Diff of the two buildlogs:
--
--- b1/build.log 2025-03-06 15:32:32.950038617 +0000
+++ b2/build.log 2025-03-06 15:34:04.277935539 +0000
@@ -1,6 +1,6 @@
I: pbuilder: network access will be disabled during build
-I: Current time: Thu Mar 6 03:30:14 -12 2025
-I: pbuilder-time-stamp: 1741275014
+I: Current time: Thu Apr 9 11:55:35 +14 2026
+I: pbuilder-time-stamp: 1775685335
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
@@ -29,54 +29,86 @@
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/20014/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/92463/tmp/hooks/D01_modify_environment starting
+debug: Running on ionos16-i386.
+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 Apr 8 21:55 /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/92463/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/92463/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='i386'
- DEBIAN_FRONTEND='noninteractive'
- DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 '
- DISTRIBUTION='unstable'
- HOME='/root'
- HOST_ARCH='i386'
+ 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]="i686-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=i386
+ DEBIAN_FRONTEND=noninteractive
+ DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 '
+ DIRSTACK=()
+ DISTRIBUTION=unstable
+ EUID=0
+ FUNCNAME=([0]="Echo" [1]="main")
+ GROUPS=()
+ HOME=/root
+ HOSTNAME=i-capture-the-hostname
+ HOSTTYPE=i686
+ HOST_ARCH=i386
IFS='
'
- INVOCATION_ID='ef0f4afc7ab649aab885a91563452df9'
- LANG='C'
- LANGUAGE='en_US:en'
- LC_ALL='C'
- LD_LIBRARY_PATH='/usr/lib/libeatmydata'
- LD_PRELOAD='libeatmydata.so'
- 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='20014'
- PS1='# '
- PS2='> '
+ INVOCATION_ID=95a74762694e487b92fb4cdec8130b9a
+ LANG=C
+ LANGUAGE=de_CH:de
+ LC_ALL=C
+ LD_LIBRARY_PATH=/usr/lib/libeatmydata
+ LD_PRELOAD=libeatmydata.so
+ MACHTYPE=i686-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=92463
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.jzHmtSz7/pbuilderrc_8iX4 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.jzHmtSz7/b1 --logfile b1/build.log subread_2.0.8+dfsg-1.dsc'
- SUDO_GID='112'
- SUDO_UID='107'
- SUDO_USER='jenkins'
- TERM='unknown'
- TZ='/usr/share/zoneinfo/Etc/GMT+12'
- USER='root'
- _='/usr/bin/systemd-run'
- http_proxy='http://46.16.76.132:3128'
+ 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.jzHmtSz7/pbuilderrc_v3E6 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.jzHmtSz7/b2 --logfile b2/build.log subread_2.0.8+dfsg-1.dsc'
+ SUDO_GID=112
+ SUDO_UID=107
+ SUDO_USER=jenkins
+ TERM=unknown
+ TZ=/usr/share/zoneinfo/Etc/GMT-14
+ UID=0
+ USER=root
+ _='I: set'
+ http_proxy=http://213.165.73.152:3128
I: uname -a
- Linux ionos12-i386 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) 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 Mar 4 11:20 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/20014/tmp/hooks/D02_print_environment finished
+ lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/92463/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
@@ -167,7 +199,7 @@
Get: 45 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 46 http://deb.debian.org/debian unstable/main i386 debhelper all 13.24.1 [920 kB]
Get: 47 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB]
-Fetched 28.4 MB in 1s (37.1 MB/s)
+Fetched 28.4 MB in 1s (31.7 MB/s)
Preconfiguring packages ...
Selecting previously unselected package libpython3.13-minimal:i386.
(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 ... 19769 files and directories currently installed.)
@@ -337,8 +369,8 @@
Setting up tzdata (2025a-2) ...
Current default time zone: 'Etc/UTC'
-Local time is now: Thu Mar 6 15:30:54 UTC 2025.
-Universal Time is now: Thu Mar 6 15:30:54 UTC 2025.
+Local time is now: Wed Apr 8 21:55:56 UTC 2026.
+Universal Time is now: Wed Apr 8 21:55:56 UTC 2026.
Run 'dpkg-reconfigure tzdata' if you wish to change it.
Setting up autotools-dev (20220109.1) ...
@@ -382,7 +414,11 @@
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/92463/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for unstable
+I: user script /srv/workspace/pbuilder/92463/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
@@ -398,7 +434,7 @@
rm -rf bin src/longread-one/make.version
find . -name "*.o" -delete
dh_auto_clean --sourcedirectory=src -- -f Makefile.Linux
- cd src && make -j11 clean -f Makefile.Linux
+ cd src && make -j21 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'
@@ -426,7 +462,7 @@
make[1]: Entering directory '/build/reproducible-path/subread-2.0.8+dfsg'
dh_auto_build --sourcedirectory=src -- -f Makefile.Linux CC=i686-linux-gnu-gcc ; \
- cd src && make -j11 "INSTALL=install --strip-program=true" -f Makefile.Linux CC=i686-linux-gnu-gcc
+ cd src && make -j21 "INSTALL=install --strip-program=true" -f Makefile.Linux CC=i686-linux-gnu-gcc
make[2]: Entering directory '/build/reproducible-path/subread-2.0.8+dfsg/src'
i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
@@ -440,6 +476,19 @@
i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 gene-value-index.o gene-value-index.c
i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 exon-algorithms.o exon-algorithms.c
i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 HelperFunctions.o HelperFunctions.c
+i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 interval_merge.o interval_merge.c
+i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 long-hashtable.o long-hashtable.c
+i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bigtable.o core-bigtable.c
+i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 seek-zlib.o seek-zlib.c
+i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 input-blc.o input-blc.c
+long-hashtable.c: In function 'lnhash_create':
+long-hashtable.c:46:60: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '8589934592' to '0' [-Woverflow]
+ 46 | the_table -> key_repeated_numbers = malloc(sizeof(short) * 0x100000000llu);
+ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+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);
+ | ^~~~
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 ))
@@ -452,6 +501,26 @@
gene-value-index.c:87:41: note: in expansion of macro 'SUBREADprintf'
87 | SUBREADprintf("INCHRO:%d ; POS:%d\n", ret, pos);
| ^~~~~~~~~~~~~
+input-files.c: In function 'reduce_SAM_to_BAM':
+input-files.c:3240:13: warning: unused variable 'seq_len' [-Wunused-variable]
+ 3240 | int seq_len = qual - seq - 1;
+ | ^~~~~~~
+In file included from input-blc.c:8:
+input-blc.c: In function 'cacheBCL_quality_test':
+input-blc.c:1422:39: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
+ 1422 | SUBREADprintf("ERROR: the cell barcodes have different lengths (%d!=%ld at %d). The program cannot process the cell barcodes.\n", known_cell_barcode_length, strlen(bcbstr),xx1);
+ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~
+ | |
+ | size_t {aka unsigned int}
+subread.h:142:44: note: in definition of macro 'SUBREADprintf'
+ 142 | #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__)
+ | ^~~~~~~~~~~
+input-blc.c:1422:95: note: format string is defined here
+ 1422 | SUBREADprintf("ERROR: the cell barcodes have different lengths (%d!=%ld at %d). The program cannot process the cell barcodes.\n", known_cell_barcode_length, strlen(bcbstr),xx1);
+ | ~~^
+ | |
+ | long int
+ | %d
core-junction.c: In function 'find_donor_receptor':
core-junction.c:2099:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
2099 | if(0&& FIXLENstrcmp("V0112_0155:7:1101:12618:2466#ACTTGA", rname) == 0)
@@ -467,20 +536,10 @@
/usr/include/i386-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;
- | ^~~~~~~
-i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 interval_merge.o interval_merge.c
input-files.c: In function 'SAM_pairer_fix_format':
input-files.c:4830:50: warning: variable 'readname' set but not used [-Wunused-but-set-variable]
4830 | char tmpfname [MAX_FILE_NAME_LENGTH+14], readname[256];
| ^~~~~~~~
-i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 long-hashtable.o long-hashtable.c
-long-hashtable.c: In function 'lnhash_create':
-long-hashtable.c:46:60: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '8589934592' to '0' [-Woverflow]
- 46 | the_table -> key_repeated_numbers = malloc(sizeof(short) * 0x100000000llu);
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
@@ -496,8 +555,6 @@
/usr/include/i386-linux-gnu/bits/string_fortified.h:81:10: warning: '__builtin___memcpy_chk' writing 256 bytes into a region of size 200 overflows the destination [-Wstringop-overflow=]
81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bigtable.o core-bigtable.c
-i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 seek-zlib.o seek-zlib.c
sambam-file.c: In function 'PBum_load_header':
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);
@@ -511,27 +568,6 @@
/usr/include/i386-linux-gnu/bits/string_fortified.h:81:10: warning: '__builtin___memcpy_chk' writing 256 bytes into a region of size 200 overflows the destination [-Wstringop-overflow=]
81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 input-blc.o input-blc.c
-input-blc.c: In function 'iCache_continuous_read_lanes':
-input-blc.c:580:59: warning: unused variable 'npos' [-Wunused-variable]
- 580 | long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET);
- | ^~~~
-In file included from input-blc.c:8:
-input-blc.c: In function 'cacheBCL_quality_test':
-input-blc.c:1422:39: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
- 1422 | SUBREADprintf("ERROR: the cell barcodes have different lengths (%d!=%ld at %d). The program cannot process the cell barcodes.\n", known_cell_barcode_length, strlen(bcbstr),xx1);
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~
- | |
- | size_t {aka unsigned int}
-subread.h:142:44: note: in definition of macro 'SUBREADprintf'
- 142 | #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__)
- | ^~~~~~~~~~~
-input-blc.c:1422:95: note: format string is defined here
- 1422 | SUBREADprintf("ERROR: the cell barcodes have different lengths (%d!=%ld at %d). The program cannot process the cell barcodes.\n", known_cell_barcode_length, strlen(bcbstr),xx1);
- | ~~^
- | |
- | long int
- | %d
input-files.c: In function 'SAM_nosort_run_once':
input-files.c:5263:37: warning: argument 1 value '4294967295' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
5263 | char * header_txt = malloc(max(1000000,pairer->BAM_l_text));
@@ -546,15 +582,25 @@
i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
-rm -f longread-one/*.o
i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
+rm -f longread-one/*.o
i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
+i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
cd longread-one && make
+i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
+i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
+i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
+i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.8"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o flattenGTF flattenAnnotations.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
make[3]: Entering directory '/build/reproducible-path/subread-2.0.8+dfsg/src/longread-one'
i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
+i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
+i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
+i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
+i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
+i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
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);
@@ -658,7 +704,6 @@
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
readSummary.c: In function 'vote_and_add_count':
-i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
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;
| ^~~~~~~~~~~~~~~~~~~~~~~~
@@ -666,20 +711,11 @@
readSummary.c:3889:32: warning: unused variable 'sample_i' [-Wunused-variable]
3889 | int xk1, xk2, ret = 0, sample_i;
| ^~~~~~~~
+i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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;
| ^~~~~~~~~~~~~~~~~~
-i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
-i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
-i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
-i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
-i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
-i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
-i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
-i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
-i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
-i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 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]
@@ -751,7 +787,7 @@
|| Repeat threshold : 100 repeats ||
|| Gapped index : no ||
|| ||
-|| Free / total memory : 2.5GB / 0.0GB ||
+|| Free / total memory : 2.7GB / 0.0GB ||
|| ||
|| Input files : 1 file in total ||
|| o chr901.fa ||
@@ -769,7 +805,7 @@
|| The notes can be found in the log file, '../small1.log'. ||
|| Scan uninformative subreads in reference sequences ... ||
subread-buildindex: hashtable.c:470: HashTablePutReplaceEx: Assertion `key != NULL' failed.
-Aborted
+subread-align-test.sh: line 7: 93837 Aborted $SUBREAD_HOME/subread-buildindex -B -F -o ../small1 -M100 ../chr901.fa
md5sum: ../small1.00.b.array: No such file or directory
md5sum: ../small1.00.b.tab: No such file or directory
@@ -800,7 +836,7 @@
|| ||
\\============================================================================//
-//================ Running (06-Mar-2025 03:31:32, pid=28863) =================\\
+//================ Running (09-Apr-2026 11:56:22, pid=93840) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
@@ -847,7 +883,7 @@
|| ||
\\============================================================================//
-//================ Running (06-Mar-2025 03:31:32, pid=28866) =================\\
+//================ Running (09-Apr-2026 11:56:22, pid=93843) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
@@ -899,7 +935,7 @@
|| ||
\\============================================================================//
-//================ Running (06-Mar-2025 03:31:33, pid=28869) =================\\
+//================ Running (09-Apr-2026 11:56:22, pid=93846) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
@@ -951,7 +987,7 @@
|| ||
\\============================================================================//
-//================ Running (06-Mar-2025 03:31:33, pid=28873) =================\\
+//================ Running (09-Apr-2026 11:56:22, pid=93849) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
@@ -1003,7 +1039,7 @@
|| ||
\\============================================================================//
-//================ Running (06-Mar-2025 03:31:33, pid=28878) =================\\
+//================ Running (09-Apr-2026 11:56:22, pid=93852) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
@@ -1056,7 +1092,7 @@
|| ||
\\============================================================================//
-//================ Running (06-Mar-2025 03:31:33, pid=28885) =================\\
+//================ Running (09-Apr-2026 11:56:22, pid=93855) =================\\
|| ||
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.
@@ -1120,7 +1156,7 @@
|| Repeat threshold : 100 repeats ||
|| Gapped index : yes ||
|| ||
-|| Free / total memory : 2.6GB / 0.0GB ||
+|| Free / total memory : 1.4GB / 0.0GB ||
|| ||
|| Input files : 1 file in total ||
|| o chr901.fa ||
@@ -1138,7 +1174,7 @@
|| The notes can be found in the log file, '../small1.log'. ||
|| Scan uninformative subreads in reference sequences ... ||
subread-buildindex: hashtable.c:470: HashTablePutReplaceEx: Assertion `key != NULL' failed.
-Aborted
+subjunc-test.sh: line 3: 93861 Aborted ../../bin/subread-buildindex -o ../small1 ../chr901.fa
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
@@ -1172,7 +1208,7 @@
|| ||
\\============================================================================//
-//================ Running (06-Mar-2025 03:31:34, pid=28906) =================\\
+//================ Running (09-Apr-2026 11:56:23, pid=93862) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
@@ -1216,7 +1252,7 @@
|| ||
\\============================================================================//
-//================ Running (06-Mar-2025 03:31:34, pid=28907) =================\\
+//================ Running (09-Apr-2026 11:56:23, pid=93863) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
@@ -1330,7 +1366,9 @@
Testing Allowing multi-mapped reads ... [[32mPASS[0m]
Testing not sorting input file ... [[32mPASS[0m]
Testing minimum overlapping length ... [[32mPASS[0m]
-Testing minimum overlapping fraction ... [[32mPASS[0m]
+Testing minimum overlapping fraction ... [data/compare.sh: line 18: 94057 Aborted nohup ../../bin/featureCounts $PARAMETERS -o $TMPF.FC -a $ANNO_FILE $SAM_FILE > /dev/null 2>&1
+cat: data/DEL4-1775685383.FC: No such file or directory
+[31mFAILED[0m]
Testing Largest Overlapping ... [[32mPASS[0m]
Testing paired-end distance ... [[32mPASS[0m]
Testing Read to position (5' end) ... [[32mPASS[0m]
@@ -1341,7 +1379,9 @@
Testing minimum mapping quality ... [[32mPASS[0m]
Testing Ignoring duplicated reads ... [[32mPASS[0m]
Testing Fraction counting ... [[32mPASS[0m]
-Testing Advanced fractions ... [[32mPASS[0m]
+Testing Advanced fractions ... [data/compare.sh: line 18: 94177 Aborted nohup ../../bin/featureCounts $PARAMETERS -o $TMPF.FC -a $ANNO_FILE $SAM_FILE > /dev/null 2>&1
+cat: data/DEL4-1775685383.FC: No such file or directory
+[31mFAILED[0m]
Testing Junction counting ... [[32mPASS[0m,[32mPASS[0m]
Skipping Junction counting (with genome).
Testing GTF format annotations ... [[32mPASS[0m]
@@ -1397,9 +1437,9 @@
|| ||
\\============================================================================//
-//====================== Running (06-Mar-2025 03:31:35) ======================\\
+//====================== Running (09-Apr-2026 11:56:24) ======================\\
|| ||
-|| Split BAM file into result/temp-snps-029532-D091970268DF-* ... ||
+|| Split BAM file into result/temp-snps-094452-ED7A8D80E65B-* ... ||
|| processed block chr901@999950 by thread 1/1 [block number=1/1] ||
|| ||
|| Completed successfully. ||
@@ -1463,10 +1503,10 @@
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'
@@ -1505,34 +1545,48 @@
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 debian/subread/usr/share/man/man1/featureCounts.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/flattenGTF.1 debian/subread/usr/share/man/man1/genRandomReads.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/propmapped.1 debian/subread/usr/share/man/man1/qualityScores.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/removeDup.1 debian/subread/usr/share/man/man1/repair.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subindel.1 debian/subread/usr/share/man/man1/subjunc.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/sublong.1 debian/subread/usr/share/man/man1/subread-align.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 debian/subread/usr/share/man/man1/subread-fullscan.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/exactSNP.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/featureCounts.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/flattenGTF.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/genRandomReads.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/propmapped.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/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/repair.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subindel.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subjunc.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/sublong.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-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/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/flattenGTF.1.dh-new debian/subread/usr/share/man/man1/flattenGTF.1
- mv debian/subread/usr/share/man/man1/genRandomReads.1.dh-new debian/subread/usr/share/man/man1/genRandomReads.1
- chmod 0644 -- debian/subread/usr/share/man/man1/flattenGTF.1 debian/subread/usr/share/man/man1/genRandomReads.1
- mv debian/subread/usr/share/man/man1/removeDup.1.dh-new debian/subread/usr/share/man/man1/removeDup.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/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/removeDup.1 debian/subread/usr/share/man/man1/repair.1
- mv debian/subread/usr/share/man/man1/sublong.1.dh-new debian/subread/usr/share/man/man1/sublong.1
+ 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/subread-align.1.dh-new debian/subread/usr/share/man/man1/subread-align.1
- chmod 0644 -- debian/subread/usr/share/man/man1/sublong.1 debian/subread/usr/share/man/man1/subread-align.1
- mv debian/subread/usr/share/man/man1/subindel.1.dh-new debian/subread/usr/share/man/man1/subindel.1
+ chmod 0644 -- debian/subread/usr/share/man/man1/subread-align.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/subjunc.1.dh-new debian/subread/usr/share/man/man1/subjunc.1
- chmod 0644 -- debian/subread/usr/share/man/man1/subindel.1 debian/subread/usr/share/man/man1/subjunc.1
+ 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/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/sublong.1.dh-new debian/subread/usr/share/man/man1/sublong.1
+ chmod 0644 -- debian/subread/usr/share/man/man1/sublong.1
mv debian/subread/usr/share/man/man1/subread-fullscan.1.dh-new debian/subread/usr/share/man/man1/subread-fullscan.1
- chmod 0644 -- debian/subread/usr/share/man/man1/subread-buildindex.1 debian/subread/usr/share/man/man1/subread-fullscan.1
- mv debian/subread/usr/share/man/man1/exactSNP.1.dh-new debian/subread/usr/share/man/man1/exactSNP.1
- mv debian/subread/usr/share/man/man1/featureCounts.1.dh-new debian/subread/usr/share/man/man1/featureCounts.1
- chmod 0644 -- debian/subread/usr/share/man/man1/exactSNP.1 debian/subread/usr/share/man/man1/featureCounts.1
- mv debian/subread/usr/share/man/man1/propmapped.1.dh-new debian/subread/usr/share/man/man1/propmapped.1
- mv debian/subread/usr/share/man/man1/qualityScores.1.dh-new debian/subread/usr/share/man/man1/qualityScores.1
- chmod 0644 -- debian/subread/usr/share/man/man1/propmapped.1 debian/subread/usr/share/man/man1/qualityScores.1
+ chmod 0644 -- debian/subread/usr/share/man/man1/subread-fullscan.1
dh_installsystemduser -O--buildsystem=makefile
dh_perl -O--buildsystem=makefile
dh_link -O--buildsystem=makefile
@@ -1543,8 +1597,8 @@
cd debian/subread
cd debian/subread-data
chmod a-x usr/share/doc/subread-data/changelog.Debian usr/share/doc/subread/examples/annotation/hg19_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/hg38_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm10_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm9_RefSeq_exon.txt
- 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-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
cd '/build/reproducible-path/subread-2.0.8+dfsg'
cd '/build/reproducible-path/subread-2.0.8+dfsg'
@@ -1555,8 +1609,8 @@
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-data -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/subread/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/subread-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
find debian/subread/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
find debian/subread/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
@@ -1567,11 +1621,61 @@
objcopy --compress-debug-sections debian/subread/usr/lib/debug/.dwz/i386-linux-gnu/subread.debug
chmod 0644 -- debian/subread/usr/lib/debug/.dwz/i386-linux-gnu/subread.debug
dh_strip -a -O--buildsystem=makefile
+ install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0e
+ objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0e/2076b28985dab39ead108cee6776809b9d4023.debug
+ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0e/2076b28985dab39ead108cee6776809b9d4023.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/0e/2076b28985dab39ead108cee6776809b9d4023.debug debian/subread/usr/bin/subindel
+ 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/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f7/a38af0f83420361882b1243000cfe5ffae64e2.debug
+ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f7/a38af0f83420361882b1243000cfe5ffae64e2.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/f7/a38af0f83420361882b1243000cfe5ffae64e2.debug debian/subread/usr/bin/subjunc
+ install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c9
+ objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c9/ab0b2ecc0098e7080a189b7afbce5b2bd8db93.debug
+ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c9/ab0b2ecc0098e7080a189b7afbce5b2bd8db93.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/c9/ab0b2ecc0098e7080a189b7afbce5b2bd8db93.debug debian/subread/usr/bin/sublong
+ install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/86
+ objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/featureCounts debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/86/287c584cc6aacd5b1e0ee58e464ae957cdcb58.debug
+ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/86/287c584cc6aacd5b1e0ee58e464ae957cdcb58.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/86/287c584cc6aacd5b1e0ee58e464ae957cdcb58.debug debian/subread/usr/bin/featureCounts
+ install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2a
+ objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2a/b637dee51f06d60f815dd786ff1ae1314fccee.debug
+ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2a/b637dee51f06d60f815dd786ff1ae1314fccee.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/2a/b637dee51f06d60f815dd786ff1ae1314fccee.debug debian/subread/usr/bin/subread-align
+ install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7e
+ objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-buildindex debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7e/4797565d61d8d09099ebd93aade4761c244548.debug
+ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7e/4797565d61d8d09099ebd93aade4761c244548.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/7e/4797565d61d8d09099ebd93aade4761c244548.debug debian/subread/usr/bin/subread-buildindex
+ install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/70
+ objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/70/81d945f067ec383086ccca1883501fe2939f9a.debug
+ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/70/81d945f067ec383086ccca1883501fe2939f9a.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/70/81d945f067ec383086ccca1883501fe2939f9a.debug debian/subread/usr/bin/exactSNP
install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/29
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/29/c75d45c4aa6d283d1f60b0f56c0f5cf1e1582f.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/29/c75d45c4aa6d283d1f60b0f56c0f5cf1e1582f.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/29/c75d45c4aa6d283d1f60b0f56c0f5cf1e1582f.debug debian/subread/usr/lib/subread/propmapped
+ install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4d
+ objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4d/c0305f14ca78275b68372185b232eb809efe09.debug
+ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4d/c0305f14ca78275b68372185b232eb809efe09.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/4d/c0305f14ca78275b68372185b232eb809efe09.debug debian/subread/usr/lib/subread/removeDup
+ install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/15
+ objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/15/4d54db67f407df47a57c8da44894f4a05d4a93.debug
+ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/15/4d54db67f407df47a57c8da44894f4a05d4a93.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/15/4d54db67f407df47a57c8da44894f4a05d4a93.debug debian/subread/usr/lib/subread/qualityScores
+ install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e0
+ objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/txUnique debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e0/226ca1de27ed2b207906c9f5fb17a225436a75.debug
+ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e0/226ca1de27ed2b207906c9f5fb17a225436a75.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/e0/226ca1de27ed2b207906c9f5fb17a225436a75.debug debian/subread/usr/lib/subread/txUnique
install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/99
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/subread-fullscan debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/99/d8fff28be5d69579c38b9da544fea3ab16fb7a.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/99/d8fff28be5d69579c38b9da544fea3ab16fb7a.debug
@@ -1587,61 +1691,11 @@
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1b/ece5c57e6c1747a3a713e01e557cdd0719b21e.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/1b/ece5c57e6c1747a3a713e01e557cdd0719b21e.debug debian/subread/usr/lib/subread/genRandomReads
- install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4d
- objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4d/c0305f14ca78275b68372185b232eb809efe09.debug
- chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4d/c0305f14ca78275b68372185b232eb809efe09.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/4d/c0305f14ca78275b68372185b232eb809efe09.debug debian/subread/usr/lib/subread/removeDup
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/flattenGTF debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5/4434b66b2f44947209e28234fe4db4ba554d05.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5/4434b66b2f44947209e28234fe4db4ba554d05.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/f5/4434b66b2f44947209e28234fe4db4ba554d05.debug debian/subread/usr/lib/subread/flattenGTF
- install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/15
- objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/15/4d54db67f407df47a57c8da44894f4a05d4a93.debug
- chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/15/4d54db67f407df47a57c8da44894f4a05d4a93.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/15/4d54db67f407df47a57c8da44894f4a05d4a93.debug debian/subread/usr/lib/subread/qualityScores
- install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e0
- objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/txUnique debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e0/226ca1de27ed2b207906c9f5fb17a225436a75.debug
- chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e0/226ca1de27ed2b207906c9f5fb17a225436a75.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/e0/226ca1de27ed2b207906c9f5fb17a225436a75.debug debian/subread/usr/lib/subread/txUnique
- install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/86
- objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/featureCounts debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/86/287c584cc6aacd5b1e0ee58e464ae957cdcb58.debug
- chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/86/287c584cc6aacd5b1e0ee58e464ae957cdcb58.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/86/287c584cc6aacd5b1e0ee58e464ae957cdcb58.debug debian/subread/usr/bin/featureCounts
- install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2a
- objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2a/b637dee51f06d60f815dd786ff1ae1314fccee.debug
- chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2a/b637dee51f06d60f815dd786ff1ae1314fccee.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/2a/b637dee51f06d60f815dd786ff1ae1314fccee.debug debian/subread/usr/bin/subread-align
- install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7e
- objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-buildindex debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7e/4797565d61d8d09099ebd93aade4761c244548.debug
- chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7e/4797565d61d8d09099ebd93aade4761c244548.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/7e/4797565d61d8d09099ebd93aade4761c244548.debug debian/subread/usr/bin/subread-buildindex
- install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/70
- objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/70/81d945f067ec383086ccca1883501fe2939f9a.debug
- chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/70/81d945f067ec383086ccca1883501fe2939f9a.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/70/81d945f067ec383086ccca1883501fe2939f9a.debug debian/subread/usr/bin/exactSNP
- 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/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f7/a38af0f83420361882b1243000cfe5ffae64e2.debug
- chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f7/a38af0f83420361882b1243000cfe5ffae64e2.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/f7/a38af0f83420361882b1243000cfe5ffae64e2.debug debian/subread/usr/bin/subjunc
- install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c9
- objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c9/ab0b2ecc0098e7080a189b7afbce5b2bd8db93.debug
- chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c9/ab0b2ecc0098e7080a189b7afbce5b2bd8db93.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/c9/ab0b2ecc0098e7080a189b7afbce5b2bd8db93.debug debian/subread/usr/bin/sublong
- install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0e
- objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0e/2076b28985dab39ead108cee6776809b9d4023.debug
- chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0e/2076b28985dab39ead108cee6776809b9d4023.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/0e/2076b28985dab39ead108cee6776809b9d4023.debug debian/subread/usr/bin/subindel
install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.dwz
cp --reflink=auto -a debian/subread/usr/lib/debug/.dwz/i386-linux-gnu debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.dwz
rm -fr debian/subread/usr/lib/debug/.dwz
@@ -1653,7 +1707,7 @@
rm -f debian/subread/DEBIAN/shlibs
dh_shlibdeps -a -O--buildsystem=makefile
install -m0755 -d debian/subread/DEBIAN
- dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/txUnique debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subread-align debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/exactSNP debian/subread/usr/bin/subjunc debian/subread/usr/bin/sublong debian/subread/usr/bin/subindel
+ dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/bin/subindel debian/subread/usr/bin/subjunc debian/subread/usr/bin/sublong debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subread-align debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/exactSNP debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/txUnique debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/flattenGTF
dh_installdeb -O--buildsystem=makefile
install -m0755 -d debian/subread/DEBIAN
install -m0755 -d debian/subread-data/DEBIAN
@@ -1668,15 +1722,15 @@
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=0e2076b28985dab39ead108cee6776809b9d4023 154d54db67f407df47a57c8da44894f4a05d4a93 1bece5c57e6c1747a3a713e01e557cdd0719b21e 29c75d45c4aa6d283d1f60b0f56c0f5cf1e1582f 2ab637dee51f06d60f815dd786ff1ae1314fccee 43aed644bac36e6ed492087711984a20248cd809 4dc0305f14ca78275b68372185b232eb809efe09 7081d945f067ec383086ccca1883501fe2939f9a 7e4797565d61d8d09099ebd93aade4761c244548 86287c584cc6aacd5b1e0ee58e464ae957cdcb58 99d8fff28be5d69579c38b9da544fea3ab16fb7a c9ab0b2ecc0098e7080a189b7afbce5b2bd8db93 e0226ca1de27ed2b207906c9f5fb17a225436a75 f54434b66b2f44947209e28234fe4db4ba554d05 f7a38af0f83420361882b1243000cfe5ffae64e2" -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
@@ -1687,8 +1741,8 @@
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_2.0.8+dfsg-1_i386.deb'.
-dpkg-deb: building package 'subread-data' in '../subread-data_2.0.8+dfsg-1_all.deb'.
dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_2.0.8+dfsg-1_i386.deb'.
+dpkg-deb: building package 'subread-data' in '../subread-data_2.0.8+dfsg-1_all.deb'.
dpkg-genbuildinfo --build=binary -O../subread_2.0.8+dfsg-1_i386.buildinfo
dpkg-genchanges --build=binary -O../subread_2.0.8+dfsg-1_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
@@ -1696,12 +1750,14 @@
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/92463/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/92463/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/20014 and its subdirectories
-I: Current time: Thu Mar 6 03:32:32 -12 2025
-I: pbuilder-time-stamp: 1741275152
+I: removing directory /srv/workspace/pbuilder/92463 and its subdirectories
+I: Current time: Thu Apr 9 11:57:02 +14 2026
+I: pbuilder-time-stamp: 1775685422