Thu Mar 6 15:30:11 UTC 2025 I: starting to build subread/unstable/i386 on jenkins on '2025-03-06 15:30'
Thu Mar 6 15:30:11 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_7/59639/console.log
Thu Mar 6 15:30:11 UTC 2025 I: Downloading source for unstable/subread=2.0.8+dfsg-1
--2025-03-06 15:30:11-- http://deb.debian.org/debian/pool/main/s/subread/subread_2.0.8%2bdfsg-1.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2333 (2.3K) [text/prs.lines.tag]
Saving to: ‘subread_2.0.8+dfsg-1.dsc’
0K .. 100% 234M=0s
2025-03-06 15:30:11 (234 MB/s) - ‘subread_2.0.8+dfsg-1.dsc’ saved [2333/2333]
Thu Mar 6 15:30:11 UTC 2025 I: subread_2.0.8+dfsg-1.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: subread
Binary: subread, subread-data
Architecture: any all
Version: 2.0.8+dfsg-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Alexandre Mestiashvili <mestia@debian.org>, Andreas Tille <tille@debian.org>
Homepage: http://sourceforge.net/projects/subread/
Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/subread
Vcs-Git: https://salsa.debian.org/med-team/subread.git
Testsuite: autopkgtest
Testsuite-Triggers: python3
Build-Depends: bc <!nocheck>, debhelper-compat (= 13), architecture-is-little-endian, python3 <!nocheck>, zlib1g-dev
Package-List:
subread deb science optional arch=any
subread-data deb science optional arch=all
Checksums-Sha1:
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Checksums-Sha256:
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427980cd515fab6f937d5a43d5f05e2f316715a3eff55c883d67e6ada35bf944 19628 subread_2.0.8+dfsg-1.debian.tar.xz
Files:
1a7e9e264eac7bdf7ee4b527b094e323 16549960 subread_2.0.8+dfsg.orig.tar.xz
ab8d12d856cb67da4695fa5672182c8f 19628 subread_2.0.8+dfsg-1.debian.tar.xz
Dgit: dabb43287de2c8140e6d570922108c6d6101d9cc debian archive/debian/2.0.8+dfsg-1 https://git.dgit.debian.org/subread
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Thu Mar 6 15:30:11 UTC 2025 I: Checking whether the package is not for us
Thu Mar 6 15:30:11 UTC 2025 I: Starting 1st build on remote node ionos12-i386.debian.net.
Thu Mar 6 15:30:11 UTC 2025 I: Preparing to do remote build '1' on ionos12-i386.debian.net.
Thu Mar 6 15:32:33 UTC 2025 I: Deleting $TMPDIR on ionos12-i386.debian.net.
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: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: using eatmydata during job
I: Copying source file
I: copying [subread_2.0.8+dfsg-1.dsc]
I: copying [./subread_2.0.8+dfsg.orig.tar.xz]
I: copying [./subread_2.0.8+dfsg-1.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./subread_2.0.8+dfsg-1.dsc: unsupported subcommand
dpkg-source: info: extracting subread in subread-2.0.8+dfsg
dpkg-source: info: unpacking subread_2.0.8+dfsg.orig.tar.xz
dpkg-source: info: unpacking subread_2.0.8+dfsg-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying typo.patch
dpkg-source: info: applying fix_ftbfs_kfreebsd.patch
dpkg-source: info: applying arch_specific_flags.patch
dpkg-source: info: applying 2to3.patch
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: 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'
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='> '
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'
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
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
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: bc, debhelper-compat (= 13), architecture-is-little-endian, python3, zlib1g-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19769 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on bc; however:
Package bc is not installed.
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on architecture-is-little-endian; however:
Package architecture-is-little-endian is not installed.
pbuilder-satisfydepends-dummy depends on python3; however:
Package python3 is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bc{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 47 newly installed, 0 to remove and 0 not upgraded.
Need to get 28.4 MB of archives. After unpacking 105 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main i386 libpython3.13-minimal i386 3.13.2-1 [859 kB]
Get: 2 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.4-1 [107 kB]
Get: 3 http://deb.debian.org/debian unstable/main i386 python3.13-minimal i386 3.13.2-1 [2266 kB]
Get: 4 http://deb.debian.org/debian unstable/main i386 python3-minimal i386 3.13.2-2 [27.1 kB]
Get: 5 http://deb.debian.org/debian unstable/main i386 media-types all 12.0.0 [28.9 kB]
Get: 6 http://deb.debian.org/debian unstable/main i386 netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian unstable/main i386 tzdata all 2025a-2 [259 kB]
Get: 8 http://deb.debian.org/debian unstable/main i386 libffi8 i386 3.4.7-1 [21.4 kB]
Get: 9 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-6 [69.4 kB]
Get: 10 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-6 [173 kB]
Get: 11 http://deb.debian.org/debian unstable/main i386 libpython3.13-stdlib i386 3.13.2-1 [1985 kB]
Get: 12 http://deb.debian.org/debian unstable/main i386 python3.13 i386 3.13.2-1 [745 kB]
Get: 13 http://deb.debian.org/debian unstable/main i386 libpython3-stdlib i386 3.13.2-2 [10.1 kB]
Get: 14 http://deb.debian.org/debian unstable/main i386 python3 i386 3.13.2-2 [28.1 kB]
Get: 15 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 16 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 17 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 18 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 19 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.23.1-1 [245 kB]
Get: 20 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 21 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-7 [1199 kB]
Get: 22 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.4-5 [96.5 kB]
Get: 23 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 24 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 25 http://deb.debian.org/debian unstable/main i386 architecture-properties i386 0.2.6 [2340 B]
Get: 26 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-7 [301 kB]
Get: 27 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB]
Get: 28 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 29 http://deb.debian.org/debian unstable/main i386 automake all 1:1.17-3 [862 kB]
Get: 30 http://deb.debian.org/debian unstable/main i386 autopoint all 0.23.1-1 [770 kB]
Get: 31 http://deb.debian.org/debian unstable/main i386 bc i386 1.07.1-4 [105 kB]
Get: 32 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 33 http://deb.debian.org/debian unstable/main i386 libtool all 2.5.4-4 [539 kB]
Get: 34 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 35 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 36 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 37 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 38 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 39 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 40 http://deb.debian.org/debian unstable/main i386 libunistring5 i386 1.3-1 [458 kB]
Get: 41 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-6 [9582 kB]
Get: 42 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b2 [734 kB]
Get: 43 http://deb.debian.org/debian unstable/main i386 gettext i386 0.23.1-1 [1714 kB]
Get: 44 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
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)
Preconfiguring packages ...
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Preparing to unpack .../libexpat1_2.6.4-1_i386.deb ...
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Setting up libpython3.13-minimal:i386 (3.13.2-1) ...
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Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
Unpacking libreadline8t64:i386 (8.2-6) ...
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Current default time zone: 'Etc/UTC'
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Run 'dpkg-reconfigure tzdata' if you wish to change it.
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-> 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
dpkg-buildpackage: info: source package subread
dpkg-buildpackage: info: source version 2.0.8+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <emollier@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
debian/rules clean
dh clean --buildsystem=makefile
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/subread-2.0.8+dfsg'
dh_auto_clean
rm -f test/subread-align/data/test-err-mut-r1.fq.gz test/subread-align/data/test-err-mut-r2.fq.gz
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
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'
make[1]: Leaving directory '/build/reproducible-path/subread-2.0.8+dfsg'
dh_autoreconf_clean -O--buildsystem=makefile
dh_clean -O--buildsystem=makefile
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/subread.substvars debian/subread-data.substvars debian/files
rm -fr -- debian/subread/ debian/tmp/ debian/subread-data/
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} + \) -o \
\( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \)
debian/rules binary
dh binary --buildsystem=makefile
dh_update_autotools_config -O--buildsystem=makefile
dh_autoreconf -O--buildsystem=makefile
dh_auto_configure -O--buildsystem=makefile
debian/rules override_dh_auto_build
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
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
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-indel.o core-indel.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 sambam-file.o sambam-file.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 sublog.o sublog.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 gene-algorithms.o gene-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 hashtable.o 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 input-files.o input-files.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 sorted-hashtable.o sorted-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 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
gene-value-index.c: In function 'is_offset_in_chro':
gene-value-index.c:85:33: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
85 | if( pos < chros -> padding || pos >= ( chros->read_offsets[n] - chros->read_offsets[n-1] - chros -> padding ))
| ^~
In file included from gene-value-index.h:24,
from gene-value-index.c:25:
subread.h:142:28: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
142 | #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__)
| ^~~~~~~
gene-value-index.c:87:41: note: in expansion of macro 'SUBREADprintf'
87 | SUBREADprintf("INCHRO:%d ; POS:%d\n", ret, pos);
| ^~~~~~~~~~~~~
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)
| ^~
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 ){
| ^~
gene-algorithms.c: In function 'miltime':
gene-algorithms.c:1395:17: warning: 'ftime' is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations]
1395 | ftime(&trp);
| ^~~~~
In file included from gene-algorithms.c:33:
/usr/include/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);
| ^
In file included from sambam-file.c:33:
subread.h:571:14: note: destination object 'chro_name' of size 200
571 | char chro_name[MAX_CHROMOSOME_NAME_LEN];
| ^~~~~~~~~
In file included from /usr/include/string.h:548,
from sambam-file.c:30:
In function 'strcpy',
inlined from 'PBam_chunk_headers' at sambam-file.c:564:6:
/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);
| ^
subread.h:571:14: note: destination object 'chro_name' of size 200
571 | char chro_name[MAX_CHROMOSOME_NAME_LEN];
| ^~~~~~~~~
In function 'strcpy',
inlined from 'PBam_chunk_headers' at sambam-file.c:564:6,
inlined from 'PBum_load_header' at sambam-file.c:1045:9:
/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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from input-files.c:24:
/usr/include/stdlib.h:672:14: note: in a call to allocation function 'malloc' declared here
672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__
| ^~~~~~
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 genRandomReads gen_rand_reads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
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 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
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
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
cd longread-one && make
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
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
detection-calls.c:154:48: note: unnamed temporary defined here
154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0};
| ^
detection-calls.c:155:109: warning: dangling pointer 'gc_2int' to an unnamed temporary may be used [-Wdangling-pointer=]
155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0);
| ^
detection-calls.c:154:48: note: unnamed temporary defined here
154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0};
| ^
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);
| ^~~~~~
In file included from /usr/include/stdio.h:970,
from SUBindel.c:20:
In function 'sprintf',
inlined from 'load_global_context_forindel' at SUBindel.c:66:2:
/usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 7 and 1006 bytes into a destination of size 1000
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
SUBindel.c: In function 'load_global_context_forindel':
SUBindel.c:77:39: warning: '.00.b.tab' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=]
77 | sprintf(tmp_fname, "%s.00.b.tab", context->config.index_prefix);
| ^~~~~~~~~
In function 'sprintf',
inlined from 'load_global_context_forindel' at SUBindel.c:77:3:
/usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
SUBindel.c: In function 'load_global_context_forindel':
SUBindel.c:75:39: warning: '.00.c.tab' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=]
75 | sprintf(tmp_fname, "%s.00.c.tab", context->config.index_prefix);
| ^~~~~~~~~
In function 'sprintf',
inlined from 'load_global_context_forindel' at SUBindel.c:75:3:
/usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
SUBindel.c: In function 'load_global_context_forindel':
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');
| ^~~~
SUBindel.c:87:36: note: directive argument in the range [-2147483647, 2147483647]
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');
| ^~~~~~~~~~~~~~~~
In function 'sprintf',
inlined from 'load_global_context_forindel' at SUBindel.c:87:3:
/usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 10 and 1018 bytes into a destination of size 1000
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
SUBindel.c: In function 'load_global_context_forindel':
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');
| ^~~~
SUBindel.c:87:36: note: directive argument in the range [-2147483647, 2147483647]
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');
| ^~~~~~~~~~~~~~~~
In function 'sprintf',
inlined from 'load_global_context_forindel' at SUBindel.c:87:3:
/usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 10 and 1018 bytes into a destination of size 1000
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
SUBindel.c: In function 'load_indexes_forindel':
SUBindel.c:110:40: warning: '%02d' directive writing between 2 and 9 bytes into a region of size between 0 and 999 [-Wformat-overflow=]
110 | sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, block_no, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b');
| ^~~~
SUBindel.c:110:36: note: directive argument in the range [0, 134217728]
110 | sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, block_no, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b');
| ^~~~~~~~~~~~~~~~~~
In function 'sprintf',
inlined from 'load_indexes_forindel' at SUBindel.c:110:3:
/usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 12 and 1018 bytes into a destination of size 1000
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
readSummary.c: In function 'vote_and_add_count':
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;
| ^~~~~~~~~~~~~~~~~~~~~~~~
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;
| ^~~~~~~~
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]
234 | ftime(&trp);
| ^~~~~
In file included from longread-mapping.c:33:
/usr/include/i386-linux-gnu/sys/timeb.h:29:12: note: declared here
29 | extern int ftime (struct timeb *__timebuf)
| ^~~~~
make[3]: Leaving directory '/build/reproducible-path/subread-2.0.8+dfsg/src/longread-one'
readSummary.c: In function 'vote_and_add_count':
readSummary.c:3752:66: warning: 'longest_overlap_score' may be used uninitialized [-Wmaybe-uninitialized]
3752 | if(longest_overlap_score > scoring_numbers[score_x1]) scoring_numbers[score_x1] = 0;
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c:3521:51: note: 'longest_overlap_score' was declared here
3521 | int scoring_count = 0, score_x1, longest_overlap_score;
| ^~~~~~~~~~~~~~~~~~~~~
mkdir -p ../bin/utilities
mv longread-one/LRM longread-one/sublong
mv longread-one/sublong subread-align subjunc featureCounts subindel exactSNP subread-buildindex ../bin/
mv detectionCall genRandomReads repair propmapped qualityScores removeDup subread-fullscan txUnique flattenGTF ../bin/utilities
###########################################################
# #
# Installation successfully completed. #
# #
# Generated executables were copied to directory ../bin/ #
# #
###########################################################
make[2]: Leaving directory '/build/reproducible-path/subread-2.0.8+dfsg/src'
make[1]: Leaving directory '/build/reproducible-path/subread-2.0.8+dfsg'
rm -f debian/subread-data.debhelper.log debian/subread.debhelper.log
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/subread-2.0.8+dfsg'
debian/tests/subread-tests /build/reproducible-path/subread-2.0.8+dfsg
[2J[0;0H[30;47m
**************************************************
**************************************************
*** ***
*** This script will test the major functions ***
*** in our package, including the index build- ***
*** er, subread-align, subjunc, featureCounts ***
*** and exactSNP. ***
*** ***
*** Test will start in seconds. ***
*** ***
**************************************************
**************************************************
[13;26H[33;44m9[13;26H8[13;26H7[13;26H6[13;26H5[13;26H4[13;26H3[13;26H2[13;26H1[13;26H0[0m[2J[0,0Hrm: cannot remove 'test-tmp.log': No such file or directory
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.8
//================================= setting ==================================\\
|| ||
|| Index name : small1 ||
|| Index space : base space ||
|| Index split : no-split ||
|| Repeat threshold : 100 repeats ||
|| Gapped index : no ||
|| ||
|| Free / total memory : 2.5GB / 0.0GB ||
|| ||
|| Input files : 1 file in total ||
|| o chr901.fa ||
|| ||
|| ||
|| WARNING: the free memory is lower than 3.0GB. ||
|| the program may run very slow or crash. ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Check the integrity of provided reference sequences ... ||
|| There were 4 notes for reference sequences. ||
|| 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
md5sum: ../small1.00.b.array: No such file or directory
md5sum: ../small1.00.b.tab: No such file or directory
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.8
//================================= setting ==================================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file : test-noerror-r1.fq ||
|| Output file : test-tmp.sam (SAM) ||
|| Index name : small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 64 ||
|| Min votes : 3 / 10 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : no ||
|| Max alignments per multi-mapping read : 1 ||
|| ||
\\============================================================================//
//================ Running (06-Mar-2025 03:31:32, pid=28863) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| The range of Phred scores observed in the data is [9,9] ||
|| Create the output SAM file. ||
|| Check the index. ||
Unable top open index '../small1'. Please make sure that the correct prefix is specified and you have the permission to read these files. For example, if there are files '/opt/my_index.reads', '/opt/my_index.files' and etc, the index prefix should be specified as '/opt/my_index' without any suffix.
Traceback (most recent call last):
File "/build/reproducible-path/subread-2.0.8+dfsg/adt_test/subread-align/readname_ora_match.py", line 83, in <module>
main()
~~~~^^
File "/build/reproducible-path/subread-2.0.8+dfsg/adt_test/subread-align/readname_ora_match.py", line 80, in main
print("accuracy=",(matched*1.)/(matched+unmatched)," ; sensitivity=",(matched+unmatched)*1./(line-NN))
~~~~~~~~~~~~^^~~~~~~~~~~~~~~~~~~
ZeroDivisionError: float division by zero
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.8
//================================= setting ==================================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file : test-noerror-r1.fq ||
|| Output file : test-tmp.sam (SAM) ||
|| Index name : small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 64 ||
|| Min votes : 3 / 10 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : no ||
|| Max alignments per multi-mapping read : 1 ||
|| ||
\\============================================================================//
//================ Running (06-Mar-2025 03:31:32, pid=28866) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| The range of Phred scores observed in the data is [9,9] ||
|| Create the output SAM file. ||
|| Check the index. ||
Unable top open index '../small1'. Please make sure that the correct prefix is specified and you have the permission to read these files. For example, if there are files '/opt/my_index.reads', '/opt/my_index.files' and etc, the index prefix should be specified as '/opt/my_index' without any suffix.
Traceback (most recent call last):
File "/build/reproducible-path/subread-2.0.8+dfsg/adt_test/subread-align/readname_ora_match.py", line 83, in <module>
main()
~~~~^^
File "/build/reproducible-path/subread-2.0.8+dfsg/adt_test/subread-align/readname_ora_match.py", line 80, in main
print("accuracy=",(matched*1.)/(matched+unmatched)," ; sensitivity=",(matched+unmatched)*1./(line-NN))
~~~~~~~~~~~~^^~~~~~~~~~~~~~~~~~~
ZeroDivisionError: float division by zero
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.8
//================================= setting ==================================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : test-noerror-r1.fq ||
|| Input file 2 : test-noerror-r2.fq ||
|| Output file : test-tmp.sam (SAM) ||
|| Index name : small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 64 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : no ||
|| Max alignments per multi-mapping read : 1 ||
|| ||
\\============================================================================//
//================ Running (06-Mar-2025 03:31:33, pid=28869) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| The range of Phred scores observed in the data is [9,9] ||
|| Create the output SAM file. ||
|| Check the index. ||
Unable top open index '../small1'. Please make sure that the correct prefix is specified and you have the permission to read these files. For example, if there are files '/opt/my_index.reads', '/opt/my_index.files' and etc, the index prefix should be specified as '/opt/my_index' without any suffix.
Traceback (most recent call last):
File "/build/reproducible-path/subread-2.0.8+dfsg/adt_test/subread-align/readname_ora_match.py", line 83, in <module>
main()
~~~~^^
File "/build/reproducible-path/subread-2.0.8+dfsg/adt_test/subread-align/readname_ora_match.py", line 80, in main
print("accuracy=",(matched*1.)/(matched+unmatched)," ; sensitivity=",(matched+unmatched)*1./(line-NN))
~~~~~~~~~~~~^^~~~~~~~~~~~~~~~~~~
ZeroDivisionError: float division by zero
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.8
//================================= setting ==================================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : test-noerror-r1.fq ||
|| Input file 2 : test-noerror-r2.fq ||
|| Output file : test-tmp.sam (SAM) ||
|| Index name : small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 64 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : no ||
|| Max alignments per multi-mapping read : 1 ||
|| ||
\\============================================================================//
//================ Running (06-Mar-2025 03:31:33, pid=28873) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| The range of Phred scores observed in the data is [9,9] ||
|| Create the output SAM file. ||
|| Check the index. ||
Unable top open index '../small1'. Please make sure that the correct prefix is specified and you have the permission to read these files. For example, if there are files '/opt/my_index.reads', '/opt/my_index.files' and etc, the index prefix should be specified as '/opt/my_index' without any suffix.
Traceback (most recent call last):
File "/build/reproducible-path/subread-2.0.8+dfsg/adt_test/subread-align/readname_ora_match.py", line 83, in <module>
main()
~~~~^^
File "/build/reproducible-path/subread-2.0.8+dfsg/adt_test/subread-align/readname_ora_match.py", line 80, in main
print("accuracy=",(matched*1.)/(matched+unmatched)," ; sensitivity=",(matched+unmatched)*1./(line-NN))
~~~~~~~~~~~~^^~~~~~~~~~~~~~~~~~~
ZeroDivisionError: float division by zero
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.8
//================================= setting ==================================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : test-error-r1.fq ||
|| Input file 2 : test-error-r2.fq ||
|| Output file : test-tmp.sam (SAM) ||
|| Index name : small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 64 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : no ||
|| Max alignments per multi-mapping read : 1 ||
|| ||
\\============================================================================//
//================ Running (06-Mar-2025 03:31:33, pid=28878) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| The range of Phred scores observed in the data is [-14,-14] ||
|| Create the output SAM file. ||
|| Check the index. ||
Unable top open index '../small1'. Please make sure that the correct prefix is specified and you have the permission to read these files. For example, if there are files '/opt/my_index.reads', '/opt/my_index.files' and etc, the index prefix should be specified as '/opt/my_index' without any suffix.
Traceback (most recent call last):
File "/build/reproducible-path/subread-2.0.8+dfsg/adt_test/subread-align/readname_ora_match.py", line 83, in <module>
main()
~~~~^^
File "/build/reproducible-path/subread-2.0.8+dfsg/adt_test/subread-align/readname_ora_match.py", line 80, in main
print("accuracy=",(matched*1.)/(matched+unmatched)," ; sensitivity=",(matched+unmatched)*1./(line-NN))
~~~~~~~~~~~~^^~~~~~~~~~~~~~~~~~~
ZeroDivisionError: float division by zero
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.8
//================================= setting ==================================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : test-err-mut-r1.fq.gz ||
|| Input file 2 : test-err-mut-r2.fq.gz ||
|| Output file : test-tmp.sam (SAM) ||
|| Index name : small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 64 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : no ||
|| Max alignments per multi-mapping read : 1 ||
|| Read group name : MyTestGroup ||
|| ||
\\============================================================================//
//================ Running (06-Mar-2025 03:31:33, pid=28885) =================\\
|| ||
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.
Traceback (most recent call last):
File "/build/reproducible-path/subread-2.0.8+dfsg/adt_test/subread-align/readname_ora_match.py", line 83, in <module>
main()
~~~~^^
File "/build/reproducible-path/subread-2.0.8+dfsg/adt_test/subread-align/readname_ora_match.py", line 80, in main
print("accuracy=",(matched*1.)/(matched+unmatched)," ; sensitivity=",(matched+unmatched)*1./(line-NN))
~~~~~~~~~~~~^^~~~~~~~~~~~~~~~~~~
ZeroDivisionError: float division by zero
*************************************************
*** SINGLE-END READS NO ERROR ******
*************************************************
unmatched= 0 ; matched= 0 ; unmapped= 0 ; reads= 0 ;NN= 0
*************************************************
*** SINGLE-END READS NO ERROR NO DUP ******
*************************************************
unmatched= 0 ; matched= 0 ; unmapped= 0 ; reads= 0 ;NN= 0
*************************************************
*** READS WITH NO ERROR ******
*************************************************
unmatched= 0 ; matched= 0 ; unmapped= 0 ; reads= 0 ;NN= 0
*************************************************
*** READS NO ERROR, NO DUPLICATED REPORT ******
*************************************************
unmatched= 0 ; matched= 0 ; unmapped= 0 ; reads= 0 ;NN= 0
*************************************************
*** READS WITH ONLY SEQUENCING ERROR ******
*************************************************
unmatched= 0 ; matched= 0 ; unmapped= 0 ; reads= 0 ;NN= 0
*************************************************
*** READS WITH SEQUENCING ERROR AND MUTATION ***
*** SUBREAD IS RUN WITH LONG INDEL DETECTION ***
*************************************************
unmatched= 0 ; matched= 0 ; unmapped= 0 ; reads= 0 ;NN= 0
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.8
//================================= setting ==================================\\
|| ||
|| Index name : small1 ||
|| Index space : base space ||
|| Memory : 3000 Mbytes ||
|| Repeat threshold : 100 repeats ||
|| Gapped index : yes ||
|| ||
|| Free / total memory : 2.6GB / 0.0GB ||
|| ||
|| Input files : 1 file in total ||
|| o chr901.fa ||
|| ||
|| ||
|| WARNING: the free memory is lower than 3.0GB. ||
|| the program may run very slow or crash. ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Check the integrity of provided reference sequences ... ||
|| There were 4 notes for reference sequences. ||
|| 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
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.8
//================================= setting ==================================\\
|| ||
|| Function : Read alignment + Junction detection (RNA-Seq) ||
|| Input file 1 : junction-reads-A.fq ||
|| Input file 2 : junction-reads-B.fq ||
|| Output file : junctions.sam (SAM) ||
|| Index name : small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 14 ||
|| Min read1 vote : 1 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : no ||
|| Max alignments per multi-mapping read : 1 ||
|| ||
\\============================================================================//
//================ Running (06-Mar-2025 03:31:34, pid=28906) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| The range of Phred scores observed in the data is [2,41] ||
|| Create the output SAM file. ||
|| Check the index. ||
Unable top open index '../small1'. Please make sure that the correct prefix is specified and you have the permission to read these files. For example, if there are files '/opt/my_index.reads', '/opt/my_index.files' and etc, the index prefix should be specified as '/opt/my_index' without any suffix.
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.8
//================================= setting ==================================\\
|| ||
|| Function : Read alignment + Junction/Fusion detection (RNA-Seq) ||
|| Input file 1 : junction-reads-A.fq ||
|| Input file 2 : junction-reads-B.fq ||
|| Output file : junctionsNfusions.bam (BAM) ||
|| Index name : small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 28 ||
|| Min read1 vote : 1 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : no ||
|| Max alignments per multi-mapping read : 1 ||
|| ||
\\============================================================================//
//================ Running (06-Mar-2025 03:31:34, pid=28907) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| The range of Phred scores observed in the data is [2,41] ||
|| Create the output BAM file. ||
|| Check the index. ||
Unable top open index '../small1'. Please make sure that the correct prefix is specified and you have the permission to read these files. For example, if there are files '/opt/my_index.reads', '/opt/my_index.files' and etc, the index prefix should be specified as '/opt/my_index' without any suffix.
================================================================================
FeatureCounts Basic Test
http://subread.sourceforge.net/
================================================================================
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.8
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 SAM file ||
|| ||
|| test-minimum.sam ||
|| ||
|| Output file : test-minimum.FC ||
|| Summary : test-minimum.FC.summary ||
|| Paired-end : yes ||
|| Count read pairs : no ||
|| Annotation : test-minimum.GTF (GTF) ||
|| Dir for temp files : result ||
|| ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Multimapping reads : not counted ||
|| Multi-overlapping reads : not counted ||
|| Min overlapping bases : 1 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file test-minimum.GTF ... ||
|| Features : 23 ||
|| Meta-features : 7 ||
|| Chromosomes/contigs : 3 ||
|| ||
|| Process SAM file test-minimum.sam... ||
|| Paired-end reads are included. ||
|| The reads are assigned on the single-end mode. ||
|| Total alignments : 998 ||
|| Successfully assigned alignments : 389 (39.0%) ||
|| Running time : 0.00 minutes ||
|| ||
|| Write the final count table. ||
|| Write the read assignment summary. ||
|| ||
|| Summary of counting results can be found in file "result/test-minimum.FC. ||
|| summary" ||
|| ||
\\============================================================================//
================================================================================
Basic Test finished.
The results are in result/test-minimum.FC
================================================================================
================================================================================
FeatureCounts Chromosome Name Aliases Tests
http://subread.sourceforge.net/
================================================================================
Testing chromosome aliases ... [[32mPASS[0m]
================================================================================
FeatureCounts Chromosome Name Inference Tests
http://subread.sourceforge.net/
================================================================================
Testing automatic inference of chromosome names ... [[32mPASS[0m]
mkdir: unrecognized option '--countReadPairs'
Try 'mkdir --help' for more information.
================================================================================
FeatureCounts Corner Case Tests
http://subread.sourceforge.net/
================================================================================
Testing indel reads ... [[32mPASS[0m]
Testing junction reads ... [[32mPASS[0m]
Testing paired-end reads (fragment counting) ... [[32mPASS[0m]
Testing paired-end reads (fragment counting, both ends mapped) ... [[32mPASS[0m]
Testing multi-overlapping reads ... [[32mPASS[0m]
Testing feature-level summarization ... [[32mPASS[0m]
Testing gene-level summarization ... [[32mPASS[0m]
Testing multi-mapping reads ... [[32mPASS[0m]
Testing multi-mapping reads (primary only) ... [[32mPASS[0m]
Testing both ends mapped ... [[32mPASS[0m]
Testing disallowing chimeric fragments ... [[32mPASS[0m]
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 Largest Overlapping ... [[32mPASS[0m]
Testing paired-end distance ... [[32mPASS[0m]
Testing Read to position (5' end) ... [[32mPASS[0m]
Testing Read to position (3' end) ... [[32mPASS[0m]
Testing Read extension to the 3' end ... [[32mPASS[0m]
Testing Read extension to the 5' end ... [[32mPASS[0m]
Testing Low maxOPs value ... [[32mPASS[0m]
Testing minimum mapping quality ... [[32mPASS[0m]
Testing Ignoring duplicated reads ... [[32mPASS[0m]
Testing Fraction counting ... [[32mPASS[0m]
Testing Advanced fractions ... [[32mPASS[0m]
Testing Junction counting ... [[32mPASS[0m,[32mPASS[0m]
Skipping Junction counting (with genome).
Testing GTF format annotations ... [[32mPASS[0m]
Testing SAF format annotations ... [[32mPASS[0m]
Testing SAM format input ... [[32mPASS[0m]
Testing BAM format input ... [[32mPASS[0m]
Testing unstranded read summarization ... [[32mPASS[0m]
Testing stranded read summarization ... [[32mPASS[0m]
Testing reversely stranded read summarization ... [[32mPASS[0m]
Testing Ignoring duplicate fragments ... [[32mPASS[0m]
Testing Junction reads only ... [[32mPASS[0m]
Testing Exonic reads only ... [[32mPASS[0m]
Testing intron_between ... [[32mPASS[0m]
Testing intron_between ... [[32mPASS[0m]
Testing intron_between ... [[32mPASS[0m]
Testing intron_between ... [[32mPASS[0m]
Testing across_genes ... [[32mPASS[0m]
Testing across_genes ... [[32mPASS[0m]
Testing across_genes ... [[32mPASS[0m]
Testing across_genes ... [[32mPASS[0m]
Testing across_intron ... [[32mPASS[0m]
Testing across_intron ... [[32mPASS[0m]
Testing across_intron ... [[32mPASS[0m]
Testing across_intron ... [[32mPASS[0m]
../../bin/exactSNP -g ../chr901.fa -o result/test-out.VCF -i data/test-in.BAM -b
Check the input format ...
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.8
//============================= exactSNP setting =============================\\
|| ||
|| Input file : test-in.BAM (BAM) ||
|| Output file : test-out.VCF ||
|| Reference genome : chr901.fa ||
|| Temp path : ||
|| ||
|| Threads : 1 ||
|| Min supporting reads : 1 ||
|| Min pct. of supporting reads : 0.0% ||
|| Min base quality score : 13 ||
|| Number of trimmed bases : 3 ||
|| ||
|| Q value cutoff : 10E-12.0 ||
|| P value upper bound : 0.00500 ||
|| Flanking windows size : 5 ||
|| ||
\\============================================================================//
//====================== Running (06-Mar-2025 03:31:35) ======================\\
|| ||
|| Split BAM file into result/temp-snps-029532-D091970268DF-* ... ||
|| processed block chr901@999950 by thread 1/1 [block number=1/1] ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed reads : 50204 ||
|| Reported SNPs : 416 ||
|| Reported indels : 22 ||
|| ||
|| Running time : 0.0 minutes ||
|| ||
\\============================================================================//
[30;47m
**************************************************
**************************************************
*** ***
*** Test finished. ***
*** ***
*** Should there be any error, please visit ***
*** [34mhttp://subread.sourceforge.net/[0;30;47m for more ***
*** information. ***
*** ***
**************************************************
**************************************************
[0m
make[1]: Leaving directory '/build/reproducible-path/subread-2.0.8+dfsg'
create-stamp debian/debhelper-build-stamp
dh_testroot -O--buildsystem=makefile
dh_prep -O--buildsystem=makefile
rm -f -- debian/subread.substvars debian/subread-data.substvars
rm -fr -- debian/.debhelper/generated/subread/ debian/subread/ debian/tmp/ debian/.debhelper/generated/subread-data/ debian/subread-data/
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/reproducible-path/subread-2.0.8+dfsg'
cp annotation/mm39_RefSeq_exon.txt.gz debian/mm39_RefSeq_exon.txt.gz.orig
find /build/reproducible-path/subread-2.0.8+dfsg -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "${name%.*}"' \;
dh_auto_install
install -m0755 -d /build/reproducible-path/subread-2.0.8\+dfsg/debian/tmp
mv debian/mm39_RefSeq_exon.txt.gz.orig annotation/mm39_RefSeq_exon.txt.gz
make[1]: Leaving directory '/build/reproducible-path/subread-2.0.8+dfsg'
dh_install -O--buildsystem=makefile
install -m0755 -d debian/subread/usr/bin
cp --reflink=auto -a ./bin/exactSNP ./bin/featureCounts ./bin/subindel ./bin/subjunc ./bin/sublong ./bin/subread-align ./bin/subread-buildindex debian/subread/usr/bin/
install -m0755 -d debian/subread/usr/lib/subread
cp --reflink=auto -a ./bin/utilities/flattenGTF ./bin/utilities/genRandomReads ./bin/utilities/propmapped ./bin/utilities/qualityScores ./bin/utilities/removeDup ./bin/utilities/repair ./bin/utilities/subread-fullscan ./bin/utilities/txUnique debian/subread/usr/lib/subread/
install -m0755 -d debian/subread-data/usr/share/doc/subread/examples
cp --reflink=auto -a ./annotation debian/subread-data/usr/share/doc/subread/examples/
dh_installdocs -O--buildsystem=makefile
install -m0755 -d debian/subread/usr/share/doc/subread
install -m0755 -d debian/subread/usr/share/doc/subread
cp --reflink=auto -a ./README.txt debian/subread/usr/share/doc/subread
chmod -R u\+rw,go=rX debian/subread/usr/share/doc
install -p -m0644 debian/README.Debian debian/subread/usr/share/doc/subread/README.Debian
install -p -m0644 debian/copyright debian/subread/usr/share/doc/subread/copyright
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
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'
tar --sort=name \
--mtime="@1741180806" \
--owner=root --group=root --numeric-owner \
--mode=go=rX,u+rw,a-s \
-cJf /build/reproducible-path/subread-2.0.8+dfsg/debian/subread-data/usr/share/doc/subread/examples/test.tar.xz test/
make[1]: Leaving directory '/build/reproducible-path/subread-2.0.8+dfsg'
dh_installman -O--buildsystem=makefile
install -m0755 -d debian/subread/usr/share/man/man1/
install -p -m0644 ./debian/exactSNP.1 debian/subread/usr/share/man/man1/exactSNP.1
install -m0755 -d debian/subread/usr/share/man/man1/
install -p -m0644 ./debian/featureCounts.1 debian/subread/usr/share/man/man1/featureCounts.1
install -m0755 -d debian/subread/usr/share/man/man1/
install -p -m0644 ./debian/flattenGTF.1 debian/subread/usr/share/man/man1/flattenGTF.1
install -m0755 -d debian/subread/usr/share/man/man1/
install -p -m0644 ./debian/genRandomReads.1 debian/subread/usr/share/man/man1/genRandomReads.1
install -m0755 -d debian/subread/usr/share/man/man1/
install -p -m0644 ./debian/propmapped.1 debian/subread/usr/share/man/man1/propmapped.1
install -m0755 -d debian/subread/usr/share/man/man1/
install -p -m0644 ./debian/qualityScores.1 debian/subread/usr/share/man/man1/qualityScores.1
install -m0755 -d debian/subread/usr/share/man/man1/
install -p -m0644 ./debian/removeDup.1 debian/subread/usr/share/man/man1/removeDup.1
install -m0755 -d debian/subread/usr/share/man/man1/
install -p -m0644 ./debian/repair.1 debian/subread/usr/share/man/man1/repair.1
install -m0755 -d debian/subread/usr/share/man/man1/
install -p -m0644 ./debian/subindel.1 debian/subread/usr/share/man/man1/subindel.1
install -m0755 -d debian/subread/usr/share/man/man1/
install -p -m0644 ./debian/subjunc.1 debian/subread/usr/share/man/man1/subjunc.1
install -m0755 -d debian/subread/usr/share/man/man1/
install -p -m0644 ./debian/sublong.1 debian/subread/usr/share/man/man1/sublong.1
install -m0755 -d debian/subread/usr/share/man/man1/
install -p -m0644 ./debian/subread-align.1 debian/subread/usr/share/man/man1/subread-align.1
install -m0755 -d debian/subread/usr/share/man/man1/
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
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
mv debian/subread/usr/share/man/man1/repair.1.dh-new debian/subread/usr/share/man/man1/repair.1
chmod 0644 -- debian/subread/usr/share/man/man1/removeDup.1 debian/subread/usr/share/man/man1/repair.1
mv debian/subread/usr/share/man/man1/sublong.1.dh-new debian/subread/usr/share/man/man1/sublong.1
mv debian/subread/usr/share/man/man1/subread-align.1.dh-new debian/subread/usr/share/man/man1/subread-align.1
chmod 0644 -- debian/subread/usr/share/man/man1/sublong.1 debian/subread/usr/share/man/man1/subread-align.1
mv debian/subread/usr/share/man/man1/subindel.1.dh-new debian/subread/usr/share/man/man1/subindel.1
mv debian/subread/usr/share/man/man1/subjunc.1.dh-new debian/subread/usr/share/man/man1/subjunc.1
chmod 0644 -- debian/subread/usr/share/man/man1/subindel.1 debian/subread/usr/share/man/man1/subjunc.1
mv debian/subread/usr/share/man/man1/subread-buildindex.1.dh-new debian/subread/usr/share/man/man1/subread-buildindex.1
mv debian/subread/usr/share/man/man1/subread-fullscan.1.dh-new debian/subread/usr/share/man/man1/subread-fullscan.1
chmod 0644 -- debian/subread/usr/share/man/man1/subread-buildindex.1 debian/subread/usr/share/man/man1/subread-fullscan.1
mv debian/subread/usr/share/man/man1/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
dh_installsystemduser -O--buildsystem=makefile
dh_perl -O--buildsystem=makefile
dh_link -O--buildsystem=makefile
dh_strip_nondeterminism -O--buildsystem=makefile
Using 1741180806 as canonical time
Normalizing debian/subread-data/usr/share/doc/subread/examples/annotation/mm39_RefSeq_exon.txt.gz using File::StripNondeterminism::handlers::gzip
dh_compress -O--buildsystem=makefile
cd debian/subread
cd debian/subread-data
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/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'
dh_fixperms -O--buildsystem=makefile
find debian/subread ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/subread-data ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/subread-data/usr/share/doc -type f -a -true -a ! -regex 'debian/subread-data/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/subread/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 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/subread/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
find debian/subread/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
dh_missing -O--buildsystem=makefile
dh_dwz -a -O--buildsystem=makefile
install -m0755 -d debian/subread/usr/lib/debug/.dwz/i386-linux-gnu
dwz -mdebian/subread/usr/lib/debug/.dwz/i386-linux-gnu/subread.debug -M/usr/lib/debug/.dwz/i386-linux-gnu/subread.debug -- debian/subread/usr/bin/exactSNP debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subindel debian/subread/usr/bin/subjunc debian/subread/usr/bin/sublong debian/subread/usr/bin/subread-align debian/subread/usr/bin/subread-buildindex debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/txUnique
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/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/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
strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/subread-fullscan
objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/99/d8fff28be5d69579c38b9da544fea3ab16fb7a.debug debian/subread/usr/lib/subread/subread-fullscan
install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/43
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/repair debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/43/aed644bac36e6ed492087711984a20248cd809.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/43/aed644bac36e6ed492087711984a20248cd809.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/43/aed644bac36e6ed492087711984a20248cd809.debug debian/subread/usr/lib/subread/repair
install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1b
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/genRandomReads debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1b/ece5c57e6c1747a3a713e01e557cdd0719b21e.debug
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
rmdir -p --ignore-fail-on-non-empty debian/subread/usr/lib/debug
install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/share/doc
ln -s subread debian/.debhelper/subread/dbgsym-root/usr/share/doc/subread-dbgsym
install -m0755 -d debian/.debhelper/subread
dh_makeshlibs -a -O--buildsystem=makefile
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
dh_installdeb -O--buildsystem=makefile
install -m0755 -d debian/subread/DEBIAN
install -m0755 -d debian/subread-data/DEBIAN
dh_gencontrol -O--buildsystem=makefile
install -m0755 -d debian/subread-data/DEBIAN
echo misc:Depends= >> debian/subread-data.substvars
echo misc:Pre-Depends= >> debian/subread-data.substvars
dpkg-gencontrol -psubread-data -ldebian/changelog -Tdebian/subread-data.substvars -cdebian/control -Pdebian/subread-data
install -m0755 -d debian/subread/DEBIAN
echo misc:Depends= >> debian/subread.substvars
echo misc:Pre-Depends= >> debian/subread.substvars
install -m0755 -d debian/.debhelper/subread/dbgsym-root/DEBIAN
dpkg-gencontrol -psubread -ldebian/changelog -Tdebian/subread.substvars -cdebian/control -Pdebian/.debhelper/subread/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=subread-dbgsym "-DDepends=subread (= \${binary:Version})" "-DDescription=debug symbols for subread" "-DBuild-Ids=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/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
chmod 0644 -- debian/subread/DEBIAN/md5sums
install -m0755 -d debian/.debhelper/subread/dbgsym-root/DEBIAN
cd debian/.debhelper/subread/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/subread-data/DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/md5sums
dh_builddeb -O--buildsystem=makefile
dpkg-deb --root-owner-group --build debian/subread ..
dpkg-deb --root-owner-group --build debian/.debhelper/subread/dbgsym-root ..
dpkg-deb --root-owner-group --build debian/subread-data ..
dpkg-deb: 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-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)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: including full source code in upload
I: copying local configuration
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
Thu Mar 6 15:32:33 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos16-i386.debian.net.
Thu Mar 6 15:32:33 UTC 2025 I: Preparing to do remote build '2' on ionos16-i386.debian.net.
Thu Mar 6 15:34:04 UTC 2025 I: Deleting $TMPDIR on ionos16-i386.debian.net.
Thu Mar 6 15:34:05 UTC 2025 I: subread_2.0.8+dfsg-1_i386.changes:
Format: 1.8
Date: Wed, 05 Mar 2025 14:20:06 +0100
Source: subread
Binary: subread subread-data subread-dbgsym
Architecture: all i386
Version: 2.0.8+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
subread - toolkit for processing next-gen sequencing data
subread-data - data files for subread package
Changes:
subread (2.0.8+dfsg-1) unstable; urgency=medium
.
* Team upload.
* New upstream version 2.0.8+dfsg
* d/control: declare compliance to standards version 4.7.2.
* typo.patch: unfuzz.
* 2to3.patch: normalise Last-Update timestamp.
Checksums-Sha1:
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52bdb6226d98992f8fd21ba2850e574d5213db5b 10021764 subread-dbgsym_2.0.8+dfsg-1_i386.deb
cf84599a386876aa84b3a5c20d81d26979fff8a9 5678 subread_2.0.8+dfsg-1_i386.buildinfo
519a73e8e46017d50f0de498327b47cf01e468e3 867512 subread_2.0.8+dfsg-1_i386.deb
Checksums-Sha256:
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Files:
4ac714bc1b0d0df1cd55416bff782d6f 19224776 science optional subread-data_2.0.8+dfsg-1_all.deb
e4c907d3d83beb852fe11397f8be4304 10021764 debug optional subread-dbgsym_2.0.8+dfsg-1_i386.deb
337050833763f190a82715b5e4c471c4 5678 science optional subread_2.0.8+dfsg-1_i386.buildinfo
644fa3122155480c1b48b4c5cb907627 867512 science optional subread_2.0.8+dfsg-1_i386.deb
Thu Mar 6 15:34:06 UTC 2025 I: diffoscope 289 will be used to compare the two builds:
Running as unit: rb-diffoscope-i386_7-59639.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.jzHmtSz7/subread_2.0.8+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.jzHmtSz7/subread_2.0.8+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.jzHmtSz7/subread_2.0.8+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.jzHmtSz7/b1/subread_2.0.8+dfsg-1_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.jzHmtSz7/b2/subread_2.0.8+dfsg-1_i386.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call diffoscope.comparators.binary.FilesystemFile
## main (total time: 0.004s)
0.004s 2 calls outputs
0.000s 1 call cleanup
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 236ms
CPU time consumed: 236ms
Thu Mar 6 15:34:06 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists.
Thu Mar 6 15:34:06 UTC 2025 I: subread from unstable built successfully and reproducibly on i386.
Thu Mar 6 15:34:07 UTC 2025 I: Submitting .buildinfo files to external archives:
Thu Mar 6 15:34:07 UTC 2025 I: Submitting 8.0K b1/subread_2.0.8+dfsg-1_i386.buildinfo.asc
Thu Mar 6 15:34:08 UTC 2025 I: Submitting 8.0K b2/subread_2.0.8+dfsg-1_i386.buildinfo.asc
Thu Mar 6 15:34:09 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Thu Mar 6 15:34:09 UTC 2025 I: Done submitting .buildinfo files.
Thu Mar 6 15:34:09 UTC 2025 I: Removing signed subread_2.0.8+dfsg-1_i386.buildinfo.asc files:
removed './b1/subread_2.0.8+dfsg-1_i386.buildinfo.asc'
removed './b2/subread_2.0.8+dfsg-1_i386.buildinfo.asc'