Sun Dec 29 16:41:07 UTC 2024 I: starting to build aegean/unstable/armhf on jenkins on '2024-12-29 16:41'
Sun Dec 29 16:41:07 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_25/12192/console.log
Sun Dec 29 16:41:07 UTC 2024 I: Downloading source for unstable/aegean=0.16.0+dfsg-4
--2024-12-29 16:41:07-- http://deb.debian.org/debian/pool/main/a/aegean/aegean_0.16.0%2bdfsg-4.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2235 (2.2K) [text/prs.lines.tag]
Saving to: ‘aegean_0.16.0+dfsg-4.dsc’
0K .. 100% 357M=0s
2024-12-29 16:41:07 (357 MB/s) - ‘aegean_0.16.0+dfsg-4.dsc’ saved [2235/2235]
Sun Dec 29 16:41:07 UTC 2024 I: aegean_0.16.0+dfsg-4.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: aegean
Binary: aegean
Architecture: amd64 arm64 armel armhf i386 mipsel powerpc ppc64el s390x hurd-i386 kfreebsd-amd64 kfreebsd-i386 ppc64 x32
Version: 0.16.0+dfsg-4
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Sascha Steinbiss <satta@debian.org>
Homepage: https://standage.github.io/AEGeAn
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/aegean
Vcs-Git: https://salsa.debian.org/med-team/aegean.git
Testsuite: autopkgtest
Testsuite-Triggers: python3
Build-Depends: debhelper-compat (= 13), libcairo2-dev, libgenometools0-dev, python3
Package-List:
aegean deb science optional arch=amd64,arm64,armel,armhf,i386,mipsel,powerpc,ppc64el,s390x,hurd-i386,kfreebsd-amd64,kfreebsd-i386,ppc64,x32
Checksums-Sha1:
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00691a8e3c55341d06cb35f66476e5f4b0a23426 9628 aegean_0.16.0+dfsg-4.debian.tar.xz
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18eaae267e4af9c076ea1679286b71f8a242d7e2124d09eb2457acd07b8e1f93 9628 aegean_0.16.0+dfsg-4.debian.tar.xz
Files:
8df4e46ed3a5e4a5e1a5d863e03ba3c9 534860 aegean_0.16.0+dfsg.orig.tar.xz
e15b076adebc76512ba2fa37111644de 9628 aegean_0.16.0+dfsg-4.debian.tar.xz
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Sun Dec 29 16:41:07 UTC 2024 I: Checking whether the package is not for us
Sun Dec 29 16:41:07 UTC 2024 I: Starting 1st build on remote node virt32c-armhf-rb.debian.net.
Sun Dec 29 16:41:07 UTC 2024 I: Preparing to do remote build '1' on virt32c-armhf-rb.debian.net.
Sun Dec 29 16:43:10 UTC 2024 I: Deleting $TMPDIR on virt32c-armhf-rb.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sun Dec 29 04:41:13 -12 2024
I: pbuilder-time-stamp: 1735490473
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [aegean_0.16.0+dfsg-4.dsc]
I: copying [./aegean_0.16.0+dfsg.orig.tar.xz]
I: copying [./aegean_0.16.0+dfsg-4.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./aegean_0.16.0+dfsg-4.dsc: unsupported subcommand
dpkg-source: info: extracting aegean in aegean-0.16.0+dfsg
dpkg-source: info: unpacking aegean_0.16.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking aegean_0.16.0+dfsg-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying add_hardening
dpkg-source: info: applying fix_m64_on_some_archs
dpkg-source: info: applying remove_license
dpkg-source: info: applying adjust_datapath
dpkg-source: info: applying follow_links
dpkg-source: info: applying includepaths
dpkg-source: info: applying 2to3.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/24843/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='armhf'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 '
DISTRIBUTION='unstable'
HOME='/root'
HOST_ARCH='armhf'
IFS='
'
INVOCATION_ID='4889bc0ee5704efeaadccb4453ad2a4e'
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='24843'
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.ESQE6Dbn/pbuilderrc_CT9S --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ESQE6Dbn/b1 --logfile b1/build.log aegean_0.16.0+dfsg-4.dsc'
SUDO_GID='113'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://10.0.0.15:3142/'
I: uname -a
Linux virt32c 6.1.0-28-armmp-lpae #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/24843/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: armhf
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), libcairo2-dev, libgenometools0-dev, python3
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19573 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 libcairo2-dev; however:
Package libcairo2-dev is not installed.
pbuilder-satisfydepends-dummy depends on libgenometools0-dev; however:
Package libgenometools0-dev is not installed.
pbuilder-satisfydepends-dummy depends on python3; however:
Package python3 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} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} genometools-common{a} gettext{a} gettext-base{a} girepository-tools{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblkid-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcairo-gobject2{a} libcairo-script-interpreter2{a} libcairo2{a} libcairo2-dev{a} libcom-err2{a} libdatrie1{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig-dev{a} libfontconfig1{a} libfreetype-dev{a} libfreetype6{a} libfribidi0{a} libgenometools0-dev{a} libgenometools0t64{a} libgio-2.0-dev{a} libgio-2.0-dev-bin{a} libgirepository-2.0-0{a} libglib2.0-0t64{a} libglib2.0-bin{a} libglib2.0-data{a} libglib2.0-dev{a} libglib2.0-dev-bin{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libice-dev{a} libice6{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblua5.1-0{a} liblzo2-2{a} libmagic-mgc{a} libmagic1t64{a} libmount-dev{a} libnsl2{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpipeline1{a} libpixman-1-0{a} libpixman-1-dev{a} libpkgconf3{a} libpng-dev{a} libpng16-16t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} libselinux1-dev{a} libsepol-dev{a} libsm-dev{a} libsm6{a} libsysprof-capture-4-dev{a} libthai-data{a} libthai0{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libtre5{a} libuchardet0{a} libunistring5{a} libx11-6{a} libx11-data{a} libx11-dev{a} libxau-dev{a} libxau6{a} libxcb-render0{a} libxcb-render0-dev{a} libxcb-shm0{a} libxcb-shm0-dev{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxml2{a} libxrender-dev{a} libxrender1{a} lua-md5{a} m4{a} man-db{a} media-types{a} native-architecture{a} netbase{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-minimal{a} python3-packaging{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} uuid-dev{a} x11-common{a} x11proto-core-dev{a} x11proto-dev{a} xorg-sgml-doctools{a} xtrans-dev{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libltdl-dev libmail-sendmail-perl libpng-tools lynx shared-mime-info wget xdg-user-dirs
0 packages upgraded, 141 newly installed, 0 to remove and 0 not upgraded.
Need to get 46.8 MB of archives. After unpacking 162 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main armhf libpython3.12-minimal armhf 3.12.8-3 [802 kB]
Get: 2 http://deb.debian.org/debian unstable/main armhf libexpat1 armhf 2.6.4-1 [83.5 kB]
Get: 3 http://deb.debian.org/debian unstable/main armhf python3.12-minimal armhf 3.12.8-3 [1794 kB]
Get: 4 http://deb.debian.org/debian unstable/main armhf python3-minimal armhf 3.12.8-1 [26.9 kB]
Get: 5 http://deb.debian.org/debian unstable/main armhf media-types all 10.1.0 [26.9 kB]
Get: 6 http://deb.debian.org/debian unstable/main armhf netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian unstable/main armhf tzdata all 2024b-4 [256 kB]
Get: 8 http://deb.debian.org/debian unstable/main armhf libffi8 armhf 3.4.6-1 [20.0 kB]
Get: 9 http://deb.debian.org/debian unstable/main armhf libkrb5support0 armhf 1.21.3-3 [30.0 kB]
Get: 10 http://deb.debian.org/debian unstable/main armhf libcom-err2 armhf 1.47.2~rc1-2 [22.9 kB]
Get: 11 http://deb.debian.org/debian unstable/main armhf libk5crypto3 armhf 1.21.3-3 [75.8 kB]
Get: 12 http://deb.debian.org/debian unstable/main armhf libkeyutils1 armhf 1.6.3-4 [8096 B]
Get: 13 http://deb.debian.org/debian unstable/main armhf libkrb5-3 armhf 1.21.3-3 [283 kB]
Get: 14 http://deb.debian.org/debian unstable/main armhf libgssapi-krb5-2 armhf 1.21.3-3 [114 kB]
Get: 15 http://deb.debian.org/debian unstable/main armhf libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get: 16 http://deb.debian.org/debian unstable/main armhf libtirpc3t64 armhf 1.3.4+ds-1.3+b1 [71.3 kB]
Get: 17 http://deb.debian.org/debian unstable/main armhf libnsl2 armhf 1.3.0-3+b3 [35.0 kB]
Get: 18 http://deb.debian.org/debian unstable/main armhf readline-common all 8.2-6 [69.4 kB]
Get: 19 http://deb.debian.org/debian unstable/main armhf libreadline8t64 armhf 8.2-6 [146 kB]
Get: 20 http://deb.debian.org/debian unstable/main armhf libpython3.12-stdlib armhf 3.12.8-3 [1824 kB]
Get: 21 http://deb.debian.org/debian unstable/main armhf python3.12 armhf 3.12.8-3 [677 kB]
Get: 22 http://deb.debian.org/debian unstable/main armhf libpython3-stdlib armhf 3.12.8-1 [9792 B]
Get: 23 http://deb.debian.org/debian unstable/main armhf python3 armhf 3.12.8-1 [27.9 kB]
Get: 24 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB]
Get: 25 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB]
Get: 26 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB]
Get: 27 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3+b1 [42.3 kB]
Get: 28 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.22.5-3 [195 kB]
Get: 29 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB]
Get: 30 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-7 [1095 kB]
Get: 31 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.2-13 [84.7 kB]
Get: 32 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB]
Get: 33 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB]
Get: 34 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-4 [264 kB]
Get: 35 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB]
Get: 36 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get: 37 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get: 38 http://deb.debian.org/debian unstable/main armhf autopoint all 0.22.5-3 [723 kB]
Get: 39 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.23 [90.6 kB]
Get: 40 http://deb.debian.org/debian unstable/main armhf libtool all 2.4.7-8 [517 kB]
Get: 41 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB]
Get: 42 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get: 43 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 44 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 45 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.192-4 [184 kB]
Get: 46 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB]
Get: 47 http://deb.debian.org/debian unstable/main armhf libunistring5 armhf 1.3-1 [444 kB]
Get: 48 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-5+b1 [9088 kB]
Get: 49 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB]
Get: 50 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.22.5-3 [1488 kB]
Get: 51 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 52 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 53 http://deb.debian.org/debian unstable/main armhf debhelper all 13.23 [919 kB]
Get: 54 http://deb.debian.org/debian unstable/main armhf libbrotli1 armhf 1.1.0-2+b6 [282 kB]
Get: 55 http://deb.debian.org/debian unstable/main armhf libpng16-16t64 armhf 1.6.44-3 [263 kB]
Get: 56 http://deb.debian.org/debian unstable/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [385 kB]
Get: 57 http://deb.debian.org/debian unstable/main armhf fonts-dejavu-mono all 2.37-8 [489 kB]
Get: 58 http://deb.debian.org/debian unstable/main armhf fonts-dejavu-core all 2.37-8 [840 kB]
Get: 59 http://deb.debian.org/debian unstable/main armhf fontconfig-config armhf 2.15.0-1.1+b1 [318 kB]
Get: 60 http://deb.debian.org/debian unstable/main armhf libfontconfig1 armhf 2.15.0-1.1+b1 [371 kB]
Get: 61 http://deb.debian.org/debian unstable/main armhf fontconfig armhf 2.15.0-1.1+b1 [461 kB]
Get: 62 http://deb.debian.org/debian unstable/main armhf liblua5.1-0 armhf 5.1.5-10 [88.7 kB]
Get: 63 http://deb.debian.org/debian unstable/main armhf libpixman-1-0 armhf 0.44.0-3 [164 kB]
Get: 64 http://deb.debian.org/debian unstable/main armhf libxau6 armhf 1:1.0.11-1 [19.7 kB]
Get: 65 http://deb.debian.org/debian unstable/main armhf libxdmcp6 armhf 1:1.1.5-1 [26.4 kB]
Get: 66 http://deb.debian.org/debian unstable/main armhf libxcb1 armhf 1.17.0-2+b1 [140 kB]
Get: 67 http://deb.debian.org/debian unstable/main armhf libx11-data all 2:1.8.10-2 [337 kB]
Get: 68 http://deb.debian.org/debian unstable/main armhf libx11-6 armhf 2:1.8.10-2 [750 kB]
Get: 69 http://deb.debian.org/debian unstable/main armhf libxcb-render0 armhf 1.17.0-2+b1 [114 kB]
Get: 70 http://deb.debian.org/debian unstable/main armhf libxcb-shm0 armhf 1.17.0-2+b1 [105 kB]
Get: 71 http://deb.debian.org/debian unstable/main armhf libxext6 armhf 2:1.3.4-1+b2 [45.2 kB]
Get: 72 http://deb.debian.org/debian unstable/main armhf libxrender1 armhf 1:0.9.10-1.1+b3 [25.0 kB]
Get: 73 http://deb.debian.org/debian unstable/main armhf libcairo2 armhf 1.18.2-2 [443 kB]
Get: 74 http://deb.debian.org/debian unstable/main armhf libfribidi0 armhf 1.0.16-1 [24.6 kB]
Get: 75 http://deb.debian.org/debian unstable/main armhf libglib2.0-0t64 armhf 2.82.4-1 [1327 kB]
Get: 76 http://deb.debian.org/debian unstable/main armhf libgraphite2-3 armhf 1.3.14-2+b1 [63.1 kB]
Get: 77 http://deb.debian.org/debian unstable/main armhf libharfbuzz0b armhf 10.1.0-2 [420 kB]
Get: 78 http://deb.debian.org/debian unstable/main armhf libthai-data all 0.1.29-2 [168 kB]
Get: 79 http://deb.debian.org/debian unstable/main armhf libdatrie1 armhf 0.2.13-3+b1 [34.7 kB]
Get: 80 http://deb.debian.org/debian unstable/main armhf libthai0 armhf 0.1.29-2+b1 [46.0 kB]
Get: 81 http://deb.debian.org/debian unstable/main armhf libpango-1.0-0 armhf 1.55.0+ds-3 [200 kB]
Get: 82 http://deb.debian.org/debian unstable/main armhf libpangoft2-1.0-0 armhf 1.55.0+ds-3 [47.7 kB]
Get: 83 http://deb.debian.org/debian unstable/main armhf libpangocairo-1.0-0 armhf 1.55.0+ds-3 [31.3 kB]
Get: 84 http://deb.debian.org/debian unstable/main armhf libtre5 armhf 0.8.0-8 [53.6 kB]
Get: 85 http://deb.debian.org/debian unstable/main armhf genometools-common all 1.6.5+ds-2.2 [195 kB]
Get: 86 http://deb.debian.org/debian unstable/main armhf native-architecture all 0.2.3 [2108 B]
Get: 87 http://deb.debian.org/debian unstable/main armhf libgirepository-2.0-0 armhf 2.82.4-1 [125 kB]
Get: 88 http://deb.debian.org/debian unstable/main armhf girepository-tools armhf 2.82.4-1 [133 kB]
Get: 89 http://deb.debian.org/debian unstable/main armhf uuid-dev armhf 2.40.2-13 [45.7 kB]
Get: 90 http://deb.debian.org/debian unstable/main armhf libblkid-dev armhf 2.40.2-13 [187 kB]
Get: 91 http://deb.debian.org/debian unstable/main armhf libbrotli-dev armhf 1.1.0-2+b6 [293 kB]
Get: 92 http://deb.debian.org/debian unstable/main armhf libbz2-dev armhf 1.0.8-6 [28.7 kB]
Get: 93 http://deb.debian.org/debian unstable/main armhf libcairo-gobject2 armhf 1.18.2-2 [129 kB]
Get: 94 http://deb.debian.org/debian unstable/main armhf liblzo2-2 armhf 2.10-3+b1 [48.5 kB]
Get: 95 http://deb.debian.org/debian unstable/main armhf libcairo-script-interpreter2 armhf 1.18.2-2 [49.9 kB]
Get: 96 http://deb.debian.org/debian unstable/main armhf libexpat1-dev armhf 2.6.4-1 [140 kB]
Get: 97 http://deb.debian.org/debian unstable/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB]
Get: 98 http://deb.debian.org/debian unstable/main armhf libpng-dev armhf 1.6.44-3 [349 kB]
Get: 99 http://deb.debian.org/debian unstable/main armhf libfreetype-dev armhf 2.13.3+dfsg-1 [561 kB]
Get: 100 http://deb.debian.org/debian unstable/main armhf libpkgconf3 armhf 1.8.1-4 [31.8 kB]
Get: 101 http://deb.debian.org/debian unstable/main armhf pkgconf-bin armhf 1.8.1-4 [29.2 kB]
Get: 102 http://deb.debian.org/debian unstable/main armhf pkgconf armhf 1.8.1-4 [26.1 kB]
Get: 103 http://deb.debian.org/debian unstable/main armhf libfontconfig-dev armhf 2.15.0-1.1+b1 [397 kB]
Get: 104 http://deb.debian.org/debian unstable/main armhf libffi-dev armhf 3.4.6-1 [55.9 kB]
Get: 105 http://deb.debian.org/debian unstable/main armhf libsepol-dev armhf 3.7-1 [338 kB]
Get: 106 http://deb.debian.org/debian unstable/main armhf libpcre2-16-0 armhf 10.44-5 [226 kB]
Get: 107 http://deb.debian.org/debian unstable/main armhf libpcre2-32-0 armhf 10.44-5 [216 kB]
Get: 108 http://deb.debian.org/debian unstable/main armhf libpcre2-posix3 armhf 10.44-5 [59.8 kB]
Get: 109 http://deb.debian.org/debian unstable/main armhf libpcre2-dev armhf 10.44-5 [702 kB]
Get: 110 http://deb.debian.org/debian unstable/main armhf libselinux1-dev armhf 3.7-3+b1 [154 kB]
Get: 111 http://deb.debian.org/debian unstable/main armhf libmount-dev armhf 2.40.2-13 [29.2 kB]
Get: 112 http://deb.debian.org/debian unstable/main armhf libsysprof-capture-4-dev armhf 47.2-1 [45.1 kB]
Get: 113 http://deb.debian.org/debian unstable/main armhf libgio-2.0-dev armhf 2.82.4-1 [1560 kB]
Get: 114 http://deb.debian.org/debian unstable/main armhf libglib2.0-data all 2.82.4-1 [1276 kB]
Get: 115 http://deb.debian.org/debian unstable/main armhf libglib2.0-bin armhf 2.82.4-1 [120 kB]
Get: 116 http://deb.debian.org/debian unstable/main armhf python3-packaging all 24.2-1 [55.3 kB]
Get: 117 http://deb.debian.org/debian unstable/main armhf libgio-2.0-dev-bin armhf 2.82.4-1 [160 kB]
Get: 118 http://deb.debian.org/debian unstable/main armhf libglib2.0-dev-bin armhf 2.82.4-1 [52.0 kB]
Get: 119 http://deb.debian.org/debian unstable/main armhf libglib2.0-dev armhf 2.82.4-1 [52.7 kB]
Get: 120 http://deb.debian.org/debian unstable/main armhf libpixman-1-dev armhf 0.44.0-3 [11.4 kB]
Get: 121 http://deb.debian.org/debian unstable/main armhf x11-common all 1:7.7+23.1 [216 kB]
Get: 122 http://deb.debian.org/debian unstable/main armhf libice6 armhf 2:1.1.1-1 [58.5 kB]
Get: 123 http://deb.debian.org/debian unstable/main armhf libsm6 armhf 2:1.2.4-1 [33.5 kB]
Get: 124 http://deb.debian.org/debian unstable/main armhf xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB]
Get: 125 http://deb.debian.org/debian unstable/main armhf x11proto-dev all 2024.1-1 [603 kB]
Get: 126 http://deb.debian.org/debian unstable/main armhf x11proto-core-dev all 2024.1-1 [3312 B]
Get: 127 http://deb.debian.org/debian unstable/main armhf libice-dev armhf 2:1.1.1-1 [69.0 kB]
Get: 128 http://deb.debian.org/debian unstable/main armhf libsm-dev armhf 2:1.2.4-1 [36.7 kB]
Get: 129 http://deb.debian.org/debian unstable/main armhf libxau-dev armhf 1:1.0.11-1 [23.0 kB]
Get: 130 http://deb.debian.org/debian unstable/main armhf libxdmcp-dev armhf 1:1.1.5-1 [42.9 kB]
Get: 131 http://deb.debian.org/debian unstable/main armhf xtrans-dev all 1.4.0-1 [98.7 kB]
Get: 132 http://deb.debian.org/debian unstable/main armhf libxcb1-dev armhf 1.17.0-2+b1 [180 kB]
Get: 133 http://deb.debian.org/debian unstable/main armhf libx11-dev armhf 2:1.8.10-2 [825 kB]
Get: 134 http://deb.debian.org/debian unstable/main armhf libxcb-render0-dev armhf 1.17.0-2+b1 [118 kB]
Get: 135 http://deb.debian.org/debian unstable/main armhf libxcb-shm0-dev armhf 1.17.0-2+b1 [108 kB]
Get: 136 http://deb.debian.org/debian unstable/main armhf libxext-dev armhf 2:1.3.4-1+b2 [100 kB]
Get: 137 http://deb.debian.org/debian unstable/main armhf libxrender-dev armhf 1:0.9.10-1.1+b3 [33.0 kB]
Get: 138 http://deb.debian.org/debian unstable/main armhf libcairo2-dev armhf 1.18.2-2 [43.0 kB]
Get: 139 http://deb.debian.org/debian unstable/main armhf lua-md5 armhf 1.2+git+1+8d87fee-2+b2 [11.8 kB]
Get: 140 http://deb.debian.org/debian unstable/main armhf libgenometools0t64 armhf 1.6.5+ds-2.2 [1266 kB]
Get: 141 http://deb.debian.org/debian unstable/main armhf libgenometools0-dev armhf 1.6.5+ds-2.2 [95.2 kB]
Fetched 46.8 MB in 1s (55.8 MB/s)
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Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3 to /lib/arm-linux-gnueabihf/libtirpc.so.3.usr-is-merged by libtirpc3t64'
Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0 to /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
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Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64'
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Setting up media-types (10.1.0) ...
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invoke-rc.d: could not determine current runlevel
Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix.
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Setting up tzdata (2024b-4) ...
Current default time zone: 'Etc/UTC'
Local time is now: Sun Dec 29 16:42:08 UTC 2024.
Universal Time is now: Sun Dec 29 16:42:08 UTC 2024.
Run 'dpkg-reconfigure tzdata' if you wish to change it.
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Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Setting up intltool-debian (0.35.0+20060710.6) ...
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No schema files found: doing nothing.
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Setting up libfontconfig1:armhf (2.15.0-1.1+b1) ...
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Setting up libmount-dev:armhf (2.40.2-13) ...
Setting up fontconfig (2.15.0-1.1+b1) ...
Regenerating fonts cache... done.
Setting up libgio-2.0-dev:armhf (2.82.4-1) ...
Setting up libxcb1-dev:armhf (1.17.0-2+b1) ...
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Setting up po-debconf (1.0.21+nmu1) ...
Setting up libpango-1.0-0:armhf (1.55.0+ds-3) ...
Setting up libx11-dev:armhf (2:1.8.10-2) ...
Setting up libglib2.0-bin (2.82.4-1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
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Setting up libxcb-render0-dev:armhf (1.17.0-2+b1) ...
Setting up libxext-dev:armhf (2:1.3.4-1+b2) ...
Setting up libnsl2:armhf (1.3.0-3+b3) ...
Setting up libcairo-gobject2:armhf (1.18.2-2) ...
Setting up libpangoft2-1.0-0:armhf (1.55.0+ds-3) ...
Setting up libxrender-dev:armhf (1:0.9.10-1.1+b3) ...
Setting up libpangocairo-1.0-0:armhf (1.55.0+ds-3) ...
Setting up libcairo-script-interpreter2:armhf (1.18.2-2) ...
Setting up girepository-tools:armhf (2.82.4-1) ...
Setting up libpython3.12-stdlib:armhf (3.12.8-3) ...
Setting up libfontconfig-dev:armhf (2.15.0-1.1+b1) ...
Setting up python3.12 (3.12.8-3) ...
Setting up debhelper (13.23) ...
Setting up genometools-common (1.6.5+ds-2.2) ...
Setting up libpython3-stdlib:armhf (3.12.8-1) ...
Setting up python3 (3.12.8-1) ...
Setting up python3-packaging (24.2-1) ...
Setting up libgenometools0t64 (1.6.5+ds-2.2) ...
Setting up libgio-2.0-dev-bin (2.82.4-1) ...
Setting up libgenometools0-dev (1.6.5+ds-2.2) ...
Setting up libglib2.0-dev-bin (2.82.4-1) ...
Setting up libglib2.0-dev:armhf (2.82.4-1) ...
Setting up libcairo2-dev:armhf (1.18.2-2) ...
Processing triggers for libc-bin (2.40-4) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/aegean-0.16.0+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 > ../aegean_0.16.0+dfsg-4_source.changes
dpkg-buildpackage: info: source package aegean
dpkg-buildpackage: info: source version 0.16.0+dfsg-4
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Sascha Steinbiss <satta@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg'
dh_auto_clean
make -j3 clean
make[2]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg'
rm -rf bin/parseval bin/canon-gff3 bin/locuspocus bin/gaeval bin/xtractore bin/pmrna bin/tidygff3 bin/unittests libaegean.a obj/AgnAttributeFilterStream.o obj/AgnCliquePair.o obj/AgnCompareReportHTML.o obj/AgnCompareReportText.o obj/AgnComparison.o obj/AgnFilterStream.o obj/AgnGaevalVisitor.o obj/AgnGeneStream.o obj/AgnInferCDSVisitor.o obj/AgnInferExonsVisitor.o obj/AgnInferParentStream.o obj/AgnLocus.o obj/AgnLocusFilterStream.o obj/AgnLocusMapVisitor.o obj/AgnLocusRefineStream.o obj/AgnLocusStream.o obj/AgnMrnaRepVisitor.o obj/AgnPseudogeneFixVisitor.o obj/AgnRemoveChildrenVisitor.o obj/AgnTranscriptClique.o obj/AgnTypecheck.o obj/AgnUnitTest.o obj/AgnUtils.o inc/core/AgnVersion.h bin/*.dSYM
make[2]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg'
rm -f /build/reproducible-path/aegean-0.16.0+dfsg/README
make[1]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg'
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg'
dh_auto_build -- prefix=/build/reproducible-path/aegean-0.16.0+dfsg/debian/tmp 64bit=no errorcheck=no
make -j3 "INSTALL=install --strip-program=true" prefix=/build/reproducible-path/aegean-0.16.0\+dfsg/debian/tmp 64bit=no errorcheck=no
make[2]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg'
[print inc/core/AgnVersion.h]
/build/reproducible-path/aegean-0.16.0+dfsg/data/scripts/version.py:31: SyntaxWarning: invalid escape sequence '\S'
sha1match = re.search('commit (\S+)', logout)
/build/reproducible-path/aegean-0.16.0+dfsg/data/scripts/version.py:37: SyntaxWarning: invalid escape sequence '\s'
yearmatch = re.search('Date:\s+.+(\d{4}) ', logout)
[compile AgnAttributeFilterStream]
[compile AgnCliquePair]
[compile AgnCompareReportHTML]
[compile AgnCompareReportText]
src/core/AgnCompareReportText.c: In function ‘compare_report_text_comp_class_summary’:
src/core/AgnCompareReportText.c:287:3: warning: ‘__builtin___strncpy_chk’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
287 | strncpy(header + 4, label, strlen(label));
| ^
src/core/AgnCompareReportText.c:287:3: note: length computed here
287 | strncpy(header + 4, label, strlen(label));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/core/AgnCompareReportText.c: In function ‘compare_report_text_summary_struc’:
src/core/AgnCompareReportText.c:589:3: warning: ‘__builtin___strncpy_chk’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
589 | strncpy(buffer + 14, units, strlen(units));
| ^
src/core/AgnCompareReportText.c:589:3: note: length computed here
589 | strncpy(buffer + 14, units, strlen(units));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/core/AgnCompareReportText.c:599:3: warning: ‘__builtin___strncpy_chk’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
599 | strncpy(buffer + 15, units, strlen(units));
| ^
src/core/AgnCompareReportText.c:599:3: note: length computed here
599 | strncpy(buffer + 15, units, strlen(units));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[compile AgnComparison]
[compile AgnFilterStream]
[compile AgnGaevalVisitor]
[compile AgnGeneStream]
[compile AgnInferCDSVisitor]
[compile AgnInferExonsVisitor]
[compile AgnInferParentStream]
src/core/AgnInferExonsVisitor.c: In function ‘infer_exons_visitor_visit_gene_collapse_feature’:
src/core/AgnInferExonsVisitor.c:325:34: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
325 | gt_logger_log(v->logger, "[AgnInferExonsVisitor::infer_exons_visitor"
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
326 | "_visit_gene_collapse_feature] mRNA ID is too long (%lu "
327 | "characters), will be truncated\n", strlen(tid));
| ~~~~~~~~~~~
| |
| size_t {aka unsigned int}
src/core/AgnInferExonsVisitor.c:326:77: note: format string is defined here
326 | "_visit_gene_collapse_feature] mRNA ID is too long (%lu "
| ~~^
| |
| long unsigned int
| %u
[compile AgnLocus]
[compile AgnLocusFilterStream]
[compile AgnLocusMapVisitor]
[compile AgnLocusRefineStream]
[compile AgnLocusStream]
[compile AgnMrnaRepVisitor]
[compile AgnPseudogeneFixVisitor]
[compile AgnRemoveChildrenVisitor]
[compile AgnTranscriptClique]
[compile AgnTypecheck]
[compile AgnUnitTest]
[compile AgnUtils]
[compile ParsEval]
[compile CanonGFF3]
[compile LocusPocus]
[compile GAEVAL]
[compile Xtractore]
[compile bin/pmrna]
[compile bin/tidygff3]
[compile unit tests]
[create libaegean]
ar: `u' modifier ignored since `D' is the default (see `U')
ar: creating libaegean.a
make[2]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg'
make[1]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg'
dh_auto_test -- useshared=yes 64bit=no testthreads=5
make -j3 test useshared=yes 64bit=no testthreads=5
make[2]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg'
AEGeAn Unit Tests
AEGeAn::AgnAttributeFilterStream | SUCCESS
| Pogonomyrmex barbatus (partial) | PASS
AEGeAn::AgnPseudogeneFixVisitor | SUCCESS
| Gene, no pseudo attribute | PASS
| Gene, bogus pseudo attribute | PASS
| Corrected pseudogene | PASS
| Uncorrected pseudogene | PASS
| iLocus with gene & pseudogene | PASS
AEGeAn::AgnInferParentStream | SUCCESS
| Test 1: basic | PASS
| Test 2: 2 top-level | PASS
| Test 3: 2 top-level, inferred parent | PASS
| Test 4: multichild | PASS
| Test 5: multichild, inferred parent | PASS
AEGeAn::AgnMrnaRepVisitor | SUCCESS
| TAIR10: test 1 | PASS
AEGeAn::AgnRemoveChildrenVisitor | SUCCESS
| Test 1: grape (Gaze) | PASS
AEGeAn::AgnTranscriptClique | SUCCESS
| simple check | PASS
| two mRNAs | PASS
| copy check | PASS
AEGeAn::AgnCliquePair | SUCCESS
| perfect match vs. self | PASS
| CDS match | PASS
| non-match | PASS
AEGeAn::AgnLocus | SUCCESS
| grape test 1 | PASS
| grape test 2 | PASS
| filter by CDS length | PASS
| filter by exon number | PASS
AEGeAn::AgnFilterStream | SUCCESS
| mRNA | PASS
| exon | PASS
| CDS | PASS
| intron | PASS
| exon+intron | PASS
| CDS+intron | PASS
AEGeAn::AgnInferCDSVisitor | SUCCESS
| grape test sans UTRs | PASS
| grape test with UTRs, strand check | PASS
| grape test 3 | PASS
| grape test 4 | PASS
AEGeAn::AgnInferExonsVisitor | SUCCESS
| grape test sans UTRs | PASS
| grape test with UTRs, strand check | PASS
| grape test 3 | PASS
| grape test 4 | PASS
AEGeAn::AgnGeneStream | SUCCESS
| 1 gene, 2 mRNAs | PASS
| 1 gene, 2 mRNAs (one sans CDS) | PASS
| mRNA only | PASS
| mRNA boundaries | PASS
AEGeAn::AgnLocusStream | SUCCESS
| grape test (pairwise) | PASS
| Pdom test (pairwise) | PASS
| Amel test (Augustus) | PASS
| Delta=200 | PASS
AEGeAn::AgnLocusRefineStream | SUCCESS
| Atta cephalotes (syndrome): coords | PASS
| Atta cephalotes (syndrome): elen | PASS
| Megachile rotundata CST: coords | PASS
| Megachile rotundata CST: elen | PASS
AEGeAn::AgnGaevalVisitor | SUCCESS
| range intersect (1) | PASS
| range intersect (2) | PASS
| range intersect (3) | PASS
| union (1) | PASS
| union (2) | PASS
| union (3) | PASS
| intersect (1) | PASS
| intersect (2) | PASS
| intersect (3) | PASS
| intersect (4) | PASS
| intersect (5) | PASS
| calculate coverage | PASS
| introns confirmed (no gaps) | PASS
| introns confirmed (gaps) | PASS
| calculate integrity | PASS
===== Unit tests passed for all 15 classes! =====
AEGeAn Functional Tests
GFF3 I/O: 'AT1G05320'
| codons | PASS
| sansexons | PASS
| sansutrs | PASS
| withprot | PASS
GFF3 I/O: 'FBgn0035002'
| codons | PASS
| sansexons | PASS
| sansutrs | PASS
AEGeAn::LocusPocus
| default | PASS
| end skip | PASS
| Apis mellifera plap | PASS
| Apis mellifera plap (CDS) | PASS
| Apis mellifera LSM | PASS
| Megachile rotundata CST (intron) | PASS
| iiLocus lengths (Amel OGS Group7.16) | PASS
| Nasonia vitripennis (intron gene) | PASS
| A. echinatior (intron gene + ncRNA) | PASS
AEGeAn::Xtractore
| major royal jelly | PASS
AEGeAn::CanonGFF3
| A. mellifera gene multitrans | PASS
AEGeAn::GAEVAL
| sans CDS | PASS
| Pdom | PASS
AEGeAn::ParsEval
| Amel Group7.16 (text) | PASS
| Amel Group7.16 (delta=500) | PASS
| Amel Group7.16 (HTML) | PASS
AEGeAn::align-convert.py
| GAEVAL example1 | PASS
| GAEVAL example5 | PASS
AEGeAn::pmrna
| A. mellifera Shal | PASS
| A. mellifera dock | PASS
| A. mellifera pseudo | PASS
AEGeAn::tidygff3
| A. dorsata exception | PASS
make[2]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg'
make[1]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg'
create-stamp debian/debhelper-build-stamp
dh_prep
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg'
dh_auto_install -- 64bit=no prefix=/build/reproducible-path/aegean-0.16.0+dfsg/debian/tmp
make -j3 install DESTDIR=/build/reproducible-path/aegean-0.16.0\+dfsg/debian/aegean AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" 64bit=no prefix=/build/reproducible-path/aegean-0.16.0\+dfsg/debian/tmp
make[2]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg'
cp bin/parseval bin/canon-gff3 bin/locuspocus bin/gaeval bin/xtractore bin/pmrna bin/tidygff3 /build/reproducible-path/aegean-0.16.0+dfsg/debian/tmp/bin/.
cp libaegean.a /build/reproducible-path/aegean-0.16.0+dfsg/debian/tmp/lib/.
cp inc/core/*.h /build/reproducible-path/aegean-0.16.0+dfsg/debian/tmp/include/aegean/.
cp -r data/share/* /build/reproducible-path/aegean-0.16.0+dfsg/debian/tmp/share/aegean/.
make[2]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg'
make[1]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg'
dh_install
debian/rules override_dh_installdocs
make[1]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg'
cp /build/reproducible-path/aegean-0.16.0+dfsg/README.md /build/reproducible-path/aegean-0.16.0+dfsg/README
dh_installdocs
make[1]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg'
dh_installchangelogs
dh_installman
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
debian/rules override_dh_missing
make[1]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg'
dh_missing --list-missing
dh_missing: warning: bin/canon-gff3 exists in debian/tmp but is not installed to anywhere (related file: "bin/canon-gff3")
dh_missing: warning: bin/gaeval exists in debian/tmp but is not installed to anywhere (related file: "bin/gaeval")
dh_missing: warning: bin/locuspocus exists in debian/tmp but is not installed to anywhere (related file: "bin/locuspocus")
dh_missing: warning: bin/parseval exists in debian/tmp but is not installed to anywhere (related file: "bin/parseval")
dh_missing: warning: bin/pmrna exists in debian/tmp but is not installed to anywhere (related file: "bin/pmrna")
dh_missing: warning: bin/tidygff3 exists in debian/tmp but is not installed to anywhere (related file: "bin/tidygff3")
dh_missing: warning: bin/xtractore exists in debian/tmp but is not installed to anywhere (related file: "bin/xtractore")
dh_missing: warning: include/aegean/AgnAttributeFilterStream.h exists in debian/tmp but is not installed to anywhere
dh_missing: warning: include/aegean/AgnCliquePair.h exists in debian/tmp but is not installed to anywhere
dh_missing: warning: include/aegean/AgnCompareReportHTML.h exists in debian/tmp but is not installed to anywhere
dh_missing: warning: include/aegean/AgnCompareReportText.h exists in debian/tmp but is not installed to anywhere
dh_missing: warning: include/aegean/AgnComparison.h exists in debian/tmp but is not installed to anywhere
dh_missing: warning: include/aegean/AgnFilterStream.h exists in debian/tmp but is not installed to anywhere
dh_missing: warning: include/aegean/AgnGaevalVisitor.h exists in debian/tmp but is not installed to anywhere
dh_missing: warning: include/aegean/AgnGeneStream.h exists in debian/tmp but is not installed to anywhere
dh_missing: warning: include/aegean/AgnInferCDSVisitor.h exists in debian/tmp but is not installed to anywhere
dh_missing: warning: include/aegean/AgnInferExonsVisitor.h exists in debian/tmp but is not installed to anywhere
dh_missing: warning: include/aegean/AgnInferParentStream.h exists in debian/tmp but is not installed to anywhere
dh_missing: warning: include/aegean/AgnLocus.h exists in debian/tmp but is not installed to anywhere
dh_missing: warning: include/aegean/AgnLocusFilterStream.h exists in debian/tmp but is not installed to anywhere
dh_missing: warning: include/aegean/AgnLocusMapVisitor.h exists in debian/tmp but is not installed to anywhere
dh_missing: warning: include/aegean/AgnLocusRefineStream.h exists in debian/tmp but is not installed to anywhere
dh_missing: warning: include/aegean/AgnLocusStream.h exists in debian/tmp but is not installed to anywhere
dh_missing: warning: include/aegean/AgnMrnaRepVisitor.h exists in debian/tmp but is not installed to anywhere
dh_missing: warning: include/aegean/AgnPseudogeneFixVisitor.h exists in debian/tmp but is not installed to anywhere
dh_missing: warning: include/aegean/AgnRemoveChildrenVisitor.h exists in debian/tmp but is not installed to anywhere
dh_missing: warning: include/aegean/AgnTranscriptClique.h exists in debian/tmp but is not installed to anywhere
dh_missing: warning: include/aegean/AgnTypecheck.h exists in debian/tmp but is not installed to anywhere
dh_missing: warning: include/aegean/AgnUnitTest.h exists in debian/tmp but is not installed to anywhere
dh_missing: warning: include/aegean/AgnUtils.h exists in debian/tmp but is not installed to anywhere
dh_missing: warning: include/aegean/AgnVersion.h exists in debian/tmp but is not installed to anywhere
dh_missing: warning: include/aegean/aegean.h exists in debian/tmp but is not installed to anywhere
dh_missing: warning: lib/libaegean.a exists in debian/tmp but is not installed to anywhere
While detecting missing files, dh_missing noted some files with a similar name to those
that were missing. This warning /might/ be resolved by replacing references to the
missing files with the similarly named ones that dh_missing found - assuming the content
is identical.
As an example, you might want to replace:
* bin/canon-gff3
with:
* bin/canon-gff3
in a file in debian/ or as argument to one of the dh_* tools called from debian/rules.
(Note it is possible the paths are not used verbatim but instead directories
containing or globs matching them are used instead)
Alternatively, add the missing file to debian/not-installed if it cannot and should not
be used.
The following debhelper tools have reported what they installed (with files per package)
* dh_install: aegean (8)
* dh_installdocs: aegean (1)
* dh_installman: aegean (7)
If the missing files are installed by another tool, please file a bug against it.
When filing the report, if the tool is not part of debhelper itself, please reference the
"Logging helpers and dh_missing" section from the "PROGRAMMING" guide for debhelper (10.6.3+).
(in the debhelper package: /usr/share/doc/debhelper/PROGRAMMING.md.gz)
Be sure to test with dpkg-buildpackage -A/-B as the results may vary when only a subset is built
If the omission is intentional or no other helper can take care of this consider adding the
paths to debian/not-installed.
make[1]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg'
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib/ld-linux-armhf.so.3
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'aegean' in '../aegean_0.16.0+dfsg-4_armhf.deb'.
dpkg-deb: building package 'aegean-dbgsym' in '../aegean-dbgsym_0.16.0+dfsg-4_armhf.deb'.
dpkg-genbuildinfo --build=binary -O../aegean_0.16.0+dfsg-4_armhf.buildinfo
dpkg-genchanges --build=binary -O../aegean_0.16.0+dfsg-4_armhf.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: 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/24843 and its subdirectories
I: Current time: Sun Dec 29 04:42:59 -12 2024
I: pbuilder-time-stamp: 1735490579
Sun Dec 29 16:43:13 UTC 2024 I: 1st build successful. Starting 2nd build on remote node virt64z-armhf-rb.debian.net.
Sun Dec 29 16:43:13 UTC 2024 I: Preparing to do remote build '2' on virt64z-armhf-rb.debian.net.
Sun Dec 29 16:46:29 UTC 2024 I: Deleting $TMPDIR on virt64z-armhf-rb.debian.net.
Sun Dec 29 16:46:31 UTC 2024 I: aegean_0.16.0+dfsg-4_armhf.changes:
Format: 1.8
Date: Mon, 01 Apr 2024 19:49:51 +0200
Source: aegean
Binary: aegean aegean-dbgsym
Architecture: armhf
Version: 0.16.0+dfsg-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Sascha Steinbiss <satta@debian.org>
Description:
aegean - integrated genome analysis toolkit
Closes: 1068178
Changes:
aegean (0.16.0+dfsg-4) unstable; urgency=medium
.
* Remove explicit runtime dependency on libgenometools0.
Closes: #1068178
* Add d/copyright information for debian/ directory.
* Bump Standards-Version.
* Add Rules-Requires-Root: no.
* Update debhelper compat level to 13.
* Only list files not installed.
* Adjust renamed lintian tag overrides.
* Bump watchfile version to 4.
Checksums-Sha1:
2d6f890fa726c989a241ac10bda60e2df06045a7 1287924 aegean-dbgsym_0.16.0+dfsg-4_armhf.deb
a3cd33acd63c34b94b715454c135f3627f1809c3 8332 aegean_0.16.0+dfsg-4_armhf.buildinfo
9625fcaaf5f26274c7970eeb2ddadab8fa721ca3 174196 aegean_0.16.0+dfsg-4_armhf.deb
Checksums-Sha256:
fb62443470bff8aa0a7a2aa02885fdaa1eb49ec6cfcb1b717fc72bb1e0f6da30 1287924 aegean-dbgsym_0.16.0+dfsg-4_armhf.deb
5a78e48e8f06ed0b3ccf6cc864ce4b4ee2e8d8579a8f8aa2ff57ed6c53bd5cb4 8332 aegean_0.16.0+dfsg-4_armhf.buildinfo
0ac8695bf678480fd7d51d529e556cf63dbcf6de7a6f7ef9f80277adecf338fd 174196 aegean_0.16.0+dfsg-4_armhf.deb
Files:
4df59d01fd9272a02ebdaf373f08fbc9 1287924 debug optional aegean-dbgsym_0.16.0+dfsg-4_armhf.deb
09acb3a910a629411c491d04655f562e 8332 science optional aegean_0.16.0+dfsg-4_armhf.buildinfo
74ae0d78d6d4d9263a5e2901e0371986 174196 science optional aegean_0.16.0+dfsg-4_armhf.deb
Sun Dec 29 16:46:32 UTC 2024 I: diffoscope 284 will be used to compare the two builds:
Running as unit: rb-diffoscope-armhf_25-12192.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ESQE6Dbn/aegean_0.16.0+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ESQE6Dbn/aegean_0.16.0+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ESQE6Dbn/aegean_0.16.0+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ESQE6Dbn/b1/aegean_0.16.0+dfsg-4_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.ESQE6Dbn/b2/aegean_0.16.0+dfsg-4_armhf.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: 0.372s)
0.372s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.032s)
0.032s 12 calls diffoscope.comparators.binary.FilesystemFile
## specialize (total time: 0.000s)
0.000s 1 call specialize
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 692ms
CPU time consumed: 683ms
Sun Dec 29 16:46:33 UTC 2024 I: diffoscope 284 found no differences in the changes files, and a .buildinfo file also exists.
Sun Dec 29 16:46:33 UTC 2024 I: aegean from unstable built successfully and reproducibly on armhf.
Sun Dec 29 16:46:35 UTC 2024 I: Submitting .buildinfo files to external archives:
Sun Dec 29 16:46:35 UTC 2024 I: Submitting 12K b1/aegean_0.16.0+dfsg-4_armhf.buildinfo.asc
Sun Dec 29 16:46:35 UTC 2024 I: Submitting 12K b2/aegean_0.16.0+dfsg-4_armhf.buildinfo.asc
Sun Dec 29 16:46:36 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sun Dec 29 16:46:36 UTC 2024 I: Done submitting .buildinfo files.
Sun Dec 29 16:46:36 UTC 2024 I: Removing signed aegean_0.16.0+dfsg-4_armhf.buildinfo.asc files:
removed './b1/aegean_0.16.0+dfsg-4_armhf.buildinfo.asc'
removed './b2/aegean_0.16.0+dfsg-4_armhf.buildinfo.asc'