Sun Jul 25 12:10:27 UTC 2021 I: starting to build stacks/bullseye/arm64 on jenkins on '2021-07-25 12:10'
Sun Jul 25 12:10:27 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_8/25243/console.log
Sun Jul 25 12:10:27 UTC 2021 I: Downloading source for bullseye/stacks=2.55+dfsg-1
--2021-07-25 12:10:28-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/stacks/stacks_2.55+dfsg-1.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2044 (2.0K)
Saving to: ‘stacks_2.55+dfsg-1.dsc’
0K . 100% 303M=0s
2021-07-25 12:10:28 (303 MB/s) - ‘stacks_2.55+dfsg-1.dsc’ saved [2044/2044]
Sun Jul 25 12:10:28 UTC 2021 I: stacks_2.55+dfsg-1.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: stacks
Binary: stacks
Architecture: any
Version: 2.55+dfsg-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Tim Booth <tbooth@ceh.ac.uk>, Andreas Tille <tille@debian.org>
Homepage: https://creskolab.uoregon.edu/stacks/
Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/stacks
Vcs-Git: https://salsa.debian.org/med-team/stacks.git
Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbam-dev, libsparsehash-dev, samtools, libhts-dev
Package-List:
stacks deb science optional arch=any
Checksums-Sha1:
b524951318872462d5280b93181c625602da55c0 321808 stacks_2.55+dfsg.orig.tar.xz
ecb80cedb021e10b33ea6fcc45b25780fb6fce8e 7540 stacks_2.55+dfsg-1.debian.tar.xz
Checksums-Sha256:
4143458fdf55874bfcd0273fb8d4c8f54fcf57c6b27ac56f907296fc4e5878cf 321808 stacks_2.55+dfsg.orig.tar.xz
dbf29f8698859be6556aa6d6a33020f9871464af671a7cfd8383db30e04da2b0 7540 stacks_2.55+dfsg-1.debian.tar.xz
Files:
becc7b543cb6d25407b164a010819cac 321808 stacks_2.55+dfsg.orig.tar.xz
2a2be29dfd0b8a45d91e2b115d2de149 7540 stacks_2.55+dfsg-1.debian.tar.xz
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Sun Jul 25 12:10:28 UTC 2021 I: Checking whether the package is not for us
Sun Jul 25 12:10:28 UTC 2021 I: Starting 1st build on remote node codethink10-arm64.debian.net.
Sun Jul 25 12:10:28 UTC 2021 I: Preparing to do remote build '1' on codethink10-arm64.debian.net.
Sun Jul 25 12:26:15 UTC 2021 I: Deleting $TMPDIR on codethink10-arm64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sun Jul 25 00:10:32 -12 2021
I: pbuilder-time-stamp: 1627215032
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 [stacks_2.55+dfsg-1.dsc]
I: copying [./stacks_2.55+dfsg.orig.tar.xz]
I: copying [./stacks_2.55+dfsg-1.debian.tar.xz]
I: Extracting source
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.bpmueB6r/trustedkeys.kbx': General error
gpgv: Signature made Sun Jan 10 05:10:16 2021 -12
gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv: issuer "npatra974@gmail.com"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./stacks_2.55+dfsg-1.dsc
dpkg-source: info: extracting stacks in stacks-2.55+dfsg
dpkg-source: info: unpacking stacks_2.55+dfsg.orig.tar.xz
dpkg-source: info: unpacking stacks_2.55+dfsg-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying RisR.patch
dpkg-source: info: applying script-exe-paths
dpkg-source: info: applying use_debian_packaged_htslib.patch
dpkg-source: info: applying 2to3.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/9579/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='arm64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8'
DISTRIBUTION=''
HOME='/var/lib/jenkins'
HOST_ARCH='arm64'
IFS='
'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='9579'
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/tmp.I0eJxwKu15/pbuilderrc_qo8c --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.I0eJxwKu15/b1 --logfile b1/build.log stacks_2.55+dfsg-1.dsc'
SUDO_GID='117'
SUDO_UID='110'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
USERNAME='root'
_='/usr/bin/systemd-run'
http_proxy='http://192.168.101.16:3128'
I: uname -a
Linux codethink10-arm64 4.15.0-151-generic #157-Ubuntu SMP Fri Jul 9 21:03:48 UTC 2021 aarch64 GNU/Linux
I: ls -l /bin
total 5252
-rwxr-xr-x 1 root root 1282512 Jun 21 14:26 bash
-rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2
-rwxr-xr-x 3 root root 34808 Jul 20 2020 bzcat
lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff
lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe
lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep
-rwxr-xr-x 3 root root 34808 Jul 20 2020 bzip2
-rwxr-xr-x 1 root root 14264 Jul 20 2020 bzip2recover
lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore
-rwxr-xr-x 1 root root 39832 Sep 22 2020 cat
-rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp
-rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod
-rwxr-xr-x 1 root root 64528 Sep 22 2020 chown
-rwxr-xr-x 1 root root 138896 Sep 22 2020 cp
-rwxr-xr-x 1 root root 129544 Dec 10 2020 dash
-rwxr-xr-x 1 root root 101384 Sep 22 2020 date
-rwxr-xr-x 1 root root 80984 Sep 22 2020 dd
-rwxr-xr-x 1 root root 89824 Sep 22 2020 df
-rwxr-xr-x 1 root root 143088 Sep 22 2020 dir
-rwxr-xr-x 1 root root 76152 Feb 7 02:38 dmesg
lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname
-rwxr-xr-x 1 root root 35632 Sep 22 2020 echo
-rwxr-xr-x 1 root root 28 Nov 9 2020 egrep
-rwxr-xr-x 1 root root 31512 Sep 22 2020 false
-rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep
-rwxr-xr-x 1 root root 64856 Feb 7 02:38 findmnt
-rwsr-xr-x 1 root root 34824 Feb 26 04:12 fusermount
-rwxr-xr-x 1 root root 178400 Nov 9 2020 grep
-rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip
-rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe
-rwxr-xr-x 1 root root 93744 Mar 2 11:30 gzip
-rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname
-rwxr-xr-x 1 root root 68720 Sep 22 2020 ln
-rwxr-xr-x 1 root root 52720 Feb 7 2020 login
-rwxr-xr-x 1 root root 143088 Sep 22 2020 ls
-rwxr-xr-x 1 root root 161960 Feb 7 02:38 lsblk
-rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir
-rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod
-rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp
-rwxr-xr-x 1 root root 51368 Feb 7 02:38 more
-rwsr-xr-x 1 root root 51360 Feb 7 02:38 mount
-rwxr-xr-x 1 root root 14496 Feb 7 02:38 mountpoint
-rwxr-xr-x 1 root root 134808 Sep 22 2020 mv
lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd
lrwxrwxrwx 1 root root 4 Jun 21 14:26 rbash -> bash
-rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink
-rwxr-xr-x 1 root root 68592 Sep 22 2020 rm
-rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir
-rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts
-rwxr-xr-x 1 root root 114016 Dec 22 2018 sed
lrwxrwxrwx 1 root root 4 Jul 24 21:26 sh -> dash
-rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep
-rwxr-xr-x 1 root root 72640 Sep 22 2020 stty
-rwsr-xr-x 1 root root 67776 Feb 7 02:38 su
-rwxr-xr-x 1 root root 35672 Sep 22 2020 sync
-rwxr-xr-x 1 root root 535768 Feb 16 21:55 tar
-rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile
-rwxr-xr-x 1 root root 89120 Sep 22 2020 touch
-rwxr-xr-x 1 root root 31512 Sep 22 2020 true
-rwxr-xr-x 1 root root 14264 Feb 26 04:12 ulockmgr_server
-rwsr-xr-x 1 root root 30880 Feb 7 02:38 umount
-rwxr-xr-x 1 root root 35640 Sep 22 2020 uname
-rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress
-rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir
-rwxr-xr-x 1 root root 59584 Feb 7 02:38 wdctl
lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat
-rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp
-rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff
-rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep
-rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep
-rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce
-rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep
-rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless
-rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore
-rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew
I: user script /srv/workspace/pbuilder/9579/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: arm64
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), zlib1g-dev, libbam-dev, libsparsehash-dev, samtools, libhts-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 ... 19646 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 zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on libbam-dev; however:
Package libbam-dev is not installed.
pbuilder-satisfydepends-dummy depends on libsparsehash-dev; however:
Package libsparsehash-dev is not installed.
pbuilder-satisfydepends-dummy depends on samtools; however:
Package samtools is not installed.
pbuilder-satisfydepends-dummy depends on libhts-dev; however:
Package libhts-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} libbam-dev{a} libbrotli1{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libhts-dev{a} libhts3{a} libicu67{a} libldap-2.4-2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsparsehash-dev{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} samtools{a} sensible-utils{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget
0 packages upgraded, 51 newly installed, 0 to remove and 0 not upgraded.
Need to get 25.2 MB of archives. After unpacking 82.1 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-7 [141 kB]
Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB]
Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB]
Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB]
Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB]
Get: 6 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB]
Get: 7 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB]
Get: 8 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB]
Get: 9 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB]
Get: 10 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB]
Get: 11 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB]
Get: 12 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB]
Get: 13 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB]
Get: 14 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get: 15 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB]
Get: 16 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB]
Get: 17 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB]
Get: 18 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB]
Get: 19 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 20 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 21 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB]
Get: 22 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get: 23 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get: 24 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB]
Get: 25 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB]
Get: 26 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB]
Get: 27 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB]
Get: 28 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB]
Get: 29 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get: 30 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 31 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB]
Get: 32 http://deb.debian.org/debian bullseye/main arm64 libbam-dev arm64 0.1.19+dfsg-1 [113 kB]
Get: 33 http://deb.debian.org/debian bullseye/main arm64 libbrotli1 arm64 1.0.9-2+b2 [267 kB]
Get: 34 http://deb.debian.org/debian bullseye/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2.1 [69.3 kB]
Get: 35 http://deb.debian.org/debian bullseye/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2.1 [105 kB]
Get: 36 http://deb.debian.org/debian bullseye/main arm64 libldap-2.4-2 arm64 2.4.57+dfsg-3 [222 kB]
Get: 37 http://deb.debian.org/debian bullseye/main arm64 libnghttp2-14 arm64 1.43.0-1 [73.8 kB]
Get: 38 http://deb.debian.org/debian bullseye/main arm64 libpsl5 arm64 0.21.0-1.2 [57.1 kB]
Get: 39 http://deb.debian.org/debian bullseye/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB]
Get: 40 http://deb.debian.org/debian bullseye/main arm64 libssh2-1 arm64 1.9.0-2 [150 kB]
Get: 41 http://deb.debian.org/debian bullseye/main arm64 libcurl3-gnutls arm64 7.74.0-1.3+b1 [318 kB]
Get: 42 http://deb.debian.org/debian bullseye/main arm64 libcurl4-gnutls-dev arm64 7.74.0-1.3+b1 [419 kB]
Get: 43 http://deb.debian.org/debian bullseye/main arm64 libdeflate0 arm64 1.7-1 [47.7 kB]
Get: 44 http://deb.debian.org/debian bullseye/main arm64 libdeflate-dev arm64 1.7-1 [44.5 kB]
Get: 45 http://deb.debian.org/debian bullseye/main arm64 libhts3 arm64 1.11-4 [346 kB]
Get: 46 http://deb.debian.org/debian bullseye/main arm64 liblzma-dev arm64 5.2.5-2 [227 kB]
Get: 47 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB]
Get: 48 http://deb.debian.org/debian bullseye/main arm64 libhts-dev arm64 1.11-4 [3856 kB]
Get: 49 http://deb.debian.org/debian bullseye/main arm64 libncurses6 arm64 6.2+20201114-2 [93.2 kB]
Get: 50 http://deb.debian.org/debian bullseye/main arm64 libsparsehash-dev all 2.0.3-2 [76.8 kB]
Get: 51 http://deb.debian.org/debian bullseye/main arm64 samtools arm64 1.11-1 [526 kB]
Fetched 25.2 MB in 1s (22.2 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package bsdextrautils.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
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Reading package lists...
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/stacks-2.55+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../stacks_2.55+dfsg-1_source.changes
dpkg-buildpackage: info: source package stacks
dpkg-buildpackage: info: source version 2.55+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Nilesh Patra <npatra974@gmail.com>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
debian/rules clean
dh clean
debian/rules override_dh_clean
make[1]: Entering directory '/build/stacks-2.55+dfsg'
dh_clean
rm -f ./constants.php
make[1]: Leaving directory '/build/stacks-2.55+dfsg'
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
configure.ac:33: installing 'config/ar-lib'
configure.ac:28: installing 'config/compile'
configure.ac:7: installing 'config/install-sh'
configure.ac:7: installing 'config/missing'
Makefile.am: installing 'config/depcomp'
parallel-tests: installing 'config/test-driver'
debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/stacks-2.55+dfsg'
dh_auto_configure -- --enable-sparsehash --enable-bam \
--with-bam-include-path=/usr/include/samtools \
--with-bam-lib-path=/usr/lib
./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-sparsehash --enable-bam --with-bam-include-path=/usr/include/samtools --with-bam-lib-path=/usr/lib
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of g++... none
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking whether g++ supports C++11 features by default... yes
checking for ranlib... ranlib
checking for ar... ar
checking the archiver (ar) interface... ar
checking for omp_set_num_threads in -lgomp... yes
checking for gzread in -lz... yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for gcc option to support OpenMP... -fopenmp
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking whether closedir returns void... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for floor... no
checking for memset... yes
checking for pow... no
checking for sqrt... no
checking for clock_gettime... yes
checking for functional regular expressions... yes
checking for gawk... (cached) mawk
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commands
make[1]: Leaving directory '/build/stacks-2.55+dfsg'
dh_auto_build
make -j8
make[1]: Entering directory '/build/stacks-2.55+dfsg'
make all-recursive
make[2]: Entering directory '/build/stacks-2.55+dfsg'
make[3]: Entering directory '/build/stacks-2.55+dfsg'
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/ustacks.o src/ustacks.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/aln_utils.o src/aln_utils.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/BamI.o src/BamI.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/catalog_utils.o src/catalog_utils.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cmb.o src/cmb.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/constants.o src/constants.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/DNANSeq.o src/DNANSeq.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/DNASeq4.o src/DNASeq4.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/DNASeq.o src/DNASeq.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/gzFasta.o src/gzFasta.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/input.o src/input.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/kmers.o src/kmers.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/locus.o src/locus.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/log_utils.o src/log_utils.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/MetaPopInfo.o src/MetaPopInfo.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/models.o src/models.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/mstack.o src/mstack.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/mst.o src/mst.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/nucleotides.o src/nucleotides.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/renz.o src/renz.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/Seq.o src/Seq.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sql_utilities.o src/sql_utilities.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/stacks.o src/stacks.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/utils.o src/utils.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/Vcf.o src/Vcf.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cstacks.o src/cstacks.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sstacks.o src/sstacks.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_radtags.o src/process_radtags.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/clean.o src/clean.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/file_io.o src/file_io.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/write.o src/write.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_shortreads.o src/process_shortreads.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/kmer_filter.o src/kmer_filter.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/clone_filter.o src/clone_filter.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations.o src/populations.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/export_formats.o src/export_formats.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/mapping_utils.o src/mapping_utils.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotype_dictionaries.o src/genotype_dictionaries.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/PopSum.o src/PopSum.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/Hwp.o src/Hwp.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/phasedstacks.o src/phasedstacks.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/tsv2bam.o src/tsv2bam.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/gstacks.o src/gstacks.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/debruijn.o src/debruijn.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/SuffixTree.o src/SuffixTree.cc
rm -f libcore.a
ar cru libcore.a src/aln_utils.o src/BamI.o src/catalog_utils.o src/cmb.o src/constants.o src/DNANSeq.o src/DNASeq4.o src/DNASeq.o src/gzFasta.o src/input.o src/kmers.o src/locus.o src/log_utils.o src/MetaPopInfo.o src/models.o src/mstack.o src/mst.o src/nucleotides.o src/renz.o src/Seq.o src/sql_utilities.o src/stacks.o src/utils.o src/Vcf.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libcore.a
rm -f libclean.a
ar cru libclean.a src/clean.o src/file_io.o src/write.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libclean.a
g++ -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o ustacks src/ustacks.o -lhts libcore.a -lz -lgomp
g++ -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o cstacks src/cstacks.o -lhts libcore.a -lz -lgomp
g++ -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o sstacks src/sstacks.o -lhts libcore.a -lz -lgomp
g++ -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o process_radtags src/process_radtags.o -lhts libcore.a libclean.a -lz -lgomp
g++ -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o process_shortreads src/process_shortreads.o -lhts libcore.a libclean.a -lz -lgomp
g++ -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o kmer_filter src/kmer_filter.o -lhts libcore.a libclean.a -lz -lgomp
g++ -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o clone_filter src/clone_filter.o -lhts libcore.a libclean.a -lz -lgomp
g++ -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o phasedstacks src/phasedstacks.o -lhts libcore.a -lz -lgomp
rm -f libpop.a
ar cru libpop.a src/export_formats.o src/mapping_utils.o src/genotype_dictionaries.o src/PopSum.o src/Hwp.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libpop.a
g++ -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o populations src/populations.o -lhts libcore.a libpop.a -lz -lgomp
g++ -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o tsv2bam src/tsv2bam.o -lhts libcore.a -lz -lgomp
g++ -g -O2 -fdebug-prefix-map=/build/stacks-2.55+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o gstacks src/gstacks.o src/debruijn.o src/SuffixTree.o -lhts libcore.a -lz -lgomp
make[3]: Leaving directory '/build/stacks-2.55+dfsg'
make[2]: Leaving directory '/build/stacks-2.55+dfsg'
make[1]: Leaving directory '/build/stacks-2.55+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/stacks-2.55+dfsg'
if [ -e /usr/share/automake-1.16/tap-driver.sh ] ; then \
ln -s /usr/share/automake-1.16/tap-driver.sh tests/tap-driver.sh ; \
else \
echo "Make sure /usr/share/automake-*/tap-driver.sh exists and is linked" ; \
false ; \
fi
# dh_auto_test
rm tests/tap-driver.sh
# FIXME: Does not work even after this trick. See
# https://groups.google.com/forum/#!msg/stacks-users/TA2tMEqb4Mg/pQy4fUCYi9kJ
true
make[1]: Leaving directory '/build/stacks-2.55+dfsg'
create-stamp debian/debhelper-build-stamp
dh_prep
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/stacks-2.55+dfsg'
dh_auto_install --no-parallel
make -j1 install DESTDIR=/build/stacks-2.55\+dfsg/debian/stacks AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/build/stacks-2.55+dfsg'
make[3]: Entering directory '/build/stacks-2.55+dfsg'
make[4]: Entering directory '/build/stacks-2.55+dfsg'
/bin/mkdir -p '/build/stacks-2.55+dfsg/debian/stacks/usr/bin'
/usr/bin/install -c ustacks cstacks sstacks process_radtags process_shortreads kmer_filter clone_filter populations phasedstacks tsv2bam gstacks '/build/stacks-2.55+dfsg/debian/stacks/usr/bin'
/bin/mkdir -p '/build/stacks-2.55+dfsg/debian/stacks/usr/bin'
/usr/bin/install -c scripts/denovo_map.pl scripts/ref_map.pl scripts/integrate_alignments.py scripts/count_fixed_catalog_snps.py scripts/stacks-integrate-alignments scripts/stacks-dist-extract scripts/stacks-gdb scripts/stacks-samtools-tview scripts/stacks-count-reads-per-sample-per-locus scripts/stacks-hist2d-loci-samples-coverage '/build/stacks-2.55+dfsg/debian/stacks/usr/bin'
make install-data-hook
make[5]: Entering directory '/build/stacks-2.55+dfsg'
sed -e 's,_VERSION_,2.55,' -e 's,_BINDIR_,/usr/lib/stacks/bin/,g' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /build/stacks-2.55+dfsg/debian/stacks/usr/bin/denovo_map.pl > /build/stacks-2.55+dfsg/debian/stacks/usr/bin/denovo_map.pl.subst
mv /build/stacks-2.55+dfsg/debian/stacks/usr/bin/denovo_map.pl.subst /build/stacks-2.55+dfsg/debian/stacks/usr/bin/denovo_map.pl
chmod +x /build/stacks-2.55+dfsg/debian/stacks/usr/bin/denovo_map.pl
sed -e 's,_VERSION_,2.55,' -e 's,_BINDIR_,/usr/lib/stacks/bin/,g' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /build/stacks-2.55+dfsg/debian/stacks/usr/bin/ref_map.pl > /build/stacks-2.55+dfsg/debian/stacks/usr/bin/ref_map.pl.subst
mv /build/stacks-2.55+dfsg/debian/stacks/usr/bin/ref_map.pl.subst /build/stacks-2.55+dfsg/debian/stacks/usr/bin/ref_map.pl
chmod +x /build/stacks-2.55+dfsg/debian/stacks/usr/bin/ref_map.pl
sed -i.bkp -e 's,_VERSION_,2.55,' /build/stacks-2.55+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments
sed -i.bkp -e 's,_VERSION_,2.55,' /build/stacks-2.55+dfsg/debian/stacks/usr/bin/stacks-samtools-tview
rm -f /build/stacks-2.55+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments.bkp
rm -f /build/stacks-2.55+dfsg/debian/stacks/usr/bin/stacks-samtools-tview.bkp
chmod +x /build/stacks-2.55+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments
chmod +x /build/stacks-2.55+dfsg/debian/stacks/usr/bin/stacks-dist-extract
chmod +x /build/stacks-2.55+dfsg/debian/stacks/usr/bin/stacks-gdb
make[5]: Leaving directory '/build/stacks-2.55+dfsg'
make[4]: Leaving directory '/build/stacks-2.55+dfsg'
make[3]: Leaving directory '/build/stacks-2.55+dfsg'
make[2]: Leaving directory '/build/stacks-2.55+dfsg'
make[1]: Leaving directory '/build/stacks-2.55+dfsg'
debian/rules override_dh_install
make[1]: Entering directory '/build/stacks-2.55+dfsg'
mkdir -p debian/stacks/usr/lib/stacks
mv debian/stacks/usr/bin debian/stacks/usr/lib/stacks
cd debian/stacks/usr/lib/stacks/bin && \
for f in *.pl ; do \
ln -s "$f" "`basename $f .pl`" ; \
sed -i '1s?^#!/usr/bin/env.*perl?#!/usr/bin/perl?' $f ; \
done
dh_install
make[1]: Leaving directory '/build/stacks-2.55+dfsg'
dh_installdocs
dh_installchangelogs
dh_perl
debian/rules override_dh_link
make[1]: Entering directory '/build/stacks-2.55+dfsg'
dh_link
mkdir -p debian/stacks/usr/lib/debian-med/bin
cd debian/stacks/usr/lib/debian-med/bin && \
for f in `ls /build/stacks-2.55+dfsg/debian/stacks/usr/lib/stacks/bin` ; do \
ln -s ../../stacks/bin/$f ; \
done
make[1]: Leaving directory '/build/stacks-2.55+dfsg'
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
dpkg-gencontrol: warning: package stacks: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package stacks: substitution variable ${perl:Depends} unused, but is defined
dh_md5sums
dh_builddeb
dpkg-deb: building package 'stacks' in '../stacks_2.55+dfsg-1_arm64.deb'.
dpkg-deb: building package 'stacks-dbgsym' in '../stacks-dbgsym_2.55+dfsg-1_arm64.deb'.
dpkg-genbuildinfo --build=binary
dpkg-genchanges --build=binary >../stacks_2.55+dfsg-1_arm64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: including full source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/9579 and its subdirectories
I: Current time: Sun Jul 25 00:26:11 -12 2021
I: pbuilder-time-stamp: 1627215971
Sun Jul 25 12:26:15 UTC 2021 I: 1st build successful. Starting 2nd build on remote node codethink15-arm64.debian.net.
Sun Jul 25 12:26:16 UTC 2021 I: Preparing to do remote build '2' on codethink15-arm64.debian.net.
Sun Jul 25 12:35:18 UTC 2021 I: Deleting $TMPDIR on codethink15-arm64.debian.net.
Sun Jul 25 12:35:19 UTC 2021 I: stacks_2.55+dfsg-1_arm64.changes:
Format: 1.8
Date: Sun, 10 Jan 2021 17:37:28 +0530
Source: stacks
Binary: stacks stacks-dbgsym
Architecture: arm64
Version: 2.55+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Nilesh Patra <npatra974@gmail.com>
Description:
stacks - pipeline for building loci from short-read DNA sequences
Changes:
stacks (2.55+dfsg-1) unstable; urgency=medium
.
* Team upload.
* New upstream version
* Standards-Version: 4.5.1 (routine-update)
Checksums-Sha1:
ccd08e28df1c4e744b31c6f2376d02fdeae382ca 26480584 stacks-dbgsym_2.55+dfsg-1_arm64.deb
516fff51075b13453a9982d7563a788398719d69 5636 stacks_2.55+dfsg-1_arm64.buildinfo
c7072bd0ae43cbd645e0e2be723a740e2898f711 932176 stacks_2.55+dfsg-1_arm64.deb
Checksums-Sha256:
85f9efaaea4b2e748d2abda6c9b00c2abc2689fb317f0071f1d197518ddf94a3 26480584 stacks-dbgsym_2.55+dfsg-1_arm64.deb
2ca55c59c2dc5a5ca8db10d23e6bfdd637946f9c773782b0124a3c712107c5a4 5636 stacks_2.55+dfsg-1_arm64.buildinfo
2c9cae6a05fa7e53fdb0dbfe25ab99983a2cba82f011cc53157f800497bfcc82 932176 stacks_2.55+dfsg-1_arm64.deb
Files:
0d8b9eda6c676a6c0cc869ac79e7e1ac 26480584 debug optional stacks-dbgsym_2.55+dfsg-1_arm64.deb
26eb36de227353d5190f0904f8bd35e1 5636 science optional stacks_2.55+dfsg-1_arm64.buildinfo
30ad4416b4945142cf4e785be5b17bae 932176 science optional stacks_2.55+dfsg-1_arm64.deb
Sun Jul 25 12:35:24 UTC 2021 I: diffoscope 177 will be used to compare the two builds:
# Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.I0eJxwKu15/stacks_2.55+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.I0eJxwKu15/stacks_2.55+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.I0eJxwKu15/stacks_2.55+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.I0eJxwKu15/b1/stacks_2.55+dfsg-1_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.I0eJxwKu15/b2/stacks_2.55+dfsg-1_arm64.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: 3.186s)
3.186s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.290s)
0.290s 10 calls diffoscope.comparators.binary.FilesystemFile
0.000s 8 calls abc.DotChangesFile
Sun Jul 25 12:35:29 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists.
Sun Jul 25 12:35:29 UTC 2021 I: stacks from bullseye built successfully and reproducibly on arm64.
Sun Jul 25 12:35:30 UTC 2021 I: Submitting .buildinfo files to external archives:
Sun Jul 25 12:35:30 UTC 2021 I: Submitting 8.0K b1/stacks_2.55+dfsg-1_arm64.buildinfo.asc
Sun Jul 25 12:35:31 UTC 2021 I: Submitting 8.0K b2/stacks_2.55+dfsg-1_arm64.buildinfo.asc
Sun Jul 25 12:35:32 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sun Jul 25 12:35:32 UTC 2021 I: Done submitting .buildinfo files.
Sun Jul 25 12:35:32 UTC 2021 I: Removing signed stacks_2.55+dfsg-1_arm64.buildinfo.asc files:
removed './b1/stacks_2.55+dfsg-1_arm64.buildinfo.asc'
removed './b2/stacks_2.55+dfsg-1_arm64.buildinfo.asc'