2.0.6+dfsg-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1970,12 +2006,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/828607/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/828607/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/4030515 and its subdirectories -I: Current time: Tue Jun 17 08:28:13 -12 2025 -I: pbuilder-time-stamp: 1750192093 +I: removing directory /srv/workspace/pbuilder/828607 and its subdirectories +I: Current time: Thu May 16 04:35:43 +14 2024 +I: pbuilder-time-stamp: 1715783743