Tue Aug 10 09:48:18 UTC 2021 I: starting to build libgff/bullseye/arm64 on jenkins on '2021-08-10 09:48'
Tue Aug 10 09:48:18 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_7/13905/console.log
Tue Aug 10 09:48:18 UTC 2021 I: Downloading source for bullseye/libgff=2.0.0-1
--2021-08-10 09:48:18-- http://cdn-fastly.deb.debian.org/debian/pool/main/libg/libgff/libgff_2.0.0-1.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 1992 (1.9K)
Saving to: ‘libgff_2.0.0-1.dsc’
0K . 100% 197M=0s
2021-08-10 09:48:18 (197 MB/s) - ‘libgff_2.0.0-1.dsc’ saved [1992/1992]
Tue Aug 10 09:48:18 UTC 2021 I: libgff_2.0.0-1.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: libgff
Binary: libgff-dev
Architecture: any
Version: 2.0.0-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Michael R. Crusoe <crusoe@debian.org>
Homepage: https://github.com/COMBINE-lab/libgff
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/libgff
Vcs-Git: https://salsa.debian.org/med-team/libgff.git
Testsuite: autopkgtest
Testsuite-Triggers: build-essential, python-pysam-tests
Build-Depends: debhelper-compat (= 13), cmake
Package-List:
libgff-dev deb libdevel optional arch=any
Checksums-Sha1:
6127e9f35dee7fc254a1ed280ff5337d42d814ba 102152 libgff_2.0.0.orig.tar.gz
4bd0a061f0e84e889f5ef887928065b24f071a69 4208 libgff_2.0.0-1.debian.tar.xz
Checksums-Sha256:
7656b19459a7ca7d2fd0fcec4f2e0fd0deec1b4f39c703a114e8f4c22d82a99c 102152 libgff_2.0.0.orig.tar.gz
4634b628861e3e7541a875e6e5bb5b1e5d1f4326a2cfb0cb87c8a08af3f979c6 4208 libgff_2.0.0-1.debian.tar.xz
Files:
2154f6c0a4ea49cea86205d9a737be84 102152 libgff_2.0.0.orig.tar.gz
85ff5fa2069459e20cfacd0e10b68f7b 4208 libgff_2.0.0-1.debian.tar.xz
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Tue Aug 10 09:48:18 UTC 2021 I: Checking whether the package is not for us
Tue Aug 10 09:48:18 UTC 2021 I: Starting 1st build on remote node codethink10-arm64.debian.net.
Tue Aug 10 09:48:18 UTC 2021 I: Preparing to do remote build '1' on codethink10-arm64.debian.net.
Tue Aug 10 09:49:20 UTC 2021 I: Deleting $TMPDIR on codethink10-arm64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Mon Aug 9 21:48:20 -12 2021
I: pbuilder-time-stamp: 1628588900
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 [libgff_2.0.0-1.dsc]
I: copying [./libgff_2.0.0.orig.tar.gz]
I: copying [./libgff_2.0.0-1.debian.tar.xz]
I: Extracting source
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.EzLEWzPq/trustedkeys.kbx': General error
gpgv: Signature made Wed Jul 15 23:54:47 2020 -12
gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./libgff_2.0.0-1.dsc
dpkg-source: info: extracting libgff in libgff-2.0.0
dpkg-source: info: unpacking libgff_2.0.0.orig.tar.gz
dpkg-source: info: unpacking libgff_2.0.0-1.debian.tar.xz
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/7001/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='7001'
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.4hTv73dZsU/pbuilderrc_HOhZ --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.4hTv73dZsU/b1 --logfile b1/build.log libgff_2.0.0-1.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 4.15.0-153-generic #160-Ubuntu SMP Thu Jul 29 07:06:07 UTC 2021 aarch64 GNU/Linux
I: ls -l /bin
total 5252
-rwxr-xr-x 1 root root 1282512 Aug 4 08:25 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 Jul 28 07:09 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 Jul 28 07:09 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 Jul 28 07:09 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 Jul 28 07:09 more
-rwsr-xr-x 1 root root 51360 Jul 28 07:09 mount
-rwxr-xr-x 1 root root 14496 Jul 28 07:09 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 Aug 4 08:25 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 Aug 8 23:21 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 Jul 28 07:09 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 Jul 28 07:09 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 Jul 28 07:09 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/7001/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), cmake
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 cmake; however:
Package cmake 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} cmake{a} cmake-data{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} libarchive13{a} libbrotli1{a} libcurl4{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libicu67{a} libjsoncpp24{a} libldap-2.4-2{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libprocps8{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} m4{a} man-db{a} po-debconf{a} procps{a} sensible-utils{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 psmisc publicsuffix wget
0 packages upgraded, 50 newly installed, 0 to remove and 0 not upgraded.
Need to get 26.0 MB of archives. After unpacking 104 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-8 [142 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 libncurses6 arm64 6.2+20201114-2 [93.2 kB]
Get: 7 http://deb.debian.org/debian bullseye/main arm64 libprocps8 arm64 2:3.3.17-5 [61.9 kB]
Get: 8 http://deb.debian.org/debian bullseye/main arm64 procps arm64 2:3.3.17-5 [497 kB]
Get: 9 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB]
Get: 10 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB]
Get: 11 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB]
Get: 12 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB]
Get: 13 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB]
Get: 14 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB]
Get: 15 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB]
Get: 16 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB]
Get: 17 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get: 18 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB]
Get: 19 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB]
Get: 20 http://deb.debian.org/debian bullseye/main arm64 cmake-data all 3.18.4-2 [1725 kB]
Get: 21 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB]
Get: 22 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB]
Get: 23 http://deb.debian.org/debian bullseye/main arm64 libarchive13 arm64 3.4.3-2+b1 [320 kB]
Get: 24 http://deb.debian.org/debian bullseye/main arm64 libbrotli1 arm64 1.0.9-2+b2 [267 kB]
Get: 25 http://deb.debian.org/debian bullseye/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2.1 [69.3 kB]
Get: 26 http://deb.debian.org/debian bullseye/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2.1 [105 kB]
Get: 27 http://deb.debian.org/debian bullseye/main arm64 libldap-2.4-2 arm64 2.4.57+dfsg-3 [222 kB]
Get: 28 http://deb.debian.org/debian bullseye/main arm64 libnghttp2-14 arm64 1.43.0-1 [73.8 kB]
Get: 29 http://deb.debian.org/debian bullseye/main arm64 libpsl5 arm64 0.21.0-1.2 [57.1 kB]
Get: 30 http://deb.debian.org/debian bullseye/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB]
Get: 31 http://deb.debian.org/debian bullseye/main arm64 libssh2-1 arm64 1.9.0-2 [150 kB]
Get: 32 http://deb.debian.org/debian bullseye/main arm64 libcurl4 arm64 7.74.0-1.3+b1 [321 kB]
Get: 33 http://deb.debian.org/debian bullseye/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB]
Get: 34 http://deb.debian.org/debian bullseye/main arm64 libjsoncpp24 arm64 1.9.4-4 [72.5 kB]
Get: 35 http://deb.debian.org/debian bullseye/main arm64 librhash0 arm64 1.4.1-2 [127 kB]
Get: 36 http://deb.debian.org/debian bullseye/main arm64 libuv1 arm64 1.40.0-2 [126 kB]
Get: 37 http://deb.debian.org/debian bullseye/main arm64 cmake arm64 3.18.4-2 [3673 kB]
Get: 38 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB]
Get: 39 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB]
Get: 40 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 41 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 42 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB]
Get: 43 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get: 44 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get: 45 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB]
Get: 46 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB]
Get: 47 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB]
Get: 48 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get: 49 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 50 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB]
Fetched 26.0 MB in 1s (49.2 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package bsdextrautils.
(Reading database ...
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(Reading database ... 19646 files and directories currently installed.)
Preparing to unpack .../00-bsdextrautils_2.36.1-8_arm64.deb ...
Unpacking bsdextrautils (2.36.1-8) ...
Selecting previously unselected package libuchardet0:arm64.
Preparing to unpack .../01-libuchardet0_0.0.7-1_arm64.deb ...
Unpacking libuchardet0:arm64 (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../02-groff-base_1.22.4-6_arm64.deb ...
Unpacking groff-base (1.22.4-6) ...
Selecting previously unselected package libpipeline1:arm64.
Preparing to unpack .../03-libpipeline1_1.5.3-1_arm64.deb ...
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/libgff-2.0.0/ && 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 > ../libgff_2.0.0-1_source.changes
dpkg-buildpackage: info: source package libgff
dpkg-buildpackage: info: source version 2.0.0-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Michael R. Crusoe <crusoe@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
debian/rules clean
dh clean
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
cd obj-aarch64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu ..
-- The C compiler identification is GNU 10.2.1
-- The CXX compiler identification is GNU 10.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Install prefix : /usr
version: 2.0.0
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
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CMAKE_INSTALL_RUNSTATEDIR
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-- Build files have been written to: /build/libgff-2.0.0/obj-aarch64-linux-gnu
dh_auto_build
cd obj-aarch64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1
make[1]: Entering directory '/build/libgff-2.0.0/obj-aarch64-linux-gnu'
/usr/bin/cmake -S/build/libgff-2.0.0 -B/build/libgff-2.0.0/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /build/libgff-2.0.0/obj-aarch64-linux-gnu/CMakeFiles /build/libgff-2.0.0/obj-aarch64-linux-gnu//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
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make -f CMakeFiles/gff.dir/build.make CMakeFiles/gff.dir/depend
make[3]: Entering directory '/build/libgff-2.0.0/obj-aarch64-linux-gnu'
cd /build/libgff-2.0.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libgff-2.0.0 /build/libgff-2.0.0 /build/libgff-2.0.0/obj-aarch64-linux-gnu /build/libgff-2.0.0/obj-aarch64-linux-gnu /build/libgff-2.0.0/obj-aarch64-linux-gnu/CMakeFiles/gff.dir/DependInfo.cmake --color=
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Scanning dependencies of target gff
make[3]: Leaving directory '/build/libgff-2.0.0/obj-aarch64-linux-gnu'
make -f CMakeFiles/gff.dir/build.make CMakeFiles/gff.dir/build
make[3]: Entering directory '/build/libgff-2.0.0/obj-aarch64-linux-gnu'
[ 9%] Building CXX object CMakeFiles/gff.dir/src/GBase.cpp.o
[ 18%] Building CXX object CMakeFiles/gff.dir/src/GArgs.cpp.o
/usr/bin/c++ -I/build/libgff-2.0.0/include -g -O2 -fdebug-prefix-map=/build/libgff-2.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -D_FILE_OFFSET_BITS=64 -std=c++14 -o CMakeFiles/gff.dir/src/GBase.cpp.o -c /build/libgff-2.0.0/src/GBase.cpp
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/usr/bin/c++ -I/build/libgff-2.0.0/include -g -O2 -fdebug-prefix-map=/build/libgff-2.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -D_FILE_OFFSET_BITS=64 -std=c++14 -o CMakeFiles/gff.dir/src/codons.cpp.o -c /build/libgff-2.0.0/src/codons.cpp
/usr/bin/c++ -I/build/libgff-2.0.0/include -g -O2 -fdebug-prefix-map=/build/libgff-2.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -D_FILE_OFFSET_BITS=64 -std=c++14 -o CMakeFiles/gff.dir/src/GArgs.cpp.o -c /build/libgff-2.0.0/src/GArgs.cpp
[ 45%] Building CXX object CMakeFiles/gff.dir/src/GFastaIndex.cpp.o
/usr/bin/c++ -I/build/libgff-2.0.0/include -g -O2 -fdebug-prefix-map=/build/libgff-2.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -D_FILE_OFFSET_BITS=64 -std=c++14 -o CMakeFiles/gff.dir/src/gdna.cpp.o -c /build/libgff-2.0.0/src/gdna.cpp
/usr/bin/c++ -I/build/libgff-2.0.0/include -g -O2 -fdebug-prefix-map=/build/libgff-2.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -D_FILE_OFFSET_BITS=64 -std=c++14 -o CMakeFiles/gff.dir/src/GFastaIndex.cpp.o -c /build/libgff-2.0.0/src/GFastaIndex.cpp
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/usr/bin/c++ -I/build/libgff-2.0.0/include -g -O2 -fdebug-prefix-map=/build/libgff-2.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -D_FILE_OFFSET_BITS=64 -std=c++14 -o CMakeFiles/gff.dir/src/GFaSeqGet.cpp.o -c /build/libgff-2.0.0/src/GFaSeqGet.cpp
[ 63%] Building CXX object CMakeFiles/gff.dir/src/gff.cpp.o
/usr/bin/c++ -I/build/libgff-2.0.0/include -g -O2 -fdebug-prefix-map=/build/libgff-2.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -D_FILE_OFFSET_BITS=64 -std=c++14 -o CMakeFiles/gff.dir/src/gff.cpp.o -c /build/libgff-2.0.0/src/gff.cpp
[ 72%] Building CXX object CMakeFiles/gff.dir/src/GStr.cpp.o
/usr/bin/c++ -I/build/libgff-2.0.0/include -g -O2 -fdebug-prefix-map=/build/libgff-2.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -D_FILE_OFFSET_BITS=64 -std=c++14 -o CMakeFiles/gff.dir/src/GStr.cpp.o -c /build/libgff-2.0.0/src/GStr.cpp
In file included from /build/libgff-2.0.0/include/GList.hh:8,
from /build/libgff-2.0.0/include/GFastaIndex.h:12,
from /build/libgff-2.0.0/include/GFaSeqGet.h:3,
from /build/libgff-2.0.0/include/gff.h:9,
from /build/libgff-2.0.0/src/gff.cpp:1:
/build/libgff-2.0.0/include/GVec.hh: In instantiation of 'void GVec<OBJ>::setCapacity(int) [with OBJ = GMapSeg]':
/build/libgff-2.0.0/include/GVec.hh:202:3: required from 'GVec<OBJ>::GVec(int) [with OBJ = GMapSeg]'
/build/libgff-2.0.0/include/gff.h:126:50: required from here
/build/libgff-2.0.0/include/GVec.hh:291:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GMapSeg'; use assignment or value-initialization instead [-Wclass-memaccess]
291 | memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/libgff-2.0.0/src/gff.cpp:1:
/build/libgff-2.0.0/include/gff.h:69:7: note: 'class GMapSeg' declared here
69 | class GMapSeg:public GSeg {
| ^~~~~~~
In file included from /build/libgff-2.0.0/include/GList.hh:8,
from /build/libgff-2.0.0/include/GFastaIndex.h:12,
from /build/libgff-2.0.0/include/GFaSeqGet.h:3,
from /build/libgff-2.0.0/include/gff.h:9,
from /build/libgff-2.0.0/src/gff.cpp:1:
/build/libgff-2.0.0/include/GVec.hh: In instantiation of 'void GVec<OBJ>::setCapacity(int) [with OBJ = GSeg]':
/build/libgff-2.0.0/include/GVec.hh:202:3: required from 'GVec<OBJ>::GVec(int) [with OBJ = GSeg]'
/build/libgff-2.0.0/include/gff.h:310:92: required from here
/build/libgff-2.0.0/include/GVec.hh:291:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess]
291 | memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/libgff-2.0.0/include/gff.h:6,
from /build/libgff-2.0.0/src/gff.cpp:1:
/build/libgff-2.0.0/include/GBase.h:308:7: note: 'class GSeg' declared here
308 | class GSeg {
| ^~~~
In file included from /build/libgff-2.0.0/include/GList.hh:8,
from /build/libgff-2.0.0/include/GFastaIndex.h:12,
from /build/libgff-2.0.0/include/GFaSeqGet.h:3,
from /build/libgff-2.0.0/include/gff.h:9,
from /build/libgff-2.0.0/src/gff.cpp:1:
/build/libgff-2.0.0/include/GVec.hh: In instantiation of 'void GVec<OBJ>::setCapacity(int) [with OBJ = GeneCDS]':
/build/libgff-2.0.0/include/GVec.hh:202:3: required from 'GVec<OBJ>::GVec(int) [with OBJ = GeneCDS]'
/build/libgff-2.0.0/include/gff.h:1349:31: required from here
/build/libgff-2.0.0/include/GVec.hh:291:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GeneCDS'; use assignment or value-initialization instead [-Wclass-memaccess]
291 | memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/libgff-2.0.0/src/gff.cpp:1:
/build/libgff-2.0.0/include/gff.h:1338:7: note: 'class GeneCDS' declared here
1338 | class GeneCDS: public GSeg {
| ^~~~~~~
In file included from /build/libgff-2.0.0/include/GList.hh:8,
from /build/libgff-2.0.0/include/GFastaIndex.h:12,
from /build/libgff-2.0.0/include/GFaSeqGet.h:3,
from /build/libgff-2.0.0/include/gff.h:9,
from /build/libgff-2.0.0/src/gff.cpp:1:
/build/libgff-2.0.0/include/GVec.hh: In instantiation of 'void GVec<OBJ>::setCapacity(int) [with OBJ = GffExon]':
/build/libgff-2.0.0/include/GVec.hh:202:3: required from 'GVec<OBJ>::GVec(int) [with OBJ = GffExon]'
/build/libgff-2.0.0/src/gff.cpp:2315:16: required from here
/build/libgff-2.0.0/include/GVec.hh:291:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GffExon'; use assignment or value-initialization instead [-Wclass-memaccess]
291 | memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/libgff-2.0.0/src/gff.cpp:1:
/build/libgff-2.0.0/include/gff.h:627:7: note: 'class GffExon' declared here
627 | class GffExon : public GSeg {
| ^~~~~~~
In file included from /build/libgff-2.0.0/include/GList.hh:8,
from /build/libgff-2.0.0/include/GFastaIndex.h:12,
from /build/libgff-2.0.0/include/GFaSeqGet.h:3,
from /build/libgff-2.0.0/include/gff.h:9,
from /build/libgff-2.0.0/src/gff.cpp:1:
/build/libgff-2.0.0/include/GVec.hh: In instantiation of 'void GVec<OBJ>::setCapacity(int) [with OBJ = GSegMatch]':
/build/libgff-2.0.0/include/GVec.hh:202:3: required from 'GVec<OBJ>::GVec(int) [with OBJ = GSegMatch]'
/build/libgff-2.0.0/include/GList.hh:191:76: required from 'GArray<OBJ>::GArray(int (*)(pointer, pointer)) [with OBJ = GSegMatch; GCompareProc = int(void*, void*); pointer = void*]'
/build/libgff-2.0.0/include/gff.h:1349:31: required from here
/build/libgff-2.0.0/include/GVec.hh:291:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSegMatch'; use assignment or value-initialization instead [-Wclass-memaccess]
291 | memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/libgff-2.0.0/src/gff.cpp:1:
/build/libgff-2.0.0/include/gff.h:1326:7: note: 'class GSegMatch' declared here
1326 | class GSegMatch { //keep track of "matching" overlaps of a GeneCDSChain with multiple GeneSegment containers
| ^~~~~~~~~
In file included from /build/libgff-2.0.0/include/GList.hh:8,
from /build/libgff-2.0.0/include/GFastaIndex.h:12,
from /build/libgff-2.0.0/include/GFaSeqGet.h:3,
from /build/libgff-2.0.0/include/gff.h:9,
from /build/libgff-2.0.0/src/gff.cpp:1:
/build/libgff-2.0.0/include/GVec.hh: In instantiation of 'void GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GSegMatch]':
/build/libgff-2.0.0/include/GVec.hh:437:9: required from 'void GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GSegMatch]'
/build/libgff-2.0.0/include/GVec.hh:69:44: required from 'void GVec<OBJ>::Insert(int, OBJ) [with OBJ = GSegMatch]'
/build/libgff-2.0.0/include/GList.hh:234:21: required from 'int GArray<OBJ>::Add(OBJ*) [with OBJ = GSegMatch]'
/build/libgff-2.0.0/include/GList.hh:51:36: required from 'int GArray<OBJ>::Add(OBJ&) [with OBJ = GSegMatch]'
/build/libgff-2.0.0/include/gff.h:1362:22: required from here
/build/libgff-2.0.0/include/GVec.hh:358:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSegMatch'; use assignment or value-initialization instead [-Wclass-memaccess]
358 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/libgff-2.0.0/src/gff.cpp:1:
/build/libgff-2.0.0/include/gff.h:1326:7: note: 'class GSegMatch' declared here
1326 | class GSegMatch { //keep track of "matching" overlaps of a GeneCDSChain with multiple GeneSegment containers
| ^~~~~~~~~
In member function 'void GStr::prep_data(uint, uint)',
inlined from 'GStr::GStr(char, int)' at /build/libgff-2.0.0/src/GStr.cpp:193:12:
/build/libgff-2.0.0/src/GStr.cpp:57:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
57 | my_data->chars[len]=0;
| ~~~~~~~~~~~~~~~~~~~^~
In file included from /build/libgff-2.0.0/src/GStr.cpp:2:
/build/libgff-2.0.0/include/GStr.h: In constructor 'GStr::GStr(char, int)':
/build/libgff-2.0.0/include/GStr.h:184:21: note: at offset 0 to object 'GStr::Data::chars' with size 1 declared here
184 | char chars[1];
| ^~~~~
In member function 'void GStr::prep_data(uint, uint)',
inlined from 'GStr GStr::operator+(int) const' at /build/libgff-2.0.0/src/GStr.cpp:666:24:
/build/libgff-2.0.0/src/GStr.cpp:57:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
57 | my_data->chars[len]=0;
| ~~~~~~~~~~~~~~~~~~~^~
In file included from /build/libgff-2.0.0/src/GStr.cpp:2:
/build/libgff-2.0.0/include/GStr.h: In member function 'GStr GStr::operator+(int) const':
/build/libgff-2.0.0/include/GStr.h:184:21: note: at offset 0 to object 'GStr::Data::chars' with size 1 declared here
184 | char chars[1];
| ^~~~~
In member function 'void GStr::prep_data(uint, uint)',
inlined from 'GStr GStr::operator+(char) const' at /build/libgff-2.0.0/src/GStr.cpp:677:24:
/build/libgff-2.0.0/src/GStr.cpp:57:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
57 | my_data->chars[len]=0;
| ~~~~~~~~~~~~~~~~~~~^~
In file included from /build/libgff-2.0.0/src/GStr.cpp:2:
/build/libgff-2.0.0/include/GStr.h: In member function 'GStr GStr::operator+(char) const':
/build/libgff-2.0.0/include/GStr.h:184:21: note: at offset 0 to object 'GStr::Data::chars' with size 1 declared here
184 | char chars[1];
| ^~~~~
In member function 'void GStr::prep_data(uint, uint)',
inlined from 'GStr GStr::operator+(double) const' at /build/libgff-2.0.0/src/GStr.cpp:688:24:
/build/libgff-2.0.0/src/GStr.cpp:57:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
57 | my_data->chars[len]=0;
| ~~~~~~~~~~~~~~~~~~~^~
In file included from /build/libgff-2.0.0/src/GStr.cpp:2:
/build/libgff-2.0.0/include/GStr.h: In member function 'GStr GStr::operator+(double) const':
/build/libgff-2.0.0/include/GStr.h:184:21: note: at offset 0 to object 'GStr::Data::chars' with size 1 declared here
184 | char chars[1];
| ^~~~~
[ 81%] Linking CXX static library libgff.a
/usr/bin/cmake -P CMakeFiles/gff.dir/cmake_clean_target.cmake
/usr/bin/cmake -E cmake_link_script CMakeFiles/gff.dir/link.txt --verbose=1
/usr/bin/ar qc libgff.a CMakeFiles/gff.dir/src/codons.cpp.o CMakeFiles/gff.dir/src/GArgs.cpp.o CMakeFiles/gff.dir/src/GBase.cpp.o CMakeFiles/gff.dir/src/gdna.cpp.o CMakeFiles/gff.dir/src/GFaSeqGet.cpp.o CMakeFiles/gff.dir/src/GFastaIndex.cpp.o CMakeFiles/gff.dir/src/gff.cpp.o CMakeFiles/gff.dir/src/GStr.cpp.o
/usr/bin/ranlib libgff.a
make[3]: Leaving directory '/build/libgff-2.0.0/obj-aarch64-linux-gnu'
[ 81%] Built target gff
make -f CMakeFiles/TestGFFParse.dir/build.make CMakeFiles/TestGFFParse.dir/depend
make[3]: Entering directory '/build/libgff-2.0.0/obj-aarch64-linux-gnu'
cd /build/libgff-2.0.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libgff-2.0.0 /build/libgff-2.0.0 /build/libgff-2.0.0/obj-aarch64-linux-gnu /build/libgff-2.0.0/obj-aarch64-linux-gnu /build/libgff-2.0.0/obj-aarch64-linux-gnu/CMakeFiles/TestGFFParse.dir/DependInfo.cmake --color=
Dependee "/build/libgff-2.0.0/obj-aarch64-linux-gnu/CMakeFiles/TestGFFParse.dir/DependInfo.cmake" is newer than depender "/build/libgff-2.0.0/obj-aarch64-linux-gnu/CMakeFiles/TestGFFParse.dir/depend.internal".
Dependee "/build/libgff-2.0.0/obj-aarch64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libgff-2.0.0/obj-aarch64-linux-gnu/CMakeFiles/TestGFFParse.dir/depend.internal".
Scanning dependencies of target TestGFFParse
make[3]: Leaving directory '/build/libgff-2.0.0/obj-aarch64-linux-gnu'
make -f CMakeFiles/TestGFFParse.dir/build.make CMakeFiles/TestGFFParse.dir/build
make[3]: Entering directory '/build/libgff-2.0.0/obj-aarch64-linux-gnu'
[ 90%] Building CXX object CMakeFiles/TestGFFParse.dir/src/TestGFFParse.cpp.o
/usr/bin/c++ -I/build/libgff-2.0.0/include -g -O2 -fdebug-prefix-map=/build/libgff-2.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -D_FILE_OFFSET_BITS=64 -std=c++14 -o CMakeFiles/TestGFFParse.dir/src/TestGFFParse.cpp.o -c /build/libgff-2.0.0/src/TestGFFParse.cpp
/build/libgff-2.0.0/src/TestGFFParse.cpp: In function 'int main(int, char**)':
/build/libgff-2.0.0/src/TestGFFParse.cpp:25:35: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
25 | for (size_t j=0; j < f->attrs->Count(); ++j) {
| ~~^~~~~~~~~~~~~~~~~~~
In file included from /build/libgff-2.0.0/include/GList.hh:8,
from /build/libgff-2.0.0/include/GFastaIndex.h:12,
from /build/libgff-2.0.0/include/GFaSeqGet.h:3,
from /build/libgff-2.0.0/include/gff.h:9,
from /build/libgff-2.0.0/src/TestGFFParse.cpp:5:
/build/libgff-2.0.0/include/GVec.hh: In instantiation of 'void GVec<OBJ>::setCapacity(int) [with OBJ = GMapSeg]':
/build/libgff-2.0.0/include/GVec.hh:202:3: required from 'GVec<OBJ>::GVec(int) [with OBJ = GMapSeg]'
/build/libgff-2.0.0/include/gff.h:126:50: required from here
/build/libgff-2.0.0/include/GVec.hh:291:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GMapSeg'; use assignment or value-initialization instead [-Wclass-memaccess]
291 | memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/libgff-2.0.0/src/TestGFFParse.cpp:5:
/build/libgff-2.0.0/include/gff.h:69:7: note: 'class GMapSeg' declared here
69 | class GMapSeg:public GSeg {
| ^~~~~~~
In file included from /build/libgff-2.0.0/include/GList.hh:8,
from /build/libgff-2.0.0/include/GFastaIndex.h:12,
from /build/libgff-2.0.0/include/GFaSeqGet.h:3,
from /build/libgff-2.0.0/include/gff.h:9,
from /build/libgff-2.0.0/src/TestGFFParse.cpp:5:
/build/libgff-2.0.0/include/GVec.hh: In instantiation of 'void GVec<OBJ>::setCapacity(int) [with OBJ = GSeg]':
/build/libgff-2.0.0/include/GVec.hh:202:3: required from 'GVec<OBJ>::GVec(int) [with OBJ = GSeg]'
/build/libgff-2.0.0/include/gff.h:310:92: required from here
/build/libgff-2.0.0/include/GVec.hh:291:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess]
291 | memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/libgff-2.0.0/include/gff.h:6,
from /build/libgff-2.0.0/src/TestGFFParse.cpp:5:
/build/libgff-2.0.0/include/GBase.h:308:7: note: 'class GSeg' declared here
308 | class GSeg {
| ^~~~
In file included from /build/libgff-2.0.0/include/GList.hh:8,
from /build/libgff-2.0.0/include/GFastaIndex.h:12,
from /build/libgff-2.0.0/include/GFaSeqGet.h:3,
from /build/libgff-2.0.0/include/gff.h:9,
from /build/libgff-2.0.0/src/TestGFFParse.cpp:5:
/build/libgff-2.0.0/include/GVec.hh: In instantiation of 'void GVec<OBJ>::setCapacity(int) [with OBJ = GeneCDS]':
/build/libgff-2.0.0/include/GVec.hh:202:3: required from 'GVec<OBJ>::GVec(int) [with OBJ = GeneCDS]'
/build/libgff-2.0.0/include/gff.h:1349:31: required from here
/build/libgff-2.0.0/include/GVec.hh:291:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GeneCDS'; use assignment or value-initialization instead [-Wclass-memaccess]
291 | memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/libgff-2.0.0/src/TestGFFParse.cpp:5:
/build/libgff-2.0.0/include/gff.h:1338:7: note: 'class GeneCDS' declared here
1338 | class GeneCDS: public GSeg {
| ^~~~~~~
In file included from /build/libgff-2.0.0/include/GList.hh:8,
from /build/libgff-2.0.0/include/GFastaIndex.h:12,
from /build/libgff-2.0.0/include/GFaSeqGet.h:3,
from /build/libgff-2.0.0/include/gff.h:9,
from /build/libgff-2.0.0/src/TestGFFParse.cpp:5:
/build/libgff-2.0.0/include/GVec.hh: In instantiation of 'void GVec<OBJ>::setCapacity(int) [with OBJ = GSegMatch]':
/build/libgff-2.0.0/include/GVec.hh:202:3: required from 'GVec<OBJ>::GVec(int) [with OBJ = GSegMatch]'
/build/libgff-2.0.0/include/GList.hh:191:76: required from 'GArray<OBJ>::GArray(int (*)(pointer, pointer)) [with OBJ = GSegMatch; GCompareProc = int(void*, void*); pointer = void*]'
/build/libgff-2.0.0/include/gff.h:1349:31: required from here
/build/libgff-2.0.0/include/GVec.hh:291:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSegMatch'; use assignment or value-initialization instead [-Wclass-memaccess]
291 | memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/libgff-2.0.0/src/TestGFFParse.cpp:5:
/build/libgff-2.0.0/include/gff.h:1326:7: note: 'class GSegMatch' declared here
1326 | class GSegMatch { //keep track of "matching" overlaps of a GeneCDSChain with multiple GeneSegment containers
| ^~~~~~~~~
In file included from /build/libgff-2.0.0/include/GList.hh:8,
from /build/libgff-2.0.0/include/GFastaIndex.h:12,
from /build/libgff-2.0.0/include/GFaSeqGet.h:3,
from /build/libgff-2.0.0/include/gff.h:9,
from /build/libgff-2.0.0/src/TestGFFParse.cpp:5:
/build/libgff-2.0.0/include/GVec.hh: In instantiation of 'void GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GSegMatch]':
/build/libgff-2.0.0/include/GVec.hh:437:9: required from 'void GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GSegMatch]'
/build/libgff-2.0.0/include/GVec.hh:69:44: required from 'void GVec<OBJ>::Insert(int, OBJ) [with OBJ = GSegMatch]'
/build/libgff-2.0.0/include/GList.hh:234:21: required from 'int GArray<OBJ>::Add(OBJ*) [with OBJ = GSegMatch]'
/build/libgff-2.0.0/include/GList.hh:51:36: required from 'int GArray<OBJ>::Add(OBJ&) [with OBJ = GSegMatch]'
/build/libgff-2.0.0/include/gff.h:1362:22: required from here
/build/libgff-2.0.0/include/GVec.hh:358:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSegMatch'; use assignment or value-initialization instead [-Wclass-memaccess]
358 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/libgff-2.0.0/src/TestGFFParse.cpp:5:
/build/libgff-2.0.0/include/gff.h:1326:7: note: 'class GSegMatch' declared here
1326 | class GSegMatch { //keep track of "matching" overlaps of a GeneCDSChain with multiple GeneSegment containers
| ^~~~~~~~~
[100%] Linking CXX executable TestGFFParse
/usr/bin/cmake -E cmake_link_script CMakeFiles/TestGFFParse.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libgff-2.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -D_FILE_OFFSET_BITS=64 -Wl,-z,relro CMakeFiles/TestGFFParse.dir/src/TestGFFParse.cpp.o -o TestGFFParse libgff.a
make[3]: Leaving directory '/build/libgff-2.0.0/obj-aarch64-linux-gnu'
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make[2]: Leaving directory '/build/libgff-2.0.0/obj-aarch64-linux-gnu'
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make[1]: Entering directory '/build/libgff-2.0.0/obj-aarch64-linux-gnu'
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I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/7001 and its subdirectories
I: Current time: Mon Aug 9 21:49:19 -12 2021
I: pbuilder-time-stamp: 1628588959
Tue Aug 10 09:49:21 UTC 2021 I: 1st build successful. Starting 2nd build on remote node codethink13-arm64.debian.net.
Tue Aug 10 09:49:21 UTC 2021 I: Preparing to do remote build '2' on codethink13-arm64.debian.net.
Tue Aug 10 09:50:16 UTC 2021 I: Deleting $TMPDIR on codethink13-arm64.debian.net.
Tue Aug 10 09:50:17 UTC 2021 I: libgff_2.0.0-1_arm64.changes:
Format: 1.8
Date: Thu, 16 Jul 2020 13:09:49 +0200
Source: libgff
Binary: libgff-dev
Architecture: arm64
Version: 2.0.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Michael R. Crusoe <crusoe@debian.org>
Description:
libgff-dev - GFF/GTF parsing from cufflinks as a library
Changes:
libgff (2.0.0-1) unstable; urgency=medium
.
* New upstream version
Checksums-Sha1:
f80e40a44375a32eb1fa114ca3d7506345e11eb0 146224 libgff-dev_2.0.0-1_arm64.deb
bd8a1cb328fc2e023bd46f516e7e9dd04f654a8f 5316 libgff_2.0.0-1_arm64.buildinfo
Checksums-Sha256:
490108174606a4f1b5002c7b908d97e1a335d95ac5209d36f74a5419f693bb51 146224 libgff-dev_2.0.0-1_arm64.deb
df049eb35f5c8b6ee4a589aab2691130fc27edfe00d329bf6cb2fa8865f53cd4 5316 libgff_2.0.0-1_arm64.buildinfo
Files:
4f67cee004fe9c21035f14c9610bb5a6 146224 libdevel optional libgff-dev_2.0.0-1_arm64.deb
63a81bc8df86e60f3e75d0465072b661 5316 libdevel optional libgff_2.0.0-1_arm64.buildinfo
Tue Aug 10 09:50:18 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.4hTv73dZsU/libgff_2.0.0-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.4hTv73dZsU/libgff_2.0.0-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.4hTv73dZsU/libgff_2.0.0-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.4hTv73dZsU/b1/libgff_2.0.0-1_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.4hTv73dZsU/b2/libgff_2.0.0-1_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: 0.271s)
0.271s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.018s)
0.018s 10 calls diffoscope.comparators.binary.FilesystemFile
0.000s 8 calls abc.DotChangesFile
Tue Aug 10 09:50:22 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists.
Tue Aug 10 09:50:22 UTC 2021 I: libgff from bullseye built successfully and reproducibly on arm64.
Tue Aug 10 09:50:23 UTC 2021 I: Submitting .buildinfo files to external archives:
Tue Aug 10 09:50:23 UTC 2021 I: Submitting 8.0K b1/libgff_2.0.0-1_arm64.buildinfo.asc
Tue Aug 10 09:50:24 UTC 2021 I: Submitting 8.0K b2/libgff_2.0.0-1_arm64.buildinfo.asc
Tue Aug 10 09:50:26 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Tue Aug 10 09:50:26 UTC 2021 I: Done submitting .buildinfo files.
Tue Aug 10 09:50:26 UTC 2021 I: Removing signed libgff_2.0.0-1_arm64.buildinfo.asc files:
removed './b1/libgff_2.0.0-1_arm64.buildinfo.asc'
removed './b2/libgff_2.0.0-1_arm64.buildinfo.asc'