Mon May 22 03:04:47 UTC 2023 I: starting to build readseq/bookworm/i386 on jenkins on '2023-05-22 03:04'
Mon May 22 03:04:47 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_9/13848/console.log
Mon May 22 03:04:47 UTC 2023 I: Downloading source for bookworm/readseq=1-14
--2023-05-22 03:04:48-- http://cdn-fastly.deb.debian.org/debian/pool/main/r/readseq/readseq_1-14.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 1955 (1.9K) [text/prs.lines.tag]
Saving to: ‘readseq_1-14.dsc’
0K . 100% 131M=0s
2023-05-22 03:04:48 (131 MB/s) - ‘readseq_1-14.dsc’ saved [1955/1955]
Mon May 22 03:04:48 UTC 2023 I: readseq_1-14.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: readseq
Binary: readseq
Architecture: any
Version: 1-14
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: http://iubio.bio.indiana.edu/soft/molbio/readseq/
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/readseq
Vcs-Git: https://salsa.debian.org/med-team/readseq.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), ncbi-tools-dev
Package-List:
readseq deb science optional arch=any
Checksums-Sha1:
474839186eec28f650ac89a33829673fa40c3bbb 54557 readseq_1.orig.tar.gz
e196c0db4e7f82412ff21a63a063a94639351627 17508 readseq_1-14.debian.tar.xz
Checksums-Sha256:
b704d7a12c5d834390f3ed4233f1409c5f1ed53b0b9accf5ab632a513de1183c 54557 readseq_1.orig.tar.gz
a735d888ceff0b59afae28ca8053d8a4cfaba36fe9db8312cd4044cba2e20211 17508 readseq_1-14.debian.tar.xz
Files:
3973daff73375953369c31c5c1661699 54557 readseq_1.orig.tar.gz
921f561313637bd04ec500297b0ec3e4 17508 readseq_1-14.debian.tar.xz
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Mon May 22 03:04:48 UTC 2023 I: Checking whether the package is not for us
Mon May 22 03:04:48 UTC 2023 I: Starting 1st build on remote node ionos2-i386.debian.net.
Mon May 22 03:04:48 UTC 2023 I: Preparing to do remote build '1' on ionos2-i386.debian.net.
Mon May 22 03:05:50 UTC 2023 I: Deleting $TMPDIR on ionos2-i386.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sun May 21 15:04:52 -12 2023
I: pbuilder-time-stamp: 1684724692
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: using eatmydata during job
I: Copying source file
I: copying [readseq_1-14.dsc]
I: copying [./readseq_1.orig.tar.gz]
I: copying [./readseq_1-14.debian.tar.xz]
I: Extracting source
gpgv: Signature made Fri Oct 30 07:23:42 2020 -12
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./readseq_1-14.dsc: no acceptable signature found
dpkg-source: info: extracting readseq in readseq-1
dpkg-source: info: unpacking readseq_1.orig.tar.gz
dpkg-source: info: unpacking readseq_1-14.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 20-Formats.patch
dpkg-source: info: applying 20-Makefile.patch
dpkg-source: info: applying 30-arb-code-patches.patch
dpkg-source: info: applying 552830.patch
dpkg-source: info: applying gcc-4.6_format-security.patch
dpkg-source: info: applying enable_tests.patch
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying buffer_overflow.patch
dpkg-source: info: applying fix_tests.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/29071/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='i386'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8 '
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='i386'
IFS='
'
INVOCATION_ID='372458332e6a416ea77185c27f4707e9'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
LD_LIBRARY_PATH='/usr/lib/libeatmydata'
LD_PRELOAD='libeatmydata.so'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='29071'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.K4Sdvd9m/pbuilderrc_uK9H --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.K4Sdvd9m/b1 --logfile b1/build.log readseq_1-14.dsc'
SUDO_GID='112'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://78.137.99.97:3128'
I: uname -a
Linux ionos2-i386 5.10.0-23-686-pae #1 SMP Debian 5.10.179-1 (2023-05-12) i686 GNU/Linux
I: ls -l /bin
total 6036
-rwxr-xr-x 1 root root 1408088 Apr 23 09:24 bash
-rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2
-rwxr-xr-x 3 root root 38404 Sep 18 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep
-rwxr-xr-x 3 root root 38404 Sep 18 2022 bzip2
-rwxr-xr-x 1 root root 17892 Sep 18 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore
-rwxr-xr-x 1 root root 42920 Sep 20 2022 cat
-rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp
-rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod
-rwxr-xr-x 1 root root 79816 Sep 20 2022 chown
-rwxr-xr-x 1 root root 162024 Sep 20 2022 cp
-rwxr-xr-x 1 root root 136916 Jan 5 01:20 dash
-rwxr-xr-x 1 root root 137160 Sep 20 2022 date
-rwxr-xr-x 1 root root 100364 Sep 20 2022 dd
-rwxr-xr-x 1 root root 108940 Sep 20 2022 df
-rwxr-xr-x 1 root root 162152 Sep 20 2022 dir
-rwxr-xr-x 1 root root 87760 Mar 22 22:20 dmesg
lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname
-rwxr-xr-x 1 root root 38760 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep
-rwxr-xr-x 1 root root 34664 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep
-rwxr-xr-x 1 root root 84272 Mar 22 22:20 findmnt
-rwsr-xr-x 1 root root 30240 Mar 22 20:38 fusermount
-rwxr-xr-x 1 root root 218680 Jan 24 02:43 grep
-rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe
-rwxr-xr-x 1 root root 100952 Apr 9 2022 gzip
-rwxr-xr-x 1 root root 21916 Dec 19 01:33 hostname
-rwxr-xr-x 1 root root 75756 Sep 20 2022 ln
-rwxr-xr-x 1 root root 55600 Mar 22 23:43 login
-rwxr-xr-x 1 root root 162152 Sep 20 2022 ls
-rwxr-xr-x 1 root root 214568 Mar 22 22:20 lsblk
-rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir
-rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod
-rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp
-rwxr-xr-x 1 root root 63016 Mar 22 22:20 more
-rwsr-xr-x 1 root root 58912 Mar 22 22:20 mount
-rwxr-xr-x 1 root root 13856 Mar 22 22:20 mountpoint
-rwxr-xr-x 1 root root 157932 Sep 20 2022 mv
lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash
-rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink
-rwxr-xr-x 1 root root 75720 Sep 20 2022 rm
-rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir
-rwxr-xr-x 1 root root 22308 Nov 2 2022 run-parts
-rwxr-xr-x 1 root root 133224 Jan 5 07:55 sed
lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash
-rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep
-rwxr-xr-x 1 root root 87976 Sep 20 2022 stty
-rwsr-xr-x 1 root root 83492 Mar 22 22:20 su
-rwxr-xr-x 1 root root 38792 Sep 20 2022 sync
-rwxr-xr-x 1 root root 598456 Apr 6 02:25 tar
-rwxr-xr-x 1 root root 13860 Nov 2 2022 tempfile
-rwxr-xr-x 1 root root 120776 Sep 20 2022 touch
-rwxr-xr-x 1 root root 34664 Sep 20 2022 true
-rwxr-xr-x 1 root root 17892 Mar 22 20:38 ulockmgr_server
-rwsr-xr-x 1 root root 30236 Mar 22 22:20 umount
-rwxr-xr-x 1 root root 38760 Sep 20 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress
-rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir
-rwxr-xr-x 1 root root 71216 Mar 22 22:20 wdctl
lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 9 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 9 2022 znew
I: user script /srv/workspace/pbuilder/29071/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), ncbi-tools-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 ... 19604 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 debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on ncbi-tools-dev; however:
Package ncbi-tools-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} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libncbi6{a} libncbi6-dev{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} ncbi-data{a} po-debconf{a} sensible-utils{a}
The following packages are RECOMMENDED but will NOT be installed:
curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx ncbi-tools-bin wget
0 packages upgraded, 33 newly installed, 0 to remove and 0 not upgraded.
Need to get 32.6 MB of archives. After unpacking 135 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 2 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB]
Get: 3 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB]
Get: 4 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB]
Get: 5 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB]
Get: 6 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB]
Get: 7 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB]
Get: 8 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB]
Get: 9 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB]
Get: 10 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB]
Get: 11 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB]
Get: 12 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB]
Get: 13 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB]
Get: 16 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 17 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB]
Get: 18 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B]
Get: 21 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 22 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 23 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB]
Get: 24 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB]
Get: 25 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB]
Get: 26 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.2 [720 kB]
Get: 27 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB]
Get: 28 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB]
Get: 31 http://deb.debian.org/debian bookworm/main i386 ncbi-data all 6.1.20170106+dfsg1-10 [3557 kB]
Get: 32 http://deb.debian.org/debian bookworm/main i386 libncbi6 i386 6.1.20170106+dfsg1-10 [4219 kB]
Get: 33 http://deb.debian.org/debian bookworm/main i386 libncbi6-dev i386 6.1.20170106+dfsg1-10 [5823 kB]
Fetched 32.6 MB in 1s (44.7 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sensible-utils.
(Reading database ...
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19604 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ...
Unpacking sensible-utils (0.0.17+nmu1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_i386.deb ...
Unpacking libmagic-mgc (1:5.44-3) ...
Selecting previously unselected package libmagic1:i386.
Preparing to unpack .../02-libmagic1_1%3a5.44-3_i386.deb ...
Unpacking libmagic1:i386 (1:5.44-3) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.44-3_i386.deb ...
Unpacking file (1:5.44-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.21-12_i386.deb ...
Unpacking gettext-base (0.21-12) ...
Selecting previously unselected package libuchardet0:i386.
Preparing to unpack .../05-libuchardet0_0.0.7-1_i386.deb ...
Unpacking libuchardet0:i386 (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.22.4-10_i386.deb ...
Unpacking groff-base (1.22.4-10) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_i386.deb ...
Unpacking bsdextrautils (2.38.1-5+b1) ...
Selecting previously unselected package libpipeline1:i386.
Preparing to unpack .../08-libpipeline1_1.5.7-1_i386.deb ...
Unpacking libpipeline1:i386 (1.5.7-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../09-man-db_2.11.2-2_i386.deb ...
Unpacking man-db (2.11.2-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.19-3_i386.deb ...
Unpacking m4 (1.4.19-3) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../11-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../14-autopoint_0.21-12_all.deb ...
Unpacking autopoint (0.21-12) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ...
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I: Building the package
I: Running cd /build/readseq-1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../readseq_1-14_source.changes
dpkg-buildpackage: info: source package readseq
dpkg-buildpackage: info: source version 1-14
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
debian/rules clean
dh clean
dh_auto_clean
make -j8 clean
make[1]: Entering directory '/build/readseq-1'
rm -f *.o core test.* readseq
make[1]: Leaving directory '/build/readseq-1'
debian/rules override_dh_clean
make[1]: Entering directory '/build/readseq-1'
dh_clean
rm -f readseq
make[1]: Leaving directory '/build/readseq-1'
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
dh_auto_build
make -j8 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/readseq-1'
Compiling readseq with NCBI toolkit support and ARB patches
gcc -o readseq -I/usr/include/ncbi -g -O2 -ffile-prefix-map=/build/readseq-1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -DNCBI -I/usr/include/ncbi -DARB readseq.c ureadseq.c ureadasn.c -lncbi -lncbiobj -lncbicdr -lncbiacc -lncbitool -lncbimmdb -lncbiid1 -lnetcli -lm -Wl,-z,relro -Wl,-z,now
readseq.c: In function 'formatstr':
readseq.c:267:41: warning: return discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers]
267 | case kASNseqset : return formats[kASN1-1];
| ~~~~~~~^~~~~~~~~
readseq.c:269:45: warning: return discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers]
269 | case kPhylipSequential: return formats[kPhylip-1];
| ~~~~~~~^~~~~~~~~~~
readseq.c:273:22: warning: return discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers]
273 | else return formats[format-1];
| ~~~~~~~^~~~~~~~~~
readseq.c: In function 'Nlm_Main':
readseq.c:801:5: warning: implicit declaration of function 'gets'; did you mean 'fgets'? [-Wimplicit-function-declaration]
801 | gets(oname= onamestore);
| ^~~~
| fgets
readseq.c:936:33: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
936 | sprintf( stemp,"%s_%d", oname, whichSeq);
| ~^ ~~~~~~~~
| | |
| int long int
| %ld
readseq.c:938:48: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
938 | fprintf( stderr,"Writing sequence %d to file %s\n", whichSeq, stemp);
| ~^ ~~~~~~~~
| | |
| int long int
| %ld
readseq.c:980:39: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
980 | fprintf( stderr, "Sequence %d, length= %d, checksum= %X, format= %s, id= %s\n",
| ~^
| |
| int
| %ld
981 | whichSeq, seqlen, checksum, formatstr(format), seqidptr);
| ~~~~~~~~
| |
| long int
readseq.c:980:51: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
980 | fprintf( stderr, "Sequence %d, length= %d, checksum= %X, format= %s, id= %s\n",
| ~^
| |
| int
| %ld
981 | whichSeq, seqlen, checksum, formatstr(format), seqidptr);
| ~~~~~~
| |
| long int
readseq.c:980:65: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=]
980 | fprintf( stderr, "Sequence %d, length= %d, checksum= %X, format= %s, id= %s\n",
| ~^
| |
| unsigned int
| %lX
981 | whichSeq, seqlen, checksum, formatstr(format), seqidptr);
| ~~~~~~~~
| |
| long unsigned int
readseq.c:998:53: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
998 | if (phylvers >= 4) fprintf(foo," %d %d\n", i, seqlen);
| ~^ ~
| | |
| int long int
| %ld
readseq.c:998:56: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
998 | if (phylvers >= 4) fprintf(foo," %d %d\n", i, seqlen);
| ~^ ~~~~~~
| | |
| int long int
| %ld
readseq.c:999:39: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
999 | else fprintf(foo," %d %d YF\n", i, seqlen);
| ~^ ~
| | |
| int long int
| %ld
readseq.c:999:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
999 | else fprintf(foo," %d %d YF\n", i, seqlen);
| ~^ ~~~~~~
| | |
| int long int
| %ld
readseq.c:1117:31: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1117 | fprintf(foo,"\n %s MSF: %d Type: N %s Check: %d ..\n\n", /* GSt + RL */
| ~^
| |
| int
| %ld
1118 | cp, seqlen, timestr, checkall);
| ~~~~~~
| |
| long int
readseq.c:1117:55: warning: format '%d' expects argument of type 'int', but argument 6 has type 'long unsigned int' [-Wformat=]
1117 | fprintf(foo,"\n %s MSF: %d Type: N %s Check: %d ..\n\n", /* GSt + RL */
| ~^
| |
| int
| %ld
1118 | cp, seqlen, timestr, checkall);
| ~~~~~~~~
| |
| long unsigned int
readseq.c:1133:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1133 | if (phylvers >= 4) fprintf(foo," %d %d\n", seqout, seqlen);
| ~^ ~~~~~~
| | |
| int long int
| %ld
readseq.c:1134:28: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1134 | else fprintf(foo," %d %d YF\n", seqout, seqlen);
| ~^ ~~~~~~
| | |
| int long int
| %ld
readseq.c:1158:49: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1158 | fprintf(foo," dimensions ntax=%d nchar=%d;\n", seqout, seqlen);
| ~^ ~~~~~~
| | |
| int long int
| %ld
ureadseq.c: In function 'seqFileFormatFp':
ureadseq.c:1535:19: warning: format '%d' expects argument of type 'int *', but argument 3 has type 'long int *' [-Wformat=]
1535 | sscanf( sp, "%d%d", &nspp, &nlen);
| ~^ ~~~~~
| | |
| int * long int *
| %ld
ureadseq.c:1535:21: warning: format '%d' expects argument of type 'int *', but argument 4 has type 'long int *' [-Wformat=]
1535 | sscanf( sp, "%d%d", &nspp, &nlen);
| ~^ ~~~~~
| | |
| int * long int *
| %ld
ureadseq.c: In function 'writeSeq':
ureadseq.c:1784:22: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
1784 | sprintf(numform, "%d", seqlen);
| ~^ ~~~~~~
| | |
| int long int
| %ld
ureadseq.c:1813:43: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1813 | fprintf(outf,"LOCUS %s %d bp\n", idword, seqlen);
| ~^ ~~~~~~
| | |
| int long int
| %ld
ureadseq.c:1814:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1814 | fprintf(outf,"DEFINITION %s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
| ~^ ~~~~~~
| | |
| int long int
| %ld
ureadseq.c:1814:48: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=]
1814 | fprintf(outf,"DEFINITION %s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
| ~^ ~~~~~~~~
| | |
| unsigned int long unsigned int
| %lX
ureadseq.c:1828:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1828 | fprintf(outf,"TITLE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
| ~^ ~~~~~~
| | |
| int long int
| %ld
ureadseq.c:1828:52: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=]
1828 | fprintf(outf,"TITLE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
| ~^ ~~~~~~~~
| | |
| unsigned int long unsigned int
| %lX
ureadseq.c:1838:53: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
1838 | for (j= 5; j<=width; j += 5) fprintf(outf,"%10d",j);
| ~~~^ ~
| | |
| | long int
| int
| %10ld
ureadseq.c:1848:26: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1848 | fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
| ~^ ~~~~~~
| | |
| int long int
| %ld
ureadseq.c:1848:36: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=]
1848 | fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
| ~^ ~~~~~~~~
| | |
| unsigned int long unsigned int
| %lX
ureadseq.c:1857:31: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1857 | fprintf(outf,"DE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
| ~^ ~~~~~~
| | |
| int long int
| %ld
ureadseq.c:1857:41: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=]
1857 | fprintf(outf,"DE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
| ~^ ~~~~~~~~
| | |
| unsigned int long unsigned int
| %lX
ureadseq.c:1858:37: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
1858 | fprintf(outf,"SQ %d BP\n", seqlen);
| ~^ ~~~~~~
| | |
| int long int
| %ld
ureadseq.c:1869:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1869 | fprintf(outf," %s Length: %d (today) Check: %d ..\n", idword, seqlen, checksum);
| ~^ ~~~~~~
| | |
| int long int
| %ld
ureadseq.c:1869:58: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long unsigned int' [-Wformat=]
1869 | fprintf(outf," %s Length: %d (today) Check: %d ..\n", idword, seqlen, checksum);
| ~^ ~~~~~~~~
| | |
| int long unsigned int
| %ld
ureadseq.c:1878:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1878 | fprintf(outf,"; DNA sequence %s, %d bases, %X checksum.\n;\n", seqname, seqlen, checksum);
| ~^ ~~~~~~
| | |
| int long int
| %ld
ureadseq.c:1878:52: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=]
1878 | fprintf(outf,"; DNA sequence %s, %d bases, %X checksum.\n;\n", seqname, seqlen, checksum);
| ~^ ~~~~~~~~
| | |
| unsigned int long unsigned int
| %lX
ureadseq.c:1884:26: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1884 | fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
| ~^ ~~~~~~
| | |
| int long int
| %ld
ureadseq.c:1884:36: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=]
1884 | fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
| ~^ ~~~~~~~~
| | |
| unsigned int long unsigned int
| %lX
ureadseq.c:1915:53: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1915 | fprintf(outf," repr raw, mol %s, length %d, topology linear,\n", cp, seqlen);
| ~^ ~~~~~~
| | |
| int long int
| %ld
ureadseq.c:1937:41: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1937 | fprintf(outf,"[Name: %-16s Len:%6d Check: %8X]\n", idword, seqlen, checksum);
| ~~^ ~~~~~~
| | |
| int long int
| %6ld
ureadseq.c:1937:53: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=]
1937 | fprintf(outf,"[Name: %-16s Len:%6d Check: %8X]\n", idword, seqlen, checksum);
| ~~^ ~~~~~~~~
| | |
| unsigned int long unsigned int
| %8lX
ureadseq.c:1954:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1954 | fprintf(outf,"Name: %-16s Len:%6d Check: %8X\n", idword, seqlen, checksum);
| ~~^ ~~~~~~
| | |
| int long int
| %6ld
ureadseq.c:1954:54: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=]
1954 | fprintf(outf,"Name: %-16s Len:%6d Check: %8X\n", idword, seqlen, checksum);
| ~~^ ~~~~~~~~
| | |
| unsigned int long unsigned int
| %8lX
ureadseq.c:1960:40: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1960 | fprintf(outf," Name: %-16s Len:%6d Check: %5d Weight: 1.00\n",
| ~~^
| |
| int
| %6ld
1961 | idword, seqlen, checksum);
| ~~~~~~
| |
| long int
ureadseq.c:1960:52: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long unsigned int' [-Wformat=]
1960 | fprintf(outf," Name: %-16s Len:%6d Check: %5d Weight: 1.00\n",
| ~~^
| |
| int
| %5ld
1961 | idword, seqlen, checksum);
| ~~~~~~~~
| |
| long unsigned int
ureadseq.c:1972:27: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1972 | fprintf(outf,";%s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
| ~^ ~~~~~~
| | |
| int long int
| %ld
ureadseq.c:1972:37: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=]
1972 | fprintf(outf,";%s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
| ~^ ~~~~~~~~
| | |
| unsigned int long unsigned int
| %lX
ureadseq.c:1979:25: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
1979 | fprintf(outf,"%4d %-60s\n",seqlen,seqname);
| ~~^ ~~~~~~
| | |
| int long int
| %4ld
ureadseq.c:2002:27: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
2002 | fprintf(outf,">%s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
| ~^ ~~~~~~
| | |
| int long int
| %ld
ureadseq.c:2002:37: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=]
2002 | fprintf(outf,">%s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
| ~^ ~~~~~~~~
| | |
| unsigned int long unsigned int
| %lX
ureadseq.c:2043:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
2043 | if (numline==1) fprintf(outf,"%-9d ",i+1);
| ~~~^ ~~~
| | |
| int long int
| %-9ld
ureadseq.c: In function 'readPAUPinterleaved':
ureadseq.c:213:22: warning: '%s' directive writing up to 255 bytes into a region of size between 246 and 251 [-Wformat-overflow=]
213 | sprintf(si, " %d) %s\n", V->nseq, s);
| ^~
In function 'addinfo',
inlined from 'readPAUPinterleaved' at ureadseq.c:813:13:
ureadseq.c:213:3: note: 'sprintf' output between 7 and 267 bytes into a destination of size 256
213 | sprintf(si, " %d) %s\n", V->nseq, s);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ureadseq.c: In function 'writeSeq':
ureadseq.c:2007:45: warning: '%d' directive writing between 1 and 6 bytes into a region of size between 2 and 7 [-Wformat-overflow=]
2007 | if (*nameform==0) sprintf(nameform, "%%%d.%ds ",namewidth,namewidth);
| ^~
ureadseq.c:2007:39: note: directive argument in the range [-32768, 32767]
2007 | if (*nameform==0) sprintf(nameform, "%%%d.%ds ",namewidth,namewidth);
| ^~~~~~~~~~~
ureadseq.c:2007:21: note: 'sprintf' output between 7 and 17 bytes into a destination of size 10
2007 | if (*nameform==0) sprintf(nameform, "%%%d.%ds ",namewidth,namewidth);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ureadasn.c: In function 'listASNSeqs':
ureadasn.c:189:24: warning: passing argument 1 of 'AsnIoOpen' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers]
189 | if ((aip = AsnIoOpen(filename, inIsBinary?"rb":"r")) == NULL) goto errxit;
| ^~~~~~~~
In file included from /usr/include/ncbi/ncbi.h:57,
from ureadasn.c:13:
/usr/include/ncbi/asn.h:384:54: note: expected 'Nlm_CharPtr' {aka 'char *'} but argument is of type 'const char *'
384 | NLM_EXTERN AsnIoPtr LIBCALL AsnIoOpen PROTO((CharPtr file_name, CharPtr mode));
/usr/include/ncbi/ncbilcl.h:192:18: note: in definition of macro 'PROTO'
192 | #define PROTO(x) x /* Prototypes are acceptable */
| ^
ureadasn.c: In function 'readASNSeq':
ureadasn.c:261:24: warning: passing argument 1 of 'AsnIoOpen' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers]
261 | if ((aip = AsnIoOpen(filename, inIsBinary?"rb":"r")) == NULL) goto errxit;
| ^~~~~~~~
/usr/include/ncbi/asn.h:384:54: note: expected 'Nlm_CharPtr' {aka 'char *'} but argument is of type 'const char *'
384 | NLM_EXTERN AsnIoPtr LIBCALL AsnIoOpen PROTO((CharPtr file_name, CharPtr mode));
/usr/include/ncbi/ncbilcl.h:192:18: note: in definition of macro 'PROTO'
192 | #define PROTO(x) x /* Prototypes are acceptable */
| ^
ureadasn.c:262:31: warning: 'fgets' writing 255 bytes into a region of size 200 overflows the destination [-Wstringop-overflow=]
262 | for (i=0; i<skiplines; i++) fgets( stemp, 255, aip->fp); /* this may mess up asn routines... */
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
ureadasn.c:241:15: note: destination object 'stemp' of size 200
241 | char *seq, stemp[200];
| ^~~~~
In file included from ureadasn.c:8:
/usr/include/stdio.h:592:14: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)'
592 | extern char *fgets (char *__restrict __s, int __n, FILE *__restrict __stream)
| ^~~~~
ureadasn.c:262:31: warning: 'fgets' writing 255 bytes into a region of size 200 overflows the destination [-Wstringop-overflow=]
262 | for (i=0; i<skiplines; i++) fgets( stemp, 255, aip->fp); /* this may mess up asn routines... */
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
ureadasn.c:241:15: note: destination object 'stemp' of size 200
241 | char *seq, stemp[200];
| ^~~~~
/usr/include/stdio.h:592:14: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)'
592 | extern char *fgets (char *__restrict __s, int __n, FILE *__restrict __stream)
| ^~~~~
ureadasn.c:262:31: warning: 'fgets' writing 255 bytes into a region of size 200 overflows the destination [-Wstringop-overflow=]
262 | for (i=0; i<skiplines; i++) fgets( stemp, 255, aip->fp); /* this may mess up asn routines... */
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
ureadasn.c:241:15: note: destination object 'stemp' of size 200
241 | char *seq, stemp[200];
| ^~~~~
/usr/include/stdio.h:592:14: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)'
592 | extern char *fgets (char *__restrict __s, int __n, FILE *__restrict __stream)
| ^~~~~
/usr/bin/ld: /tmp/cc2F5ls0.o: in function `Nlm_Main':
././readseq.c:783: warning: the use of `tmpnam' is dangerous, better use `mkstemp'
/usr/bin/ld: ././readseq.c:801: warning: the `gets' function is dangerous and should not be used.
make[1]: Leaving directory '/build/readseq-1'
dh_auto_test
make -j8 test
make[1]: Entering directory '/build/readseq-1'
Test for general read/write of all chars:
./readseq -p alphabet.std -otest.alpha
diff test.alpha alphabet.std
Test for valid format conversions:
./readseq -v -p -f=ig nucleic.std -otest.ig
Sequence 1, length= 228, checksum= 1B5655D0, format= 20. Vienna, id= nucleic/amino test
./readseq -v -p -f=gb test.ig -otest.gb
Sequence 1, length= 228, checksum= 1B5655D0, format= 1. IG/Stanford, id= nucleic/amino
./readseq -v -p -f=nbrf test.gb -otest.nbrf
Sequence 1, length= 228, checksum= 1B5655D0, format= 2. GenBank/GB, id= nucleic/amino 228 bp
./readseq -v -p -f=embl test.nbrf -otest.embl
Sequence 1, length= 228, checksum= 1B5655D0, format= 3. NBRF, id= nucleic/amino
./readseq -v -p -f=gcg test.embl -otest.gcg
Sequence 1, length= 228, checksum= 1B5655D0, format= 4. EMBL, id= nucleic/amino
./readseq -v -p -f=strider test.gcg -otest.strider
Sequence 1, length= 228, checksum= 1B5655D0, format= 5. GCG, id= nucleic/amino
./readseq -v -p -f=fitch test.strider -otest.fitch
Sequence 1, length= 228, checksum= 1B5655D0, format= 6. DNAStrider, id= nucleic/amino, 228 bases, 1B5655D0 checksum.
./readseq -v -p -f=fasta test.fitch -otest.fasta
Sequence 1, length= 228, checksum= 1B5655D0, format= 7. Fitch, id= nucleic/amino, 228 bases, 1B5655D0 checksum.
./readseq -v -p -f=pir test.fasta -otest.pir
Sequence 1, length= 228, checksum= 1B5655D0, format= 8. Pearson/Fasta, id= nucleic/amino, 228 bases, 1B5655D0 checksum.
./readseq -v -p -f=ig test.pir -otest.ig-b
Sequence 1, length= 228, checksum= 1B5655D0, format= 14. PIR/CODATA, id= nucleic/amino,
diff test.ig test.ig-b
1,2c1,2
< ;nucleic/amino test, 228 bases, 1B5655D0 checksum.
< nucleic/amino
---
> ;nucleic/amino, , 228 bases, 1B5655D0 checksum.
> nucleic/amino,
make[1]: [Makefile:70: test] Error 1 (ignored)
Test for multiple-sequence format conversions:
./readseq -p -f=ig multi.std -otest.m-ig
./readseq -p -f=gb test.m-ig -otest.m-gb
./readseq -p -f=nbrf test.m-gb -otest.m-nbrf
./readseq -p -f=embl test.m-nbrf -otest.m-embl
./readseq -p -f=fasta test.m-embl -otest.m-fasta
./readseq -p -f=pir test.m-fasta -otest.m-pir
./readseq -p -f=msf test.m-pir -otest.m-msf
./readseq -p -f=paup test.m-msf -otest.m-paup
./readseq -p -f=ig test.m-paup -otest.m-ig-b
diff test.m-ig test.m-ig-b
1,2c1,2
< ;acarr58sst , 183 bases, 64754A4D checksum.
< acarr58sst
---
> ;acarr58ss, 183 bases, 64754A4D checksum.
> acarr58ss
7c7
< ;amgrrbst , 183 bases, C886D2FB checksum.
---
> ;amgrrbst, 183 bases, C886D2FB checksum.
13c13
< ;bmorrbst , 183 bases, 3E9C23D6 checksum.
---
> ;bmorrbst, 183 bases, 3E9C23D6 checksum.
19c19
< ;crerrbst , 183 bases, AC88A337 checksum.
---
> ;crerrbst, 183 bases, AC88A337 checksum.
25,26c25,26
< ;ddirr58sst , 183 bases, 1E3D23B8 checksum.
< ddirr58sst
---
> ;ddirr58ss, 183 bases, 1E3D23B8 checksum.
> ddirr58ss
make[1]: [Makefile:82: test] Error 1 (ignored)
Expect differences in the header lines due to
different format headers. If any sequence lines
differ, or if the checksums differ, there is a problem.
----------------------
To clean up test files, command me:
make clean
make[1]: Leaving directory '/build/readseq-1'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_installdirs
dh_auto_install --destdir=debian/readseq/
make -j8 install DESTDIR=/build/readseq-1/debian/readseq AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/readseq-1'
install readseq /build/readseq-1/debian/readseq/usr/bin
install *.std /build/readseq-1/debian/readseq/usr/share/doc/readseq/tests
install Makefile /build/readseq-1/debian/readseq/usr/share/doc/readseq/tests
make[1]: Leaving directory '/build/readseq-1'
dh_install
dh_installdocs
dh_installchangelogs
dh_installman
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'readseq' in '../readseq_1-14_i386.deb'.
dpkg-deb: building package 'readseq-dbgsym' in '../readseq-dbgsym_1-14_i386.deb'.
dpkg-genbuildinfo --build=binary -O../readseq_1-14_i386.buildinfo
dpkg-genchanges --build=binary -O../readseq_1-14_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/29071 and its subdirectories
I: Current time: Sun May 21 15:05:50 -12 2023
I: pbuilder-time-stamp: 1684724750
Mon May 22 03:05:50 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos6-i386.debian.net.
Mon May 22 03:05:50 UTC 2023 I: Preparing to do remote build '2' on ionos6-i386.debian.net.
Mon May 22 03:06:14 UTC 2023 I: Deleting $TMPDIR on ionos6-i386.debian.net.
Mon May 22 03:06:14 UTC 2023 I: readseq_1-14_i386.changes:
Format: 1.8
Date: Fri, 30 Oct 2020 20:20:15 +0100
Source: readseq
Binary: readseq readseq-dbgsym
Architecture: i386
Version: 1-14
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
readseq - Conversion between sequence formats
Changes:
readseq (1-14) unstable; urgency=medium
.
* Standards-Version: 4.5.0 (routine-update)
* debhelper-compat 13 (routine-update)
* Remove trailing whitespace in debian/changelog (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* Trim trailing whitespace.
* Refer to specific version of license GPL-2+.
Checksums-Sha1:
bb9cb462237905d7f8ef98cee2f759bbfc2fcad7 59392 readseq-dbgsym_1-14_i386.deb
730d9c491fcc8c7eae82eca0973ded5da9759522 5333 readseq_1-14_i386.buildinfo
7074132880565cb88b7bbb98ffa85f6c623fa74c 57080 readseq_1-14_i386.deb
Checksums-Sha256:
102cd5dbf9a3503e489ef02d9ce772215d9da0a79596c811f0bea9a68172938d 59392 readseq-dbgsym_1-14_i386.deb
539395b865925ecc06bddc195c56745301dc859f538b221ee06ab2b6284814f4 5333 readseq_1-14_i386.buildinfo
c782a7f7114fb8e2578d055582f386597efffd357b5b0415575ac5a783cf4c14 57080 readseq_1-14_i386.deb
Files:
a2c4b394573bd58ddb2b703a0206ed86 59392 debug optional readseq-dbgsym_1-14_i386.deb
19e3339f6a0cdc5e20daa43fd27fa3b4 5333 science optional readseq_1-14_i386.buildinfo
4a546eda8fbc1824d5901671e3ef2b03 57080 science optional readseq_1-14_i386.deb
Mon May 22 03:06:15 UTC 2023 I: diffoscope 242 will be used to compare the two builds:
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.K4Sdvd9m/readseq_1-14.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.K4Sdvd9m/readseq_1-14.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.K4Sdvd9m/readseq_1-14.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.K4Sdvd9m/b1/readseq_1-14_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.K4Sdvd9m/b2/readseq_1-14_i386.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call abc.DotChangesFile
## main (total time: 0.347s)
0.347s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.017s)
0.017s 12 calls diffoscope.comparators.binary.FilesystemFile
0.000s 10 calls abc.DotChangesFile
## specialize (total time: 0.000s)
0.000s 1 call specialize
Mon May 22 03:06:16 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists.
Mon May 22 03:06:16 UTC 2023 I: readseq from bookworm built successfully and reproducibly on i386.
Mon May 22 03:06:18 UTC 2023 I: Submitting .buildinfo files to external archives:
Mon May 22 03:06:18 UTC 2023 I: Submitting 8.0K b1/readseq_1-14_i386.buildinfo.asc
Mon May 22 03:06:18 UTC 2023 I: Submitting 8.0K b2/readseq_1-14_i386.buildinfo.asc
Mon May 22 03:06:19 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Mon May 22 03:06:19 UTC 2023 I: Done submitting .buildinfo files.
Mon May 22 03:06:19 UTC 2023 I: Removing signed readseq_1-14_i386.buildinfo.asc files:
removed './b1/readseq_1-14_i386.buildinfo.asc'
removed './b2/readseq_1-14_i386.buildinfo.asc'