I: pbuilder: network access will be disabled during build
I: Current time: Mon Aug 16 16:46:30 +14 2021
I: pbuilder-time-stamp: 1629081990
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz]
I: copying local configuration
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: Copying source file
I: copying [subread_2.0.1+dfsg-1.dsc]
I: copying [./subread_2.0.1+dfsg.orig.tar.xz]
I: copying [./subread_2.0.1+dfsg-1.debian.tar.xz]
I: Extracting source
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.7vWeAgjj/trustedkeys.kbx': General error
gpgv: Signature made Sat May 23 07:56:50 2020 +14
gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1
gpgv: issuer "moeller@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./subread_2.0.1+dfsg-1.dsc
dpkg-source: info: extracting subread in subread-2.0.1+dfsg
dpkg-source: info: unpacking subread_2.0.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking subread_2.0.1+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 gcc10.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/1957/tmp/hooks/D01_modify_environment starting
debug: Running on jtx1b.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
Removing 'diversion of /bin/sh to /bin/sh.distrib by dash'
Adding 'diversion of /bin/sh to /bin/sh.distrib by bash'
Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash'
Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash'
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/1957/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/1957/tmp/hooks/D02_print_environment starting
I: set
BASH=/bin/sh
BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath
BASH_ALIASES=()
BASH_ARGC=()
BASH_ARGV=()
BASH_CMDS=()
BASH_LINENO=([0]="12" [1]="0")
BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf")
BASH_VERSION='5.1.4(1)-release'
BUILDDIR=/build
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=armhf
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=4'
DIRSTACK=()
DISTRIBUTION=
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=arm
HOST_ARCH=armhf
IFS='
'
INVOCATION_ID=135e08156a7c4b8fadfa2acbeae78bf8
LANG=C
LANGUAGE=it_CH:it
LC_ALL=C
MACHTYPE=arm-unknown-linux-gnueabihf
MAIL=/var/mail/root
OPTERR=1
OPTIND=1
OSTYPE=linux-gnueabihf
PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
PBCURRENTCOMMANDLINEOPERATION=build
PBUILDER_OPERATION=build
PBUILDER_PKGDATADIR=/usr/share/pbuilder
PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
PBUILDER_SYSCONFDIR=/etc
PIPESTATUS=([0]="0")
POSIXLY_CORRECT=y
PPID=1957
PS4='+ '
PWD=/
SHELL=/bin/bash
SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
SHLVL=3
SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.eq6MdHPpVQ/pbuilderrc_wA00 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.eq6MdHPpVQ/b2 --logfile b2/build.log --extrapackages usrmerge subread_2.0.1+dfsg-1.dsc'
SUDO_GID=114
SUDO_UID=110
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://10.0.0.15:8000/
I: uname -a
Linux i-capture-the-hostname 5.10.0-8-arm64 #1 SMP Debian 5.10.46-4 (2021-08-03) aarch64 GNU/Linux
I: ls -l /bin
total 3580
-rwxr-xr-x 1 root root 816764 Aug 5 10:25 bash
-rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2
-rwxr-xr-x 3 root root 26052 Jul 21 2020 bzcat
lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff
lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe
lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep
-rwxr-xr-x 3 root root 26052 Jul 21 2020 bzip2
-rwxr-xr-x 1 root root 9636 Jul 21 2020 bzip2recover
lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore
-rwxr-xr-x 1 root root 26668 Sep 23 2020 cat
-rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp
-rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod
-rwxr-xr-x 1 root root 43112 Sep 23 2020 chown
-rwxr-xr-x 1 root root 92616 Sep 23 2020 cp
-rwxr-xr-x 1 root root 75524 Dec 11 2020 dash
-rwxr-xr-x 1 root root 75880 Sep 23 2020 date
-rwxr-xr-x 1 root root 55436 Sep 23 2020 dd
-rwxr-xr-x 1 root root 59912 Sep 23 2020 df
-rwxr-xr-x 1 root root 96764 Sep 23 2020 dir
-rwxr-xr-x 1 root root 55012 Jul 29 09:09 dmesg
lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname
-rwxr-xr-x 1 root root 22508 Sep 23 2020 echo
-rwxr-xr-x 1 root root 28 Nov 10 2020 egrep
-rwxr-xr-x 1 root root 22496 Sep 23 2020 false
-rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep
-rwxr-xr-x 1 root root 47492 Jul 29 09:09 findmnt
-rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount
-rwxr-xr-x 1 root root 124508 Nov 10 2020 grep
-rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip
-rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe
-rwxr-xr-x 1 root root 64212 Mar 3 13:30 gzip
-rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname
-rwxr-xr-x 1 root root 43180 Sep 23 2020 ln
-rwxr-xr-x 1 root root 35068 Feb 8 2020 login
-rwxr-xr-x 1 root root 96764 Sep 23 2020 ls
-rwxr-xr-x 1 root root 99940 Jul 29 09:09 lsblk
-rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir
-rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod
-rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp
-rwxr-xr-x 1 root root 34408 Jul 29 09:09 more
-rwsr-xr-x 1 root root 34400 Jul 29 09:09 mount
-rwxr-xr-x 1 root root 9824 Jul 29 09:09 mountpoint
-rwxr-xr-x 1 root root 88524 Sep 23 2020 mv
lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd
lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash
-rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink
-rwxr-xr-x 1 root root 43104 Sep 23 2020 rm
-rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir
-rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts
-rwxr-xr-x 1 root root 76012 Dec 23 2018 sed
lrwxrwxrwx 1 root root 4 Aug 16 16:46 sh -> bash
lrwxrwxrwx 1 root root 4 Aug 14 23:35 sh.distrib -> dash
-rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep
-rwxr-xr-x 1 root root 55360 Sep 23 2020 stty
-rwsr-xr-x 1 root root 46704 Jul 29 09:09 su
-rwxr-xr-x 1 root root 22532 Sep 23 2020 sync
-rwxr-xr-x 1 root root 340872 Feb 17 23:55 tar
-rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile
-rwxr-xr-x 1 root root 67696 Sep 23 2020 touch
-rwxr-xr-x 1 root root 22496 Sep 23 2020 true
-rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server
-rwsr-xr-x 1 root root 22108 Jul 29 09:09 umount
-rwxr-xr-x 1 root root 22520 Sep 23 2020 uname
-rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress
-rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir
-rwxr-xr-x 1 root root 38512 Jul 29 09:09 wdctl
lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat
-rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp
-rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff
-rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep
-rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep
-rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce
-rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep
-rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless
-rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore
-rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew
I: user script /srv/workspace/pbuilder/1957/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: armhf
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 (= 12), help2man, 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 ... 19398 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 (= 12); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on help2man; however:
Package help2man 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:
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} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libicu67{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libmpdec3{a} libncurses6{a} libpipeline1{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-minimal{a} python3.9{a} python3.9-minimal{a} readline-common{a} sensible-utils{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl libarchive-cpio-perl libgpm2 libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 48 newly installed, 0 to remove and 0 not upgraded.
Need to get 23.3 MB of archives. After unpacking 82.4 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bullseye/main armhf bsdextrautils armhf 2.36.1-8 [138 kB]
Get: 2 http://deb.debian.org/debian bullseye/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get: 3 http://deb.debian.org/debian bullseye/main armhf groff-base armhf 1.22.4-6 [847 kB]
Get: 4 http://deb.debian.org/debian bullseye/main armhf libpipeline1 armhf 1.5.3-1 [30.1 kB]
Get: 5 http://deb.debian.org/debian bullseye/main armhf man-db armhf 2.9.4-2 [1319 kB]
Get: 6 http://deb.debian.org/debian bullseye/main armhf liblocale-gettext-perl armhf 1.07-4+b1 [18.3 kB]
Get: 7 http://deb.debian.org/debian bullseye/main armhf libpython3.9-minimal armhf 3.9.2-1 [790 kB]
Get: 8 http://deb.debian.org/debian bullseye/main armhf libexpat1 armhf 2.2.10-2 [76.3 kB]
Get: 9 http://deb.debian.org/debian bullseye/main armhf python3.9-minimal armhf 3.9.2-1 [1630 kB]
Get: 10 http://deb.debian.org/debian bullseye/main armhf python3-minimal armhf 3.9.2-3 [38.2 kB]
Get: 11 http://deb.debian.org/debian bullseye/main armhf media-types all 4.0.0 [30.3 kB]
Get: 12 http://deb.debian.org/debian bullseye/main armhf libmpdec3 armhf 2.5.1-1 [74.9 kB]
Get: 13 http://deb.debian.org/debian bullseye/main armhf readline-common all 8.1-1 [73.7 kB]
Get: 14 http://deb.debian.org/debian bullseye/main armhf libreadline8 armhf 8.1-1 [147 kB]
Get: 15 http://deb.debian.org/debian bullseye/main armhf libpython3.9-stdlib armhf 3.9.2-1 [1608 kB]
Get: 16 http://deb.debian.org/debian bullseye/main armhf python3.9 armhf 3.9.2-1 [466 kB]
Get: 17 http://deb.debian.org/debian bullseye/main armhf libpython3-stdlib armhf 3.9.2-3 [21.4 kB]
Get: 18 http://deb.debian.org/debian bullseye/main armhf python3 armhf 3.9.2-3 [37.9 kB]
Get: 19 http://deb.debian.org/debian bullseye/main armhf sensible-utils all 0.0.14 [14.8 kB]
Get: 20 http://deb.debian.org/debian bullseye/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get: 21 http://deb.debian.org/debian bullseye/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get: 22 http://deb.debian.org/debian bullseye/main armhf file armhf 1:5.39-3 [68.1 kB]
Get: 23 http://deb.debian.org/debian bullseye/main armhf gettext-base armhf 0.21-4 [171 kB]
Get: 24 http://deb.debian.org/debian bullseye/main armhf libsigsegv2 armhf 2.13-1 [34.0 kB]
Get: 25 http://deb.debian.org/debian bullseye/main armhf m4 armhf 1.4.18-5 [192 kB]
Get: 26 http://deb.debian.org/debian bullseye/main armhf autoconf all 2.69-14 [313 kB]
Get: 27 http://deb.debian.org/debian bullseye/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get: 28 http://deb.debian.org/debian bullseye/main armhf automake all 1:1.16.3-2 [814 kB]
Get: 29 http://deb.debian.org/debian bullseye/main armhf autopoint all 0.21-4 [510 kB]
Get: 30 http://deb.debian.org/debian bullseye/main armhf libncurses6 armhf 6.2+20201114-2 [80.5 kB]
Get: 31 http://deb.debian.org/debian bullseye/main armhf bc armhf 1.07.1-2+b2 [104 kB]
Get: 32 http://deb.debian.org/debian bullseye/main armhf libdebhelper-perl all 13.3.4 [189 kB]
Get: 33 http://deb.debian.org/debian bullseye/main armhf libtool all 2.4.6-15 [513 kB]
Get: 34 http://deb.debian.org/debian bullseye/main armhf dh-autoreconf all 20 [17.1 kB]
Get: 35 http://deb.debian.org/debian bullseye/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get: 36 http://deb.debian.org/debian bullseye/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get: 37 http://deb.debian.org/debian bullseye/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get: 38 http://deb.debian.org/debian bullseye/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get: 39 http://deb.debian.org/debian bullseye/main armhf libelf1 armhf 0.183-1 [161 kB]
Get: 40 http://deb.debian.org/debian bullseye/main armhf dwz armhf 0.13+20210201-1 [179 kB]
Get: 41 http://deb.debian.org/debian bullseye/main armhf libicu67 armhf 67.1-7 [8319 kB]
Get: 42 http://deb.debian.org/debian bullseye/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [602 kB]
Get: 43 http://deb.debian.org/debian bullseye/main armhf gettext armhf 0.21-4 [1243 kB]
Get: 44 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get: 45 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 46 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB]
Get: 47 http://deb.debian.org/debian bullseye/main armhf help2man armhf 1.48.1 [190 kB]
Get: 48 http://deb.debian.org/debian bullseye/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [185 kB]
Fetched 23.3 MB in 4s (5323 kB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package bsdextrautils.
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(Reading database ... 19398 files and directories currently installed.)
Preparing to unpack .../0-bsdextrautils_2.36.1-8_armhf.deb ...
Unpacking bsdextrautils (2.36.1-8) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../1-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../2-groff-base_1.22.4-6_armhf.deb ...
Unpacking groff-base (1.22.4-6) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../3-libpipeline1_1.5.3-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.3-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../4-man-db_2.9.4-2_armhf.deb ...
Unpacking man-db (2.9.4-2) ...
Selecting previously unselected package liblocale-gettext-perl.
Preparing to unpack .../5-liblocale-gettext-perl_1.07-4+b1_armhf.deb ...
Unpacking liblocale-gettext-perl (1.07-4+b1) ...
Selecting previously unselected package libpython3.9-minimal:armhf.
Preparing to unpack .../6-libpython3.9-minimal_3.9.2-1_armhf.deb ...
Unpacking libpython3.9-minimal:armhf (3.9.2-1) ...
Selecting previously unselected package libexpat1:armhf.
Preparing to unpack .../7-libexpat1_2.2.10-2_armhf.deb ...
Unpacking libexpat1:armhf (2.2.10-2) ...
Selecting previously unselected package python3.9-minimal.
Preparing to unpack .../8-python3.9-minimal_3.9.2-1_armhf.deb ...
Unpacking python3.9-minimal (3.9.2-1) ...
Setting up libpython3.9-minimal:armhf (3.9.2-1) ...
Setting up libexpat1:armhf (2.2.10-2) ...
Setting up python3.9-minimal (3.9.2-1) ...
Selecting previously unselected package python3-minimal.
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Unpacking python3-minimal (3.9.2-3) ...
Selecting previously unselected package media-types.
Preparing to unpack .../1-media-types_4.0.0_all.deb ...
Unpacking media-types (4.0.0) ...
Selecting previously unselected package libmpdec3:armhf.
Preparing to unpack .../2-libmpdec3_2.5.1-1_armhf.deb ...
Unpacking libmpdec3:armhf (2.5.1-1) ...
Selecting previously unselected package readline-common.
Preparing to unpack .../3-readline-common_8.1-1_all.deb ...
Unpacking readline-common (8.1-1) ...
Selecting previously unselected package libreadline8:armhf.
Preparing to unpack .../4-libreadline8_8.1-1_armhf.deb ...
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The following additional packages will be installed:
libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl
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I: Building the package
hostname: Name or service not known
I: Running cd /build/subread-2.0.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../subread_2.0.1+dfsg-1_source.changes
dpkg-buildpackage: info: source package subread
dpkg-buildpackage: info: source version 2.0.1+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Steffen Moeller <moeller@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/subread-2.0.1+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
make[1]: Leaving directory '/build/subread-2.0.1+dfsg'
debian/rules override_dh_clean
make[1]: Entering directory '/build/subread-2.0.1+dfsg'
cd src; make -f Makefile.Linux clean
make[2]: Entering directory '/build/subread-2.0.1+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/subread-2.0.1+dfsg/src'
dh_clean
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 \
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
make[1]: Leaving directory '/build/subread-2.0.1+dfsg'
debian/rules binary
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make[1]: Entering directory '/build/subread-2.0.1+dfsg'
cd src; make -f Makefile.Linux
make[2]: Entering directory '/build/subread-2.0.1+dfsg/src'
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core.o core.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-junction.o core-junction.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-indel.o core-indel.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sambam-file.o sambam-file.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sublog.o sublog.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-algorithms.o gene-algorithms.c
gene-algorithms.c: In function 'miltime':
gene-algorithms.c:1579:2: warning: 'ftime' is deprecated [-Wdeprecated-declarations]
1579 | ftime(&trp);
| ^~~~~
In file included from gene-algorithms.c:32:
/usr/include/arm-linux-gnueabihf/sys/timeb.h:39:12: note: declared here
39 | extern int ftime (struct timeb *__timebuf)
| ^~~~~
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-files.o input-files.c
input-files.c: In function 'f_subr_open':
input-files.c:54:10: warning: implicit declaration of function 'fopen64'; did you mean 'gzopen64'? [-Wimplicit-function-declaration]
54 | return fopen64(fname, mode);
| ^~~~~~~
| gzopen64
input-files.c:54:10: warning: returning 'int' from a function with return type 'FILE *' makes pointer from integer without a cast [-Wint-conversion]
54 | return fopen64(fname, mode);
| ^~~~~~~~~~~~~~~~~~~~
input-files.c: In function 'SAM_nosort_run_once':
input-files.c:5267:23: warning: argument 1 value '4294967295' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
5267 | char * header_txt = malloc(max(1000000,pairer->BAM_l_text));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from input-files.c:24:
/usr/include/stdlib.h:539:14: note: in a call to allocation function 'malloc' declared here
539 | extern void *malloc (size_t __size) __THROW __attribute_malloc__
| ^~~~~~
input-files.c: In function 'is_SAM_unsorted':
input-files.c:6237:33: warning: 'read_name[0]' may be used uninitialized in this function [-Wmaybe-uninitialized]
6237 | for(field_cursor = 0; read_name[field_cursor] ; field_cursor++)
| ~~~~~~~~~^~~~~~~~~~~~~~
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sorted-hashtable.o sorted-hashtable.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-value-index.o gene-value-index.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o exon-algorithms.o exon-algorithms.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HelperFunctions.o HelperFunctions.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o interval_merge.o interval_merge.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o long-hashtable.o long-hashtable.c
long-hashtable.c: In function 'lnhash_create':
long-hashtable.c:46:46: 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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seek-zlib.o seek-zlib.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-blc.o input-blc.c
In file included from input-blc.c:7:
input-blc.c: In function 'cacheBCL_quality_test':
input-blc.c:910:18: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
910 | 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:132:44: note: in definition of macro 'SUBREADprintf'
132 | #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__)
| ^~~~~~~~~~~
input-blc.c:910:74: note: format string is defined here
910 | 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
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o detectionCall detection-calls.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
echo " " > longread-one/make.version
rm -f longread-one/*.o
cd longread-one && make
make[3]: Entering directory '/build/subread-2.0.1+dfsg/src/longread-one'
gcc -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" -fmessage-length=0 -ggdb -o LRMsorted-hashtable.o -c LRMsorted-hashtable.c
gcc -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" -fmessage-length=0 -ggdb -o LRMbase-index.o -c LRMbase-index.c
gcc -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" -fmessage-length=0 -ggdb -o LRMchro-event.o -c LRMchro-event.c
gcc -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" -fmessage-length=0 -ggdb -o LRMhelper.o -c LRMhelper.c
gcc -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" -fmessage-length=0 -ggdb -o LRMseek-zlib.o -c LRMseek-zlib.c
gcc -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" -fmessage-length=0 -ggdb -o LRMfile-io.o -c LRMfile-io.c
gcc -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" -fmessage-length=0 -ggdb -o LRMhashtable.o -c LRMhashtable.c
gcc -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" -fmessage-length=0 -ggdb -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:227:2: warning: 'ftime' is deprecated [-Wdeprecated-declarations]
227 | ftime(&trp);
| ^~~~~
In file included from longread-mapping.c:33:
/usr/include/arm-linux-gnueabihf/sys/timeb.h:39:12: note: declared here
39 | extern int ftime (struct timeb *__timebuf)
| ^~~~~
make[3]: Leaving directory '/build/subread-2.0.1+dfsg/src/longread-one'
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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
readSummary.c: In function 'fc_thread_start_threads':
readSummary.c:5194:28: warning: '%s' directive writing up to 1019 bytes into a region of size between 100 and 1099 [-Wformat-overflow=]
5194 | sprintf(tmp_fname2, "%s/%s", applied_detail_path, modified_fname);
| ^~
In file included from /usr/include/stdio.h:867,
from readSummary.c:23:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 2 and 2020 bytes into a destination of size 1100
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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
SUBindel.c: In function 'load_global_context_forindel':
SUBindel.c:66:24: 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:867,
from SUBindel.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 1006 bytes into a destination of size 1000
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SUBindel.c:77:25: 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 file included from /usr/include/stdio.h:867,
from SUBindel.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SUBindel.c:75:25: 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 file included from /usr/include/stdio.h:867,
from SUBindel.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SUBindel.c:87:26: 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');
| ^~~~
In file included from /usr/include/stdio.h:867,
from SUBindel.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 10 and 1018 bytes into a destination of size 1000
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SUBindel.c:87:26: 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');
| ^~~~
In file included from /usr/include/stdio.h:867,
from SUBindel.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 10 and 1018 bytes into a destination of size 1000
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SUBindel.c: In function 'load_indexes_forindel':
SUBindel.c:110:26: 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:110:22: 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 file included from /usr/include/stdio.h:867,
from SUBindel.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 12 and 1018 bytes into a destination of size 1000
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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
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/subread-2.0.1+dfsg/src'
dh_auto_build -- CC=arm-linux-gnueabihf-gcc
make[1]: Leaving directory '/build/subread-2.0.1+dfsg'
rm -f debian/subread-data.debhelper.log debian/subread.debhelper.log
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/subread-2.0.1+dfsg'
debian/tests/subread-tests /build/subread-2.0.1+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[0,0H
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.1
//================================= setting ==================================\\
|| ||
|| Index name : small1 ||
|| Index space : base space ||
|| Index split : no-split ||
|| Repeat threshold : 100 repeats ||
|| Gapped index : no ||
|| ||
|| Free / total memory : 2.3GB / 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:444: HashTablePutReplaceEx: Assertion `key != NULL' failed.
subread-align-test.sh: line 7: 31538 Aborted $SUBREAD_HOME/subread-buildindex -B -F -o ../small1 -M100 ../chr901.fa
md5sum: ../small1.00.b.array: No such file or directory
md5sum: ../small1.00.b.tab: No such file or directory
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.1
//================================= 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 (16-Aug-2021 16:51:51, pid=31577) =================\\
|| ||
|| 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/subread-2.0.1+dfsg/adt_test/subread-align/readname_ora_match.py", line 83, in <module>
main()
File "/build/subread-2.0.1+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
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.1
//================================= 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 (16-Aug-2021 16:51:52, pid=31585) =================\\
|| ||
|| 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/subread-2.0.1+dfsg/adt_test/subread-align/readname_ora_match.py", line 83, in <module>
main()
File "/build/subread-2.0.1+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
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.1
//================================= 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 (16-Aug-2021 16:51:52, pid=31589) =================\\
|| ||
|| 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/subread-2.0.1+dfsg/adt_test/subread-align/readname_ora_match.py", line 83, in <module>
main()
File "/build/subread-2.0.1+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
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.1
//================================= 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 (16-Aug-2021 16:51:52, pid=31595) =================\\
|| ||
|| 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/subread-2.0.1+dfsg/adt_test/subread-align/readname_ora_match.py", line 83, in <module>
main()
File "/build/subread-2.0.1+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
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.1
//================================= 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 (16-Aug-2021 16:51:52, pid=31598) =================\\
|| ||
|| 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/subread-2.0.1+dfsg/adt_test/subread-align/readname_ora_match.py", line 83, in <module>
main()
File "/build/subread-2.0.1+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
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.1
//================================= 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 (16-Aug-2021 16:51:52, pid=31601) =================\\
|| ||
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/subread-2.0.1+dfsg/adt_test/subread-align/readname_ora_match.py", line 83, in <module>
main()
File "/build/subread-2.0.1+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
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.1
//================================= setting ==================================\\
|| ||
|| Index name : small1 ||
|| Index space : base space ||
|| Memory : 3000 Mbytes ||
|| Repeat threshold : 100 repeats ||
|| Gapped index : yes ||
|| ||
|| Free / total memory : 1.4GB / 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:444: HashTablePutReplaceEx: Assertion `key != NULL' failed.
subjunc-test.sh: line 3: 31607 Aborted ../../bin/subread-buildindex -o ../small1 ../chr901.fa
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.1
//================================= 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 (16-Aug-2021 16:51:53, pid=31630) =================\\
|| ||
|| 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.
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.1
//================================= 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 (16-Aug-2021 16:51:53, pid=31631) =================\\
|| ||
|| 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/
================================================================================
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.1
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 SAM file ||
|| o test-minimum.sam ||
|| ||
|| Output file : test-minimum.FC ||
|| Summary : test-minimum.FC.summary ||
|| Annotation : test-minimum.GTF (GTF) ||
|| Dir for temp files : result ||
|| ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : no ||
|| 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... ||
|| WARNING: Paired-end reads were found. ||
|| 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]
================================================================================
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
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.1
//============================= 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 (16-Aug-2021 16:51:55) ======================\\
|| ||
|| Split BAM file into result/temp-snps-032179-32E6C10C73D5-* ... ||
|| 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/subread-2.0.1+dfsg'
create-stamp debian/debhelper-build-stamp
dh_prep
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/subread-2.0.1+dfsg'
find /build/subread-2.0.1+dfsg -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "${name%.*}"' \;
mkdir -p /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1
help2man --no-info --help-option="''" --no-discard-stderr --name='an accurate and efficient aligner for mapping both genomic \
DNA-seq reads and RNA-seq reads (for the purpose of expression analysis)' \
/build/subread-2.0.1+dfsg/bin/subread-align | debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/subread-align.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='builds an base-space or color-space index using the reference sequences' \
/build/subread-2.0.1+dfsg/bin/subread-buildindex | debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/subread-buildindex.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='an RNA-seq aligner suitable for all purposes of RNA-seq analyses' \
/build/subread-2.0.1+dfsg/bin/subjunc | debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/subjunc.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='a highly efficient and accurate read summarization program' \
/build/subread-2.0.1+dfsg/bin/featureCounts | debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/featureCounts.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='a SNP caller that discovers SNPs by testing signals against local background noises' \
/build/subread-2.0.1+dfsg/bin/exactSNP | debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/exactSNP.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='detect short and long indels' \
/build/subread-2.0.1+dfsg/bin/subindel | debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/subindel.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='long-read aligner that is designed based on seed-and-vote' \
/build/subread-2.0.1+dfsg/bin/sublong| debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/sublong.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='scans the entire genome and reports all matches of a specified sequence' \
/build/subread-2.0.1+dfsg/bin/utilities/subread-fullscan | debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/subread-fullscan.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='calculate the proportion of mapped reads/fragments' \
/build/subread-2.0.1+dfsg/bin/utilities/propmapped | debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/propmapped.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='retrieve Phred score for read bases' \
/build/subread-2.0.1+dfsg/bin/utilities/qualityScores| debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/qualityScores.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='Find reads that are from the same pair in the input and then place them next \
to each other in the output. A dummy read is added for each singleton read that does not have a pair. \
The output file is compatible with featureCounts program' \
/build/subread-2.0.1+dfsg/bin/utilities/repair| debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/repair.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='Remove duplicated reads' \
/build/subread-2.0.1+dfsg/bin/utilities/removeDup| debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/removeDup.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='Flatten features included in a GTF annotation and save the modified annotation \
to a SAF format file.' \
/build/subread-2.0.1+dfsg/bin/utilities/flattenGTF| debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/flattenGTF.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='helper tool from subread suite' \
/build/subread-2.0.1+dfsg/bin/utilities/genRandomReads| debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/genRandomReads.1;
dh_auto_install
install -d /build/subread-2.0.1\+dfsg/debian/tmp
make[1]: Leaving directory '/build/subread-2.0.1+dfsg'
dh_install
install -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 -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 -d debian/.debhelper/generated/subread
install -d debian/subread-data/usr/share/doc/subread/examples
cp --reflink=auto -a ./annotation debian/subread-data/usr/share/doc/subread/examples/
install -d debian/.debhelper/generated/subread-data
dh_installdocs
install -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 -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
install -p -m0644 debian/changelog debian/subread/usr/share/doc/subread/changelog.Debian
install -p -m0644 debian/changelog 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/subread-2.0.1+dfsg'
tar --sort=name \
--mtime="@1590168680" \
--owner=root --group=root --numeric-owner \
--mode=go=rX,u+rw,a-s \
-cJf /build/subread-2.0.1+dfsg/debian/subread-data/usr/share/doc/subread/examples/test.tar.xz test/
make[1]: Leaving directory '/build/subread-2.0.1+dfsg'
dh_installman
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 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/exactSNP.1 debian/subread/usr/share/man/man1/featureCounts.1 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 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/subread-buildindex.1 debian/subread/usr/share/man/man1/subread-fullscan.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/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
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/subindel.1 debian/subread/usr/share/man/man1/subjunc.1 debian/subread/usr/share/man/man1/sublong.1 debian/subread/usr/share/man/man1/subread-align.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
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/exactSNP.1 debian/subread/usr/share/man/man1/featureCounts.1 debian/subread/usr/share/man/man1/flattenGTF.1 debian/subread/usr/share/man/man1/genRandomReads.1
mv debian/subread/usr/share/man/man1/propmapped.1.dh-new debian/subread/usr/share/man/man1/propmapped.1
mv debian/subread/usr/share/man/man1/qualityScores.1.dh-new debian/subread/usr/share/man/man1/qualityScores.1
mv debian/subread/usr/share/man/man1/removeDup.1.dh-new debian/subread/usr/share/man/man1/removeDup.1
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/propmapped.1 debian/subread/usr/share/man/man1/qualityScores.1 debian/subread/usr/share/man/man1/removeDup.1 debian/subread/usr/share/man/man1/repair.1
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
cd debian/subread
cd debian/subread-data
chmod a-x usr/share/doc/subread/README.txt 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/README.txt 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
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
cd '/build/subread-2.0.1+dfsg'
cd '/build/subread-2.0.1+dfsg'
dh_fixperms
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/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/subread-data -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/subread -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/subread/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
find debian/subread/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
dh_missing
dh_dwz
install -d debian/subread/usr/lib/debug/.dwz/arm-linux-gnueabihf
dwz -mdebian/subread/usr/lib/debug/.dwz/arm-linux-gnueabihf/subread.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/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/arm-linux-gnueabihf/subread.debug
dh_strip
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/53
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/53/51fc03514bf41b92a401aa3e4d8c08b6a53bf1.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/53/51fc03514bf41b92a401aa3e4d8c08b6a53bf1.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/53/51fc03514bf41b92a401aa3e4d8c08b6a53bf1.debug debian/subread/usr/bin/subindel
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/48
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/48/ba35c6e12ce171c44695853e0487010b701680.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/48/ba35c6e12ce171c44695853e0487010b701680.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/48/ba35c6e12ce171c44695853e0487010b701680.debug debian/subread/usr/bin/sublong
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7f
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7f/bf9cee128428f7c85b01b033a1798fc5112fb1.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7f/bf9cee128428f7c85b01b033a1798fc5112fb1.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/7f/bf9cee128428f7c85b01b033a1798fc5112fb1.debug debian/subread/usr/bin/subread-align
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b5
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b5/eb278f0ac8e00780ba7a5f56588d19806ac5a4.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b5/eb278f0ac8e00780ba7a5f56588d19806ac5a4.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/b5/eb278f0ac8e00780ba7a5f56588d19806ac5a4.debug debian/subread/usr/bin/subjunc
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/29
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-buildindex debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/29/fbc97b1f78fdb74854633191743a1f9b18e4e0.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/29/fbc97b1f78fdb74854633191743a1f9b18e4e0.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/29/fbc97b1f78fdb74854633191743a1f9b18e4e0.debug debian/subread/usr/bin/subread-buildindex
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/83
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/83/eaa75bc78a65dd3282abf6a05f69f89bff83b9.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/83/eaa75bc78a65dd3282abf6a05f69f89bff83b9.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/83/eaa75bc78a65dd3282abf6a05f69f89bff83b9.debug debian/subread/usr/bin/exactSNP
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4f
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/featureCounts debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4f/23b2226eae1f4b04fb20a00fda8fb89e6f57fb.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4f/23b2226eae1f4b04fb20a00fda8fb89e6f57fb.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/4f/23b2226eae1f4b04fb20a00fda8fb89e6f57fb.debug debian/subread/usr/bin/featureCounts
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/8c
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/8c/a1b56178518b58d46a0d91b2255f03d04f8938.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/8c/a1b56178518b58d46a0d91b2255f03d04f8938.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/8c/a1b56178518b58d46a0d91b2255f03d04f8938.debug debian/subread/usr/lib/subread/qualityScores
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1e
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/subread-fullscan debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1e/80c448b7e8f1759ce076695b6a05c68466a755.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1e/80c448b7e8f1759ce076695b6a05c68466a755.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/1e/80c448b7e8f1759ce076695b6a05c68466a755.debug debian/subread/usr/lib/subread/subread-fullscan
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a7
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/txUnique debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a7/f05d47fcad89690a92804c371887b9c60e912f.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a7/f05d47fcad89690a92804c371887b9c60e912f.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/a7/f05d47fcad89690a92804c371887b9c60e912f.debug debian/subread/usr/lib/subread/txUnique
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/3a
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/genRandomReads debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/3a/ce17d877a824a303df52588e7972430bc87675.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/3a/ce17d877a824a303df52588e7972430bc87675.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/3a/ce17d877a824a303df52588e7972430bc87675.debug debian/subread/usr/lib/subread/genRandomReads
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9f
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/flattenGTF debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9f/9ddcbbc844dc29eb0e315343a331eefcda7dd4.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9f/9ddcbbc844dc29eb0e315343a331eefcda7dd4.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/9f/9ddcbbc844dc29eb0e315343a331eefcda7dd4.debug debian/subread/usr/lib/subread/flattenGTF
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/58
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/58/1482dffa2b83ba88434afac298df046b62b224.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/58/1482dffa2b83ba88434afac298df046b62b224.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/58/1482dffa2b83ba88434afac298df046b62b224.debug debian/subread/usr/lib/subread/propmapped
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2a
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2a/0a8962b5fe397ecdccb27fadd84fef0958dd50.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2a/0a8962b5fe397ecdccb27fadd84fef0958dd50.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/2a/0a8962b5fe397ecdccb27fadd84fef0958dd50.debug debian/subread/usr/lib/subread/removeDup
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/91
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/repair debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/91/1795a2ab6cf5513f3a73627ef63e5930a56f95.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/91/1795a2ab6cf5513f3a73627ef63e5930a56f95.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/91/1795a2ab6cf5513f3a73627ef63e5930a56f95.debug debian/subread/usr/lib/subread/repair
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.dwz
cp --reflink=auto -a debian/subread/usr/lib/debug/.dwz/arm-linux-gnueabihf 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 -d debian/.debhelper/subread/dbgsym-root/usr/share/doc
ln -s subread debian/.debhelper/subread/dbgsym-root/usr/share/doc/subread-dbgsym
dh_makeshlibs
rm -f debian/subread/DEBIAN/shlibs
rm -f debian/subread-data/DEBIAN/shlibs
dh_shlibdeps
install -d debian/subread/DEBIAN
dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/bin/subindel debian/subread/usr/bin/sublong debian/subread/usr/bin/subread-align debian/subread/usr/bin/subjunc debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/exactSNP debian/subread/usr/bin/featureCounts debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/txUnique debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/repair
dh_installdeb
install -d debian/subread-data/DEBIAN
dh_gencontrol
echo misc:Depends= >> debian/subread-data.substvars
echo misc:Pre-Depends= >> debian/subread-data.substvars
dpkg-gencontrol -psubread-data -ldebian/changelog -Tdebian/subread-data.substvars -Pdebian/subread-data
echo misc:Depends= >> debian/subread.substvars
echo misc:Pre-Depends= >> debian/subread.substvars
install -d debian/.debhelper/subread/dbgsym-root/DEBIAN
dpkg-gencontrol -psubread -ldebian/changelog -Tdebian/subread.substvars -Pdebian/.debhelper/subread/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=subread-dbgsym "-DDepends=subread (= \${binary:Version})" "-DDescription=debug symbols for subread" "-DBuild-Ids=1e80c448b7e8f1759ce076695b6a05c68466a755 29fbc97b1f78fdb74854633191743a1f9b18e4e0 2a0a8962b5fe397ecdccb27fadd84fef0958dd50 3ace17d877a824a303df52588e7972430bc87675 48ba35c6e12ce171c44695853e0487010b701680 4f23b2226eae1f4b04fb20a00fda8fb89e6f57fb 5351fc03514bf41b92a401aa3e4d8c08b6a53bf1 581482dffa2b83ba88434afac298df046b62b224 7fbf9cee128428f7c85b01b033a1798fc5112fb1 83eaa75bc78a65dd3282abf6a05f69f89bff83b9 8ca1b56178518b58d46a0d91b2255f03d04f8938 911795a2ab6cf5513f3a73627ef63e5930a56f95 9f9ddcbbc844dc29eb0e315343a331eefcda7dd4 a7f05d47fcad89690a92804c371887b9c60e912f b5eb278f0ac8e00780ba7a5f56588d19806ac5a4" -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 -Pdebian/subread
chmod 0644 -- debian/subread/DEBIAN/control
dh_md5sums
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
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
dpkg-deb --root-owner-group --build debian/subread ..
dpkg-deb: building package 'subread' in '../subread_2.0.1+dfsg-1_armhf.deb'.
dpkg-deb --root-owner-group --build debian/subread-data ..
dpkg-deb --root-owner-group --build debian/.debhelper/subread/dbgsym-root ..
dpkg-deb: building package 'subread-data' in '../subread-data_2.0.1+dfsg-1_all.deb'.
dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_2.0.1+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=binary
dpkg-genchanges --build=binary >../subread_2.0.1+dfsg-1_armhf.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: user script /srv/workspace/pbuilder/1957/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/1957/tmp/hooks/B01_cleanup finished
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/1957 and its subdirectories
I: Current time: Mon Aug 16 16:55:05 +14 2021
I: pbuilder-time-stamp: 1629082505