Diff of the two buildlogs:
--
--- b1/build.log 2025-03-09 01:01:03.510889878 +0000
+++ b2/build.log 2025-03-09 01:09:25.420266246 +0000
@@ -1,6 +1,6 @@
I: pbuilder: network access will be disabled during build
-I: Current time: Fri Apr 10 19:16:30 -12 2026
-I: pbuilder-time-stamp: 1775891790
+I: Current time: Sun Mar 9 15:01:06 +14 2025
+I: pbuilder-time-stamp: 1741482066
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
@@ -28,52 +28,84 @@
dpkg-source: info: applying 0001-src-Makefile.Linux-Do-not-set-CFLAGS-and-CXXFLAGS-to.patch
I: Not using root during the build.
I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/374784/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/817158/tmp/hooks/D01_modify_environment starting
+debug: Running on ionos11-amd64.
+I: Changing host+domainname to test build reproducibility
+I: Adding a custom variable just for the fun of it...
+I: Changing /bin/sh to bash
+'/bin/sh' -> '/bin/bash'
+lrwxrwxrwx 1 root root 9 Mar 9 01:01 /bin/sh -> /bin/bash
+I: Setting pbuilder2's login shell to /bin/bash
+I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
+I: user script /srv/workspace/pbuilder/817158/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/817158/tmp/hooks/D02_print_environment starting
I: set
- BUILDDIR='/build/reproducible-path'
- BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
- BUILDUSERNAME='pbuilder1'
- BUILD_ARCH='amd64'
- DEBIAN_FRONTEND='noninteractive'
- DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 '
- DISTRIBUTION='trixie'
- HOME='/root'
- HOST_ARCH='amd64'
+ BASH=/bin/sh
+ BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
+ BASH_ALIASES=()
+ BASH_ARGC=()
+ BASH_ARGV=()
+ BASH_CMDS=()
+ BASH_LINENO=([0]="12" [1]="0")
+ BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
+ BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
+ BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
+ BASH_VERSION='5.2.37(1)-release'
+ BUILDDIR=/build/reproducible-path
+ BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+ BUILDUSERNAME=pbuilder2
+ BUILD_ARCH=amd64
+ DEBIAN_FRONTEND=noninteractive
+ DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 '
+ DIRSTACK=()
+ DISTRIBUTION=trixie
+ EUID=0
+ FUNCNAME=([0]="Echo" [1]="main")
+ GROUPS=()
+ HOME=/root
+ HOSTNAME=i-capture-the-hostname
+ HOSTTYPE=x86_64
+ HOST_ARCH=amd64
IFS='
'
- INVOCATION_ID='f8fdf4f7bd4845d8a16b55d7faf7c8a5'
- LANG='C'
- LANGUAGE='en_US:en'
- LC_ALL='C'
- MAIL='/var/mail/root'
- OPTIND='1'
- PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
- PBCURRENTCOMMANDLINEOPERATION='build'
- PBUILDER_OPERATION='build'
- PBUILDER_PKGDATADIR='/usr/share/pbuilder'
- PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
- PBUILDER_SYSCONFDIR='/etc'
- PPID='374784'
- PS1='# '
- PS2='> '
+ INVOCATION_ID=a697d3395c8a4020bb69d8d9b8efebfd
+ LANG=C
+ LANGUAGE=et_EE:et
+ LC_ALL=C
+ MACHTYPE=x86_64-pc-linux-gnu
+ MAIL=/var/mail/root
+ OPTERR=1
+ OPTIND=1
+ OSTYPE=linux-gnu
+ PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
+ PBCURRENTCOMMANDLINEOPERATION=build
+ PBUILDER_OPERATION=build
+ PBUILDER_PKGDATADIR=/usr/share/pbuilder
+ PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
+ PBUILDER_SYSCONFDIR=/etc
+ PIPESTATUS=([0]="0")
+ POSIXLY_CORRECT=y
+ PPID=817158
PS4='+ '
- PWD='/'
- SHELL='/bin/bash'
- SHLVL='2'
- SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.HHfEzPHc/pbuilderrc_zZHD --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HHfEzPHc/b1 --logfile b1/build.log subread_2.0.8+dfsg-1.dsc'
- SUDO_GID='110'
- SUDO_UID='105'
- SUDO_USER='jenkins'
- TERM='unknown'
- TZ='/usr/share/zoneinfo/Etc/GMT+12'
- USER='root'
- _='/usr/bin/systemd-run'
- http_proxy='http://213.165.73.152:3128'
+ PWD=/
+ SHELL=/bin/bash
+ SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
+ SHLVL=3
+ SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.HHfEzPHc/pbuilderrc_NkWC --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HHfEzPHc/b2 --logfile b2/build.log subread_2.0.8+dfsg-1.dsc'
+ SUDO_GID=111
+ SUDO_UID=106
+ SUDO_USER=jenkins
+ TERM=unknown
+ TZ=/usr/share/zoneinfo/Etc/GMT-14
+ UID=0
+ USER=root
+ _='I: set'
+ http_proxy=http://46.16.76.132:3128
I: uname -a
- Linux ionos5-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux
+ Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
I: ls -l /bin
- lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/374784/tmp/hooks/D02_print_environment finished
+ lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/817158/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
@@ -164,7 +196,7 @@
Get: 45 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 46 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB]
Get: 47 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
-Fetched 28.1 MB in 0s (140 MB/s)
+Fetched 28.1 MB in 0s (63.0 MB/s)
Preconfiguring packages ...
Selecting previously unselected package libpython3.13-minimal:amd64.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19800 files and directories currently installed.)
@@ -334,8 +366,8 @@
Setting up tzdata (2025a-2) ...
Current default time zone: 'Etc/UTC'
-Local time is now: Sat Apr 11 07:17:01 UTC 2026.
-Universal Time is now: Sat Apr 11 07:17:01 UTC 2026.
+Local time is now: Sun Mar 9 01:02:00 UTC 2025.
+Universal Time is now: Sun Mar 9 01:02:00 UTC 2025.
Run 'dpkg-reconfigure tzdata' if you wish to change it.
Setting up autotools-dev (20220109.1) ...
@@ -379,7 +411,11 @@
Building tag database...
-> Finished parsing the build-deps
I: Building the package
-I: Running cd /build/reproducible-path/subread-2.0.8+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../subread_2.0.8+dfsg-1_source.changes
+I: user script /srv/workspace/pbuilder/817158/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for trixie
+I: user script /srv/workspace/pbuilder/817158/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/subread-2.0.8+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../subread_2.0.8+dfsg-1_source.changes
dpkg-buildpackage: info: source package subread
dpkg-buildpackage: info: source version 2.0.8+dfsg-1
dpkg-buildpackage: info: source distribution unstable
@@ -395,7 +431,7 @@
rm -rf bin src/longread-one/make.version
find . -name "*.o" -delete
dh_auto_clean --sourcedirectory=src -- -f Makefile.Linux
- cd src && make -j42 clean -f Makefile.Linux
+ cd src && make -j20 clean -f Makefile.Linux
make[2]: Entering directory '/build/reproducible-path/subread-2.0.8+dfsg/src'
rm -f core featureCounts exactSNP removeDup subread-buildindex core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o
make[2]: Leaving directory '/build/reproducible-path/subread-2.0.8+dfsg/src'
@@ -423,7 +459,7 @@
make[1]: Entering directory '/build/reproducible-path/subread-2.0.8+dfsg'
dh_auto_build --sourcedirectory=src -- -f Makefile.Linux CC=x86_64-linux-gnu-gcc ; \
- cd src && make -j42 "INSTALL=install --strip-program=true" -f Makefile.Linux CC=x86_64-linux-gnu-gcc
+ cd src && make -j20 "INSTALL=install --strip-program=true" -f Makefile.Linux CC=x86_64-linux-gnu-gcc
make[2]: Entering directory '/build/reproducible-path/subread-2.0.8+dfsg/src'
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core.o core.c
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-junction.o core-junction.c
@@ -454,17 +490,25 @@
gene-value-index.c:87:41: note: in expansion of macro 'SUBREADprintf'
87 | SUBREADprintf("INCHRO:%d ; POS:%d\n", ret, pos);
| ^~~~~~~~~~~~~
-input-blc.c: In function 'iCache_continuous_read_lanes':
-input-blc.c:580:59: warning: unused variable 'npos' [-Wunused-variable]
- 580 | long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET);
- | ^~~~
+input-files.c: In function 'reduce_SAM_to_BAM':
core-junction.c: In function 'find_donor_receptor':
+input-files.c:3240:13: warning: unused variable 'seq_len' [-Wunused-variable]
+ 3240 | int seq_len = qual - seq - 1;
+ | ^~~~~~~
core-junction.c:2099:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
2099 | if(0&& FIXLENstrcmp("V0112_0155:7:1101:12618:2466#ACTTGA", rname) == 0)
| ^~
core-junction.c:2103:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
2103 | if( (end_site_mismatches + start_site_mismatches) * 500 + insertion_in_between_i < best_testing_score ){
| ^~
+input-blc.c: In function 'iCache_continuous_read_lanes':
+input-blc.c:580:59: warning: unused variable 'npos' [-Wunused-variable]
+ 580 | long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET);
+ | ^~~~
+input-files.c: In function 'SAM_pairer_fix_format':
+input-files.c:4830:50: warning: variable 'readname' set but not used [-Wunused-but-set-variable]
+ 4830 | char tmpfname [MAX_FILE_NAME_LENGTH+14], readname[256];
+ | ^~~~~~~~
gene-algorithms.c: In function 'miltime':
gene-algorithms.c:1395:17: warning: 'ftime' is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations]
1395 | ftime(&trp);
@@ -473,14 +517,6 @@
/usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here
29 | extern int ftime (struct timeb *__timebuf)
| ^~~~~
-input-files.c: In function 'reduce_SAM_to_BAM':
-input-files.c:3240:13: warning: unused variable 'seq_len' [-Wunused-variable]
- 3240 | int seq_len = qual - seq - 1;
- | ^~~~~~~
-input-files.c: In function 'SAM_pairer_fix_format':
-input-files.c:4830:50: warning: variable 'readname' set but not used [-Wunused-but-set-variable]
- 4830 | char tmpfname [MAX_FILE_NAME_LENGTH+14], readname[256];
- | ^~~~~~~~
sambam-file.c: In function 'PBam_chunk_headers':
sambam-file.c:564:41: warning: '__builtin___strcpy_chk' writing 256 bytes into a region of size 200 [-Wstringop-overflow=]
564 | strcpy(new_event->chro_name, chro_name);
@@ -513,28 +549,26 @@
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o detectionCall detection-calls.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
echo " " > longread-one/make.version
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o repair read-repair.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
-rm -f longread-one/*.o
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o txUnique tx-unique.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o removeDup removeDupReads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
-cd longread-one && make
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o exactSNP SNPCalling.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
+rm -f longread-one/*.o
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-buildindex index-builder.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
-make[3]: Entering directory '/build/reproducible-path/subread-2.0.8+dfsg/src/longread-one'
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subindel SUBindel.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
+cd longread-one && make
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
-x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMsorted-hashtable.o -c LRMsorted-hashtable.c
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
+make[3]: Entering directory '/build/reproducible-path/subread-2.0.8+dfsg/src/longread-one'
+x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMsorted-hashtable.o -c LRMsorted-hashtable.c
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-fullscan fullscan.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
+x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o flattenGTF flattenAnnotations.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMbase-index.o -c LRMbase-index.c
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMchro-event.o -c LRMchro-event.c
-x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o flattenGTF flattenAnnotations.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhelper.o -c LRMhelper.c
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMseek-zlib.o -c LRMseek-zlib.c
-x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMfile-io.o -c LRMfile-io.c
-x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhashtable.o -c LRMhashtable.c
detection-calls.c: In function 'DTCwrite_annotations':
detection-calls.c:155:9: warning: dangling pointer 'gc_2int' to an unnamed temporary may be used [-Wdangling-pointer=]
155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0);
@@ -548,22 +582,6 @@
detection-calls.c:154:48: note: unnamed temporary defined here
154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0};
| ^
-In file included from readSummary.c:41:
-readSummary.c: In function 'get_RG_tables':
-readSummary.c:2505:31: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
- 2505 | SUBREADprintf("cannot allocate memory for %s (%d)\n", rg_name, strlen(rg_name));
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~
- | |
- | size_t {aka long unsigned int}
-subread.h:142:44: note: in definition of macro 'SUBREADprintf'
- 142 | #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__)
- | ^~~~~~~~~~~
-readSummary.c:2505:64: note: format string is defined here
- 2505 | SUBREADprintf("cannot allocate memory for %s (%d)\n", rg_name, strlen(rg_name));
- | ~^
- | |
- | int
- | %ld
SUBindel.c: In function 'load_global_context_forindel':
SUBindel.c:66:31: warning: '.reads' directive writing 6 bytes into a region of size between 1 and 1000 [-Wformat-overflow=]
66 | sprintf(tmp_fname, "%s.reads", context->config.index_prefix);
@@ -622,6 +640,16 @@
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
SUBindel.c: In function 'load_global_context_forindel':
+In file included from readSummary.c:41:
+readSummary.c: In function 'get_RG_tables':
+readSummary.c:2505:31: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
+ 2505 | SUBREADprintf("cannot allocate memory for %s (%d)\n", rg_name, strlen(rg_name));
+ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~
+ | |
+ | size_t {aka long unsigned int}
+subread.h:142:44: note: in definition of macro 'SUBREADprintf'
+ 142 | #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__)
+ | ^~~~~~~~~~~
SUBindel.c:87:40: warning: '%02d' directive writing between 2 and 11 bytes into a region of size between 0 and 999 [-Wformat-overflow=]
87 | sprintf(tmp_fname, "%s.%02d.%c.tab", context->config.index_prefix, context->index_block_number, context->config.space_type == GENE_SPACE_COLOR?'c':'b');
| ^~~~
@@ -637,7 +665,17 @@
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
+readSummary.c:2505:64: note: format string is defined here
+ 2505 | SUBREADprintf("cannot allocate memory for %s (%d)\n", rg_name, strlen(rg_name));
+ | ~^
+ | |
+ | int
+ | %ld
+readSummary.c: In function 'vote_and_add_count':
SUBindel.c: In function 'load_indexes_forindel':
+readSummary.c:3819:58: warning: variable 'assignment_target_number' set but not used [-Wunused-but-set-variable]
+ 3819 | srInt_64 assignment_target_number = tmp_voter_id;
+ | ^~~~~~~~~~~~~~~~~~~~~~~~
SUBindel.c:110:40: warning: '%02d' directive writing between 2 and 10 bytes into a region of size between 0 and 999 [-Wformat-overflow=]
110 | sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, block_no, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b');
| ^~~~
@@ -653,14 +691,12 @@
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
-readSummary.c: In function 'vote_and_add_count':
-readSummary.c:3819:58: warning: variable 'assignment_target_number' set but not used [-Wunused-but-set-variable]
- 3819 | srInt_64 assignment_target_number = tmp_voter_id;
- | ^~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c: In function 'fc_thread_merge_results':
readSummary.c:3889:32: warning: unused variable 'sample_i' [-Wunused-variable]
3889 | int xk1, xk2, ret = 0, sample_i;
| ^~~~~~~~
+x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMfile-io.o -c LRMfile-io.c
+x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhashtable.o -c LRMhashtable.c
readSummary.c: In function 'readSummary':
readSummary.c:5645:52: warning: variable 'scrna_total_BAM_no' set but not used [-Wunused-but-set-variable]
5645 | int isGTF, n_input_files=0,is_dual_index, scrna_total_BAM_no;
@@ -736,7 +772,7 @@
|| Repeat threshold : 100 repeats ||
|| Gapped index : no ||
|| ||
-|| Free / total memory : 70.6GB / 78.5GB ||
+|| Free / total memory : 70.8GB / 79.0GB ||
|| ||
|| Input files : 1 file in total ||
|| o chr901.fa ||
@@ -752,30 +788,30 @@
|| 52 uninformative subreads were found. ||
|| These subreads were excluded from index building. ||
|| Estimate the index size... ||
-|| 8%, 0 mins elapsed, rate=490.2k bps/s ||
-|| 16%, 0 mins elapsed, rate=901.4k bps/s ||
-|| 25%, 0 mins elapsed, rate=1238.9k bps/s ||
-|| 33%, 0 mins elapsed, rate=1531.2k bps/s ||
-|| 41%, 0 mins elapsed, rate=1791.3k bps/s ||
-|| 50%, 0 mins elapsed, rate=2012.0k bps/s ||
-|| 58%, 0 mins elapsed, rate=2206.1k bps/s ||
-|| 66%, 0 mins elapsed, rate=2378.2k bps/s ||
-|| 75%, 0 mins elapsed, rate=2531.8k bps/s ||
-|| 83%, 0 mins elapsed, rate=2669.8k bps/s ||
-|| 91%, 0 mins elapsed, rate=2794.4k bps/s ||
+|| 8%, 0 mins elapsed, rate=275.8k bps/s ||
+|| 16%, 0 mins elapsed, rate=520.7k bps/s ||
+|| 25%, 0 mins elapsed, rate=744.1k bps/s ||
+|| 33%, 0 mins elapsed, rate=941.9k bps/s ||
+|| 41%, 0 mins elapsed, rate=1123.8k bps/s ||
+|| 50%, 0 mins elapsed, rate=1286.4k bps/s ||
+|| 58%, 0 mins elapsed, rate=1438.3k bps/s ||
+|| 66%, 0 mins elapsed, rate=1578.0k bps/s ||
+|| 75%, 0 mins elapsed, rate=1710.9k bps/s ||
+|| 83%, 0 mins elapsed, rate=1826.4k bps/s ||
+|| 91%, 0 mins elapsed, rate=1937.3k bps/s ||
|| 3.0 GB of memory is needed for index building. ||
|| Build the index... ||
-|| 8%, 0 mins elapsed, rate=46.5k bps/s ||
-|| 16%, 0 mins elapsed, rate=91.0k bps/s ||
-|| 25%, 0 mins elapsed, rate=133.5k bps/s ||
-|| 33%, 0 mins elapsed, rate=174.2k bps/s ||
-|| 41%, 0 mins elapsed, rate=213.2k bps/s ||
-|| 50%, 0 mins elapsed, rate=250.6k bps/s ||
-|| 58%, 0 mins elapsed, rate=286.4k bps/s ||
-|| 66%, 0 mins elapsed, rate=320.7k bps/s ||
-|| 75%, 0 mins elapsed, rate=353.9k bps/s ||
-|| 83%, 0 mins elapsed, rate=385.6k bps/s ||
-|| 91%, 0 mins elapsed, rate=416.3k bps/s ||
+|| 8%, 0 mins elapsed, rate=32.0k bps/s ||
+|| 16%, 0 mins elapsed, rate=63.0k bps/s ||
+|| 25%, 0 mins elapsed, rate=93.0k bps/s ||
+|| 33%, 0 mins elapsed, rate=122.1k bps/s ||
+|| 41%, 0 mins elapsed, rate=150.0k bps/s ||
+|| 50%, 0 mins elapsed, rate=176.9k bps/s ||
+|| 58%, 0 mins elapsed, rate=202.9k bps/s ||
+|| 66%, 0 mins elapsed, rate=228.1k bps/s ||
+|| 75%, 0 mins elapsed, rate=252.3k bps/s ||
+|| 83%, 0 mins elapsed, rate=276.0k bps/s ||
+|| 91%, 0 mins elapsed, rate=298.9k bps/s ||
|| Save current index block... ||
|| [ 0.0% finished ] ||
|| [ 10.0% finished ] ||
@@ -789,7 +825,7 @@
|| [ 90.0% finished ] ||
|| [ 100.0% finished ] ||
|| ||
-|| Total running time: 0.3 minutes. ||
+|| Total running time: 0.5 minutes. ||
|| Index ../small1 was successfully built. ||
|| ||
\\============================================================================//
@@ -822,7 +858,7 @@
|| ||
\\============================================================================//
-//================ Running (10-Apr-2026 19:17:50, pid=386116) ================\\
+//================ Running (09-Mar-2025 15:03:15, pid=894586) ================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
@@ -836,10 +872,10 @@
|| Load the 1-th index block... ||
|| The index block has been loaded. ||
|| Start read mapping in chunk. ||
-|| 33% completed, 1.3 mins elapsed, rate=57.5k reads per second ||
-|| 74% completed, 1.3 mins elapsed, rate=0.2k reads per second ||
-|| 83% completed, 1.3 mins elapsed, rate=0.2k reads per second ||
-|| 91% completed, 1.4 mins elapsed, rate=0.2k reads per second ||
+|| 33% completed, 0.8 mins elapsed, rate=43.0k reads per second ||
+|| 74% completed, 0.8 mins elapsed, rate=0.3k reads per second ||
+|| 83% completed, 0.8 mins elapsed, rate=0.4k reads per second ||
+|| 91% completed, 0.8 mins elapsed, rate=0.4k reads per second ||
|| ||
|| Completed successfully. ||
|| ||
@@ -856,7 +892,7 @@
|| ||
|| Indels : 0 ||
|| ||
-|| Running time : 1.4 minutes ||
+|| Running time : 0.8 minutes ||
|| ||
\\============================================================================//
@@ -888,7 +924,7 @@
|| ||
\\============================================================================//
-//================ Running (10-Apr-2026 19:19:12, pid=391589) ================\\
+//================ Running (09-Mar-2025 15:04:01, pid=936681) ================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
@@ -902,10 +938,10 @@
|| Load the 1-th index block... ||
|| The index block has been loaded. ||
|| Start read mapping in chunk. ||
-|| 33% completed, 1.1 mins elapsed, rate=63.5k reads per second ||
-|| 74% completed, 1.1 mins elapsed, rate=0.2k reads per second ||
-|| 83% completed, 1.1 mins elapsed, rate=0.3k reads per second ||
-|| 91% completed, 1.1 mins elapsed, rate=0.3k reads per second ||
+|| 33% completed, 0.9 mins elapsed, rate=43.9k reads per second ||
+|| 74% completed, 0.9 mins elapsed, rate=0.3k reads per second ||
+|| 83% completed, 0.9 mins elapsed, rate=0.3k reads per second ||
+|| 91% completed, 0.9 mins elapsed, rate=0.4k reads per second ||
|| ||
|| Completed successfully. ||
|| ||
@@ -922,7 +958,7 @@
|| ||
|| Indels : 0 ||
|| ||
-|| Running time : 1.1 minutes ||
+|| Running time : 0.9 minutes ||
|| ||
\\============================================================================//
@@ -959,7 +995,7 @@
|| ||
\\============================================================================//
-//================ Running (10-Apr-2026 19:20:16, pid=402126) ================\\
+//================ Running (09-Mar-2025 15:04:53, pid=982512) ================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
@@ -973,7 +1009,7 @@
|| Load the 1-th index block... ||
|| The index block has been loaded. ||
|| Start read mapping in chunk. ||
-|| 33% completed, 0.9 mins elapsed, rate=28.7k fragments per second ||
+|| 33% completed, 0.9 mins elapsed, rate=21.0k fragments per second ||
|| Estimated fragment length : 495 bp ||
|| 74% completed, 0.9 mins elapsed, rate=0.3k fragments per second ||
|| 83% completed, 0.9 mins elapsed, rate=0.3k fragments per second ||
@@ -1002,7 +1038,7 @@
|| ||
|| Indels : 0 ||
|| ||
-|| Running time : 1.0 minutes ||
+|| Running time : 0.9 minutes ||
|| ||
\\============================================================================//
@@ -1039,7 +1075,7 @@
|| ||
\\============================================================================//
-//================ Running (10-Apr-2026 19:21:13, pid=406494) ================\\
+//================ Running (09-Mar-2025 15:05:47, pid=997513) ================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
@@ -1053,11 +1089,11 @@
|| Load the 1-th index block... ||
|| The index block has been loaded. ||
|| Start read mapping in chunk. ||
-|| 33% completed, 0.9 mins elapsed, rate=30.6k fragments per second ||
+|| 33% completed, 0.8 mins elapsed, rate=19.9k fragments per second ||
|| Estimated fragment length : 495 bp ||
|| 74% completed, 0.9 mins elapsed, rate=0.3k fragments per second ||
|| 83% completed, 0.9 mins elapsed, rate=0.3k fragments per second ||
-|| 91% completed, 0.9 mins elapsed, rate=0.3k fragments per second ||
+|| 91% completed, 0.9 mins elapsed, rate=0.4k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
@@ -1119,7 +1155,7 @@
|| ||
\\============================================================================//
-//================ Running (10-Apr-2026 19:22:10, pid=408010) ================\\
+//=============== Running (09-Mar-2025 15:06:39, pid=1027422) ================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
@@ -1133,11 +1169,11 @@
|| Load the 1-th index block... ||
|| The index block has been loaded. ||
|| Start read mapping in chunk. ||
-|| 33% completed, 0.9 mins elapsed, rate=33.0k fragments per second ||
+|| 33% completed, 1.3 mins elapsed, rate=19.3k fragments per second ||
|| Estimated fragment length : 497 bp ||
-|| 74% completed, 0.9 mins elapsed, rate=0.3k fragments per second ||
-|| 83% completed, 1.0 mins elapsed, rate=0.3k fragments per second ||
-|| 91% completed, 1.0 mins elapsed, rate=0.3k fragments per second ||
+|| 74% completed, 1.4 mins elapsed, rate=0.2k fragments per second ||
+|| 83% completed, 1.4 mins elapsed, rate=0.2k fragments per second ||
+|| 91% completed, 1.4 mins elapsed, rate=0.2k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
@@ -1162,7 +1198,7 @@
|| ||
|| Indels : 15 ||
|| ||
-|| Running time : 1.0 minutes ||
+|| Running time : 1.4 minutes ||
|| ||
\\============================================================================//
@@ -1200,7 +1236,7 @@
|| ||
\\============================================================================//
-//================ Running (10-Apr-2026 19:23:07, pid=412987) ================\\
+//=============== Running (09-Mar-2025 15:08:02, pid=1044723) ================\\
|| ||
ERROR: unable to open file 'data/test-err-mut-r1.fq.gz'. File name might be incorrect, or you do not have the permission to read the file.
ERROR: unable to open file 'data/test-err-mut-r2.fq.gz'. File name might be incorrect, or you do not have the permission to read the file.
@@ -1270,7 +1306,7 @@
|| Repeat threshold : 100 repeats ||
|| Gapped index : yes ||
|| ||
-|| Free / total memory : 74.4GB / 78.5GB ||
+|| Free / total memory : 70.7GB / 79.0GB ||
|| ||
|| Input files : 1 file in total ||
|| o chr901.fa ||
@@ -1286,30 +1322,30 @@
|| 2 uninformative subreads were found. ||
|| These subreads were excluded from index building. ||
|| Estimate the index size... ||
-|| 8%, 0 mins elapsed, rate=3644.9k bps/s ||
-|| 16%, 0 mins elapsed, rate=5988.0k bps/s ||
-|| 25%, 0 mins elapsed, rate=7859.2k bps/s ||
-|| 33%, 0 mins elapsed, rate=9062.9k bps/s ||
-|| 41%, 0 mins elapsed, rate=9980.0k bps/s ||
-|| 50%, 0 mins elapsed, rate=10934.6k bps/s ||
-|| 58%, 0 mins elapsed, rate=11506.4k bps/s ||
-|| 66%, 0 mins elapsed, rate=12193.7k bps/s ||
-|| 75%, 0 mins elapsed, rate=12574.8k bps/s ||
-|| 83%, 0 mins elapsed, rate=13098.8k bps/s ||
-|| 91%, 0 mins elapsed, rate=13561.0k bps/s ||
+|| 8%, 0 mins elapsed, rate=2704.2k bps/s ||
+|| 16%, 0 mins elapsed, rate=4299.1k bps/s ||
+|| 25%, 0 mins elapsed, rate=5239.5k bps/s ||
+|| 33%, 0 mins elapsed, rate=5988.0k bps/s ||
+|| 41%, 0 mins elapsed, rate=6448.6k bps/s ||
+|| 50%, 0 mins elapsed, rate=6797.2k bps/s ||
+|| 58%, 0 mins elapsed, rate=7156.4k bps/s ||
+|| 66%, 0 mins elapsed, rate=7369.8k bps/s ||
+|| 75%, 0 mins elapsed, rate=7621.1k bps/s ||
+|| 83%, 0 mins elapsed, rate=7762.2k bps/s ||
+|| 91%, 0 mins elapsed, rate=7949.6k bps/s ||
|| 0.8 GB of memory is needed for index building. ||
|| Build the index... ||
-|| 8%, 0 mins elapsed, rate=438.9k bps/s ||
-|| 16%, 0 mins elapsed, rate=842.5k bps/s ||
-|| 25%, 0 mins elapsed, rate=1215.0k bps/s ||
-|| 33%, 0 mins elapsed, rate=1567.0k bps/s ||
-|| 41%, 0 mins elapsed, rate=1888.1k bps/s ||
-|| 50%, 0 mins elapsed, rate=2196.5k bps/s ||
-|| 58%, 0 mins elapsed, rate=2476.1k bps/s ||
-|| 66%, 0 mins elapsed, rate=2748.6k bps/s ||
-|| 75%, 0 mins elapsed, rate=3005.9k bps/s ||
-|| 83%, 0 mins elapsed, rate=3236.8k bps/s ||
-|| 91%, 0 mins elapsed, rate=3466.7k bps/s ||
+|| 8%, 0 mins elapsed, rate=262.0k bps/s ||
+|| 16%, 0 mins elapsed, rate=500.5k bps/s ||
+|| 25%, 0 mins elapsed, rate=718.6k bps/s ||
+|| 33%, 0 mins elapsed, rate=918.7k bps/s ||
+|| 41%, 0 mins elapsed, rate=1103.1k bps/s ||
+|| 50%, 0 mins elapsed, rate=1273.4k bps/s ||
+|| 58%, 0 mins elapsed, rate=1431.3k bps/s ||
+|| 66%, 0 mins elapsed, rate=1578.0k bps/s ||
+|| 75%, 0 mins elapsed, rate=1714.7k bps/s ||
+|| 83%, 0 mins elapsed, rate=1842.5k bps/s ||
+|| 91%, 0 mins elapsed, rate=1957.9k bps/s ||
|| Save current index block... ||
|| [ 0.0% finished ] ||
|| [ 10.0% finished ] ||
@@ -1323,7 +1359,7 @@
|| [ 90.0% finished ] ||
|| [ 100.0% finished ] ||
|| ||
-|| Total running time: 0.0 minutes. ||
+|| Total running time: 0.1 minutes. ||
|| Index ../small1 was successfully built. ||
|| ||
\\============================================================================//
@@ -1361,7 +1397,7 @@
|| ||
\\============================================================================//
-//================ Running (10-Apr-2026 19:23:10, pid=412994) ================\\
+//=============== Running (09-Mar-2025 15:08:07, pid=1045488) ================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
@@ -1375,11 +1411,11 @@
|| Load the 1-th index block... ||
|| The index block has been loaded. ||
|| Start read mapping in chunk. ||
-|| 41% completed, 0.1 mins elapsed, rate=19.9k fragments per second ||
+|| 41% completed, 0.1 mins elapsed, rate=11.0k fragments per second ||
|| Estimated fragment length : 173 bp ||
-|| 77% completed, 0.1 mins elapsed, rate=1.6k fragments per second ||
-|| 87% completed, 0.1 mins elapsed, rate=1.8k fragments per second ||
-|| 97% completed, 0.1 mins elapsed, rate=1.9k fragments per second ||
+|| 77% completed, 0.1 mins elapsed, rate=1.7k fragments per second ||
+|| 87% completed, 0.1 mins elapsed, rate=1.9k fragments per second ||
+|| 97% completed, 0.1 mins elapsed, rate=2.0k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
@@ -1442,7 +1478,7 @@
|| ||
\\============================================================================//
-//================ Running (10-Apr-2026 19:23:18, pid=413103) ================\\
+//=============== Running (09-Mar-2025 15:08:14, pid=1046357) ================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
@@ -1456,10 +1492,10 @@
|| Load the 1-th index block... ||
|| The index block has been loaded. ||
|| Start read mapping in chunk. ||
-|| 41% completed, 0.1 mins elapsed, rate=11.9k fragments per second ||
+|| 41% completed, 0.1 mins elapsed, rate=5.7k fragments per second ||
|| Estimated fragment length : 174 bp ||
|| 77% completed, 0.1 mins elapsed, rate=1.5k fragments per second ||
-|| 87% completed, 0.1 mins elapsed, rate=1.6k fragments per second ||
+|| 87% completed, 0.1 mins elapsed, rate=1.7k fragments per second ||
|| 97% completed, 0.1 mins elapsed, rate=1.8k fragments per second ||
|| ||
|| Completed successfully. ||
@@ -1661,9 +1697,9 @@
|| ||
\\============================================================================//
-//====================== Running (10-Apr-2026 19:23:28) ======================\\
+//====================== Running (09-Mar-2025 15:08:25) ======================\\
|| ||
-|| Split BAM file into result/temp-snps-413705-47B5F4B701E8-* ... ||
+|| Split BAM file into result/temp-snps-1047801-67DECA8CFE9F-* ... ||
|| processed block chr901@999950 by thread 1/1 [block number=1/1] ||
|| ||
|| Completed successfully. ||
@@ -1727,10 +1763,10 @@
install -m0755 -d debian/subread-data/usr/share/doc/subread-data
install -p -m0644 debian/copyright debian/subread-data/usr/share/doc/subread-data/copyright
dh_installchangelogs -O--buildsystem=makefile
- install -m0755 -d debian/subread/usr/share/doc/subread
- install -p -m0644 debian/.debhelper/generated/subread/dh_installchangelogs.dch.trimmed debian/subread/usr/share/doc/subread/changelog.Debian
install -m0755 -d debian/subread-data/usr/share/doc/subread-data
install -p -m0644 debian/.debhelper/generated/subread-data/dh_installchangelogs.dch.trimmed debian/subread-data/usr/share/doc/subread-data/changelog.Debian
+ install -m0755 -d debian/subread/usr/share/doc/subread
+ install -p -m0644 debian/.debhelper/generated/subread/dh_installchangelogs.dch.trimmed debian/subread/usr/share/doc/subread/changelog.Debian
rm -f debian/subread-data.debhelper.log debian/subread.debhelper.log
debian/rules override_dh_installexamples-indep
make[1]: Entering directory '/build/reproducible-path/subread-2.0.8+dfsg'
@@ -1783,28 +1819,28 @@
man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-align.1
man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-buildindex.1
man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-fullscan.1
+ mv debian/subread/usr/share/man/man1/propmapped.1.dh-new debian/subread/usr/share/man/man1/propmapped.1
+ chmod 0644 -- debian/subread/usr/share/man/man1/propmapped.1
mv debian/subread/usr/share/man/man1/exactSNP.1.dh-new debian/subread/usr/share/man/man1/exactSNP.1
chmod 0644 -- debian/subread/usr/share/man/man1/exactSNP.1
- mv debian/subread/usr/share/man/man1/featureCounts.1.dh-new debian/subread/usr/share/man/man1/featureCounts.1
- chmod 0644 -- debian/subread/usr/share/man/man1/featureCounts.1
- mv debian/subread/usr/share/man/man1/flattenGTF.1.dh-new debian/subread/usr/share/man/man1/flattenGTF.1
- chmod 0644 -- debian/subread/usr/share/man/man1/flattenGTF.1
mv debian/subread/usr/share/man/man1/genRandomReads.1.dh-new debian/subread/usr/share/man/man1/genRandomReads.1
chmod 0644 -- debian/subread/usr/share/man/man1/genRandomReads.1
- mv debian/subread/usr/share/man/man1/propmapped.1.dh-new debian/subread/usr/share/man/man1/propmapped.1
- chmod 0644 -- debian/subread/usr/share/man/man1/propmapped.1
- mv debian/subread/usr/share/man/man1/subindel.1.dh-new debian/subread/usr/share/man/man1/subindel.1
- chmod 0644 -- debian/subread/usr/share/man/man1/subindel.1
+ mv debian/subread/usr/share/man/man1/flattenGTF.1.dh-new debian/subread/usr/share/man/man1/flattenGTF.1
+ chmod 0644 -- debian/subread/usr/share/man/man1/flattenGTF.1
+ mv debian/subread/usr/share/man/man1/featureCounts.1.dh-new debian/subread/usr/share/man/man1/featureCounts.1
+ chmod 0644 -- debian/subread/usr/share/man/man1/featureCounts.1
+ mv debian/subread/usr/share/man/man1/qualityScores.1.dh-new debian/subread/usr/share/man/man1/qualityScores.1
+ chmod 0644 -- debian/subread/usr/share/man/man1/qualityScores.1
mv debian/subread/usr/share/man/man1/removeDup.1.dh-new debian/subread/usr/share/man/man1/removeDup.1
chmod 0644 -- debian/subread/usr/share/man/man1/removeDup.1
+ mv debian/subread/usr/share/man/man1/subjunc.1.dh-new debian/subread/usr/share/man/man1/subjunc.1
+ chmod 0644 -- debian/subread/usr/share/man/man1/subjunc.1
+ mv debian/subread/usr/share/man/man1/subindel.1.dh-new debian/subread/usr/share/man/man1/subindel.1
+ chmod 0644 -- debian/subread/usr/share/man/man1/subindel.1
mv debian/subread/usr/share/man/man1/repair.1.dh-new debian/subread/usr/share/man/man1/repair.1
chmod 0644 -- debian/subread/usr/share/man/man1/repair.1
- mv debian/subread/usr/share/man/man1/qualityScores.1.dh-new debian/subread/usr/share/man/man1/qualityScores.1
- chmod 0644 -- debian/subread/usr/share/man/man1/qualityScores.1
mv debian/subread/usr/share/man/man1/sublong.1.dh-new debian/subread/usr/share/man/man1/sublong.1
chmod 0644 -- debian/subread/usr/share/man/man1/sublong.1
- mv debian/subread/usr/share/man/man1/subjunc.1.dh-new debian/subread/usr/share/man/man1/subjunc.1
- chmod 0644 -- debian/subread/usr/share/man/man1/subjunc.1
mv debian/subread/usr/share/man/man1/subread-align.1.dh-new debian/subread/usr/share/man/man1/subread-align.1
chmod 0644 -- debian/subread/usr/share/man/man1/subread-align.1
mv debian/subread/usr/share/man/man1/subread-buildindex.1.dh-new debian/subread/usr/share/man/man1/subread-buildindex.1
@@ -1829,10 +1865,10 @@
dh_fixperms -O--buildsystem=makefile
find debian/subread ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/subread-data ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
- find debian/subread/usr/share/doc -type f -a -true -a ! -regex 'debian/subread/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/subread-data/usr/share/doc -type f -a -true -a ! -regex 'debian/subread-data/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
- find debian/subread/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
+ find debian/subread/usr/share/doc -type f -a -true -a ! -regex 'debian/subread/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/subread-data/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
+ find debian/subread/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/subread/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/subread-data -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/subread -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
@@ -1845,71 +1881,26 @@
objcopy --compress-debug-sections debian/subread/usr/lib/debug/.dwz/x86_64-linux-gnu/subread.debug
chmod 0644 -- debian/subread/usr/lib/debug/.dwz/x86_64-linux-gnu/subread.debug
dh_strip -a -O--buildsystem=makefile
- install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/af
- objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/af/86d5cd40ab2f6896c069f377df687ca07899b9.debug
- chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/af/86d5cd40ab2f6896c069f377df687ca07899b9.debug
- strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subread-align
- objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/af/86d5cd40ab2f6896c069f377df687ca07899b9.debug debian/subread/usr/bin/subread-align
- install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ba
- objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/featureCounts debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ba/9ec00a5feb854ebea072a71ceacce4f16c807b.debug
- chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ba/9ec00a5feb854ebea072a71ceacce4f16c807b.debug
- strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/featureCounts
- objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ba/9ec00a5feb854ebea072a71ceacce4f16c807b.debug debian/subread/usr/bin/featureCounts
- install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c6
- objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c6/7e563bfbceae3df89a2e763a3e16830fc7d6f1.debug
- chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c6/7e563bfbceae3df89a2e763a3e16830fc7d6f1.debug
- strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subindel
- objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c6/7e563bfbceae3df89a2e763a3e16830fc7d6f1.debug debian/subread/usr/bin/subindel
- install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/df
- objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/df/b79cf83e2e4eefa739c7bd1e0286c2330badf2.debug
- chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/df/b79cf83e2e4eefa739c7bd1e0286c2330badf2.debug
- strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/sublong
- objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/df/b79cf83e2e4eefa739c7bd1e0286c2330badf2.debug debian/subread/usr/bin/sublong
- install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/17
- objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/17/e5fb9733a4e27115ae9f50e30a23cb8216c140.debug
- chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/17/e5fb9733a4e27115ae9f50e30a23cb8216c140.debug
- strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subjunc
- objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/17/e5fb9733a4e27115ae9f50e30a23cb8216c140.debug debian/subread/usr/bin/subjunc
- install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/eb
- objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-buildindex debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/eb/95f93c14404e614a9e99d8c4473e0b9a34c944.debug
- chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/eb/95f93c14404e614a9e99d8c4473e0b9a34c944.debug
- strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subread-buildindex
- objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/eb/95f93c14404e614a9e99d8c4473e0b9a34c944.debug debian/subread/usr/bin/subread-buildindex
- install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26
- objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26/3e3a7d353f54ef9e013eefea0ed9ab3772bf9a.debug
- chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26/3e3a7d353f54ef9e013eefea0ed9ab3772bf9a.debug
- strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/exactSNP
- objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26/3e3a7d353f54ef9e013eefea0ed9ab3772bf9a.debug debian/subread/usr/bin/exactSNP
- install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/40
- objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/genRandomReads debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/40/d17561a4178aa2e7d5b32f4022b788c942fe94.debug
- chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/40/d17561a4178aa2e7d5b32f4022b788c942fe94.debug
- strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/genRandomReads
- objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/40/d17561a4178aa2e7d5b32f4022b788c942fe94.debug debian/subread/usr/lib/subread/genRandomReads
- install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c3
- objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c3/2378f625c13e8486fbc4a67b031e53166dfd0a.debug
- chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c3/2378f625c13e8486fbc4a67b031e53166dfd0a.debug
- strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/qualityScores
- objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c3/2378f625c13e8486fbc4a67b031e53166dfd0a.debug debian/subread/usr/lib/subread/qualityScores
install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c1
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/txUnique debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c1/54f615f002a43fd730f93851192eb3ea3733a4.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c1/54f615f002a43fd730f93851192eb3ea3733a4.debug
strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/txUnique
objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c1/54f615f002a43fd730f93851192eb3ea3733a4.debug debian/subread/usr/lib/subread/txUnique
- install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/54
- objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/54/d892b37e74c7629769bf9e36cec2f9f75ac9b4.debug
- chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/54/d892b37e74c7629769bf9e36cec2f9f75ac9b4.debug
- strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/propmapped
- objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/54/d892b37e74c7629769bf9e36cec2f9f75ac9b4.debug debian/subread/usr/lib/subread/propmapped
- install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ac
- objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/flattenGTF debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ac/d1db8bda83b3cc336baa0449ccfab407c81e35.debug
- chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ac/d1db8bda83b3cc336baa0449ccfab407c81e35.debug
- strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/flattenGTF
- objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ac/d1db8bda83b3cc336baa0449ccfab407c81e35.debug debian/subread/usr/lib/subread/flattenGTF
install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9e
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9e/684bba40f22a949afcb671a10194407d3be7ea.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9e/684bba40f22a949afcb671a10194407d3be7ea.debug
strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/removeDup
objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9e/684bba40f22a949afcb671a10194407d3be7ea.debug debian/subread/usr/lib/subread/removeDup
+ install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ac
+ objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/flattenGTF debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ac/d1db8bda83b3cc336baa0449ccfab407c81e35.debug
+ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ac/d1db8bda83b3cc336baa0449ccfab407c81e35.debug
+ strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/flattenGTF
+ objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ac/d1db8bda83b3cc336baa0449ccfab407c81e35.debug debian/subread/usr/lib/subread/flattenGTF
+ install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/40
+ objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/genRandomReads debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/40/d17561a4178aa2e7d5b32f4022b788c942fe94.debug
+ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/40/d17561a4178aa2e7d5b32f4022b788c942fe94.debug
+ strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/genRandomReads
+ objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/40/d17561a4178aa2e7d5b32f4022b788c942fe94.debug debian/subread/usr/lib/subread/genRandomReads
install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/82
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/subread-fullscan debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/82/c0db4b6065c61dc9c3bdae61dfa5919bc6e881.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/82/c0db4b6065c61dc9c3bdae61dfa5919bc6e881.debug
@@ -1920,6 +1911,51 @@
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/82/03931b059e770bf1e7b95ef249c79652776d76.debug
strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/repair
objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/82/03931b059e770bf1e7b95ef249c79652776d76.debug debian/subread/usr/lib/subread/repair
+ install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/54
+ objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/54/d892b37e74c7629769bf9e36cec2f9f75ac9b4.debug
+ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/54/d892b37e74c7629769bf9e36cec2f9f75ac9b4.debug
+ strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/propmapped
+ objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/54/d892b37e74c7629769bf9e36cec2f9f75ac9b4.debug debian/subread/usr/lib/subread/propmapped
+ install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c3
+ objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c3/2378f625c13e8486fbc4a67b031e53166dfd0a.debug
+ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c3/2378f625c13e8486fbc4a67b031e53166dfd0a.debug
+ strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/qualityScores
+ objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c3/2378f625c13e8486fbc4a67b031e53166dfd0a.debug debian/subread/usr/lib/subread/qualityScores
+ install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/eb
+ objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-buildindex debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/eb/95f93c14404e614a9e99d8c4473e0b9a34c944.debug
+ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/eb/95f93c14404e614a9e99d8c4473e0b9a34c944.debug
+ strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subread-buildindex
+ objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/eb/95f93c14404e614a9e99d8c4473e0b9a34c944.debug debian/subread/usr/bin/subread-buildindex
+ install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/17
+ objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/17/e5fb9733a4e27115ae9f50e30a23cb8216c140.debug
+ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/17/e5fb9733a4e27115ae9f50e30a23cb8216c140.debug
+ strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subjunc
+ objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/17/e5fb9733a4e27115ae9f50e30a23cb8216c140.debug debian/subread/usr/bin/subjunc
+ install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c6
+ objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c6/7e563bfbceae3df89a2e763a3e16830fc7d6f1.debug
+ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c6/7e563bfbceae3df89a2e763a3e16830fc7d6f1.debug
+ strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subindel
+ objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c6/7e563bfbceae3df89a2e763a3e16830fc7d6f1.debug debian/subread/usr/bin/subindel
+ install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ba
+ objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/featureCounts debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ba/9ec00a5feb854ebea072a71ceacce4f16c807b.debug
+ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ba/9ec00a5feb854ebea072a71ceacce4f16c807b.debug
+ strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/featureCounts
+ objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ba/9ec00a5feb854ebea072a71ceacce4f16c807b.debug debian/subread/usr/bin/featureCounts
+ install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/df
+ objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/df/b79cf83e2e4eefa739c7bd1e0286c2330badf2.debug
+ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/df/b79cf83e2e4eefa739c7bd1e0286c2330badf2.debug
+ strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/sublong
+ objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/df/b79cf83e2e4eefa739c7bd1e0286c2330badf2.debug debian/subread/usr/bin/sublong
+ install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26
+ objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26/3e3a7d353f54ef9e013eefea0ed9ab3772bf9a.debug
+ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26/3e3a7d353f54ef9e013eefea0ed9ab3772bf9a.debug
+ strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/exactSNP
+ objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26/3e3a7d353f54ef9e013eefea0ed9ab3772bf9a.debug debian/subread/usr/bin/exactSNP
+ install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/af
+ objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/af/86d5cd40ab2f6896c069f377df687ca07899b9.debug
+ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/af/86d5cd40ab2f6896c069f377df687ca07899b9.debug
+ strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subread-align
+ objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/af/86d5cd40ab2f6896c069f377df687ca07899b9.debug debian/subread/usr/bin/subread-align
install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.dwz
cp --reflink=auto -a debian/subread/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.dwz
rm -fr debian/subread/usr/lib/debug/.dwz
@@ -1931,7 +1967,7 @@
rm -f debian/subread/DEBIAN/shlibs
dh_shlibdeps -a -O--buildsystem=makefile
install -m0755 -d debian/subread/DEBIAN
- dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/bin/subread-align debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subindel debian/subread/usr/bin/sublong debian/subread/usr/bin/subjunc debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/exactSNP debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/txUnique debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/repair
+ dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/lib/subread/txUnique debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/qualityScores debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/subjunc debian/subread/usr/bin/subindel debian/subread/usr/bin/featureCounts debian/subread/usr/bin/sublong debian/subread/usr/bin/exactSNP debian/subread/usr/bin/subread-align
dh_installdeb -O--buildsystem=makefile
install -m0755 -d debian/subread/DEBIAN
install -m0755 -d debian/subread-data/DEBIAN
@@ -1946,15 +1982,15 @@
install -m0755 -d debian/.debhelper/subread/dbgsym-root/DEBIAN
dpkg-gencontrol -psubread -ldebian/changelog -Tdebian/subread.substvars -cdebian/control -Pdebian/.debhelper/subread/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=subread-dbgsym "-DDepends=subread (= \${binary:Version})" "-DDescription=debug symbols for subread" "-DBuild-Ids=17e5fb9733a4e27115ae9f50e30a23cb8216c140 263e3a7d353f54ef9e013eefea0ed9ab3772bf9a 40d17561a4178aa2e7d5b32f4022b788c942fe94 54d892b37e74c7629769bf9e36cec2f9f75ac9b4 8203931b059e770bf1e7b95ef249c79652776d76 82c0db4b6065c61dc9c3bdae61dfa5919bc6e881 9e684bba40f22a949afcb671a10194407d3be7ea acd1db8bda83b3cc336baa0449ccfab407c81e35 af86d5cd40ab2f6896c069f377df687ca07899b9 ba9ec00a5feb854ebea072a71ceacce4f16c807b c154f615f002a43fd730f93851192eb3ea3733a4 c32378f625c13e8486fbc4a67b031e53166dfd0a c67e563bfbceae3df89a2e763a3e16830fc7d6f1 dfb79cf83e2e4eefa739c7bd1e0286c2330badf2 eb95f93c14404e614a9e99d8c4473e0b9a34c944" -DSection=debug -UMulti-Arch -UReplaces -UBreaks
dpkg-gencontrol: warning: Depends field of package subread-data: substitution variable ${shlibs:Depends} used, but is not defined
+ chmod 0644 -- debian/subread-data/DEBIAN/control
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/control
dpkg-gencontrol -psubread -ldebian/changelog -Tdebian/subread.substvars -cdebian/control -Pdebian/subread
- chmod 0644 -- debian/subread-data/DEBIAN/control
chmod 0644 -- debian/subread/DEBIAN/control
dh_md5sums -O--buildsystem=makefile
install -m0755 -d debian/subread/DEBIAN
install -m0755 -d debian/subread-data/DEBIAN
- cd debian/subread >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
cd debian/subread-data >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
+ cd debian/subread >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/subread/DEBIAN/md5sums
install -m0755 -d debian/.debhelper/subread/dbgsym-root/DEBIAN
cd debian/.debhelper/subread/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
@@ -1974,12 +2010,14 @@
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: including full source code in upload
I: copying local configuration
+I: user script /srv/workspace/pbuilder/817158/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/817158/tmp/hooks/B01_cleanup finished
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
-I: removing directory /srv/workspace/pbuilder/374784 and its subdirectories
-I: Current time: Fri Apr 10 19:24:01 -12 2026
-I: pbuilder-time-stamp: 1775892241
+I: removing directory /srv/workspace/pbuilder/817158 and its subdirectories
+I: Current time: Sun Mar 9 15:09:23 +14 2025
+I: pbuilder-time-stamp: 1741482563