gubbins →
2.3.5-1 →
armhf → 2019-12-23 05:18:12
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01
+==============================================================================+
| gubbins 2.3.5-1 (armhf) Mon, 23 Dec 2019 05:01:09 +0000 |
+==============================================================================+
Package: gubbins
Version: 2.3.5-1
Source Version: 2.3.5-1
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bullseye-staging-armhf-sbuild-638f5c9c-6945-4986-bc19-9fc4d5e86a1b' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.7 MB]
Fetched 24.2 MB in 26s (932 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'gubbins' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/gubbins.git
Please use:
git clone https://salsa.debian.org/med-team/gubbins.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 705 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main gubbins 2.3.5-1 (dsc) [2163 B]
Get:2 http://172.17.0.1/private bullseye-staging/main gubbins 2.3.5-1 (tar) [696 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main gubbins 2.3.5-1 (diff) [6116 B]
Fetched 705 kB in 0s (8133 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/gubbins-QvodJm/gubbins-2.3.5' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/gubbins-QvodJm' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-SV9FF7/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-SV9FF7/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-SV9FF7/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-SV9FF7/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-SV9FF7/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-SV9FF7/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-SV9FF7/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-SV9FF7/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-SV9FF7/apt_archive ./ Packages [435 B]
Fetched 2111 B in 1s (2908 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-SV9FF7/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-SV9FF7/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 29 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-SV9FF7/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12199 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 12), dh-python, fasttree, raxml, python3-setuptools, zlib1g-dev, check, python3, python3-biopython, python3-dendropy, python3-reportlab, python3-nose, pkg-config
Filtered Build-Depends: debhelper-compat (= 12), dh-python, fasttree, raxml, python3-setuptools, zlib1g-dev, check, python3, python3-biopython, python3-dendropy, python3-reportlab, python3-nose, pkg-config
dpkg-deb: building package 'sbuild-build-depends-gubbins-dummy' in '/<<BUILDDIR>>/resolver-SV9FF7/apt_archive/sbuild-build-depends-gubbins-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-gubbins-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-SV9FF7/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-SV9FF7/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-SV9FF7/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-SV9FF7/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-SV9FF7/apt_archive ./ Sources [569 B]
Get:5 copy:/<<BUILDDIR>>/resolver-SV9FF7/apt_archive ./ Packages [656 B]
Fetched 2558 B in 1s (3184 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-SV9FF7/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-SV9FF7/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install gubbins build dependencies (apt-based resolver)
-------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils check cpp-9 debhelper
dh-autoreconf dh-python dh-strip-nondeterminism dwz fasttree file g++-9
gcc-9 gcc-9-base gettext gettext-base groff-base intltool-debian
libarchive-zip-perl libasan5 libatomic1 libblas3 libbsd0 libcc1-0 libcroco3
libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl
libfreetype6 libgcc-9-dev libgcc1 libgfortran5 libglib2.0-0 libgomp1
libicu63 libimagequant0 libjbig0 libjpeg62-turbo liblapack3 liblcms2-2
libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpng16-16 libpython3-stdlib
libpython3.7-minimal libpython3.7-stdlib libsigsegv2 libssl1.1
libstdc++-9-dev libstdc++6 libsub-override-perl libsubunit-dev libsubunit0
libtiff5 libtinfo5 libtool libubsan1 libuchardet0 libwebp6 libwebpdemux2
libwebpmux3 libxml2 m4 man-db mime-support pkg-config po-debconf python3
python3-biopython python3-dendropy python3-distutils python3-lib2to3
python3-minimal python3-nose python3-numpy python3-pil python3-pkg-resources
python3-reportlab python3-reportlab-accel python3-setuptools python3.7
python3.7-minimal raxml sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation gcc-9-locales dh-make gcc-9-doc gettext-doc libasprintf-dev
libgettextpo-dev groff liblcms2-utils libstdc++-9-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl python3-doc python3-tk python3-venv clustalo clustalw
dialign dssp emboss mafft muscle phylip phyml prank probcons python3-mysqldb
python3-matplotlib python3-rdflib python3-renderpm python3-psycopg2
python3-scipy samtools t-coffee wise w3-dtd-mathml python-nose-doc gfortran
python-numpy-doc python3-dev python3-pytest python3-numpy-dbg python-pil-doc
python3-pil-dbg pdf-viewer python3-egenix-mxtexttools python-reportlab-doc
python-setuptools-doc python3.7-venv python3.7-doc binfmt-support
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libmail-sendmail-perl python-biopython-doc
ncbi-blast+ python3-olefile python3-renderpm
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils check debhelper
dh-autoreconf dh-python dh-strip-nondeterminism dwz fasttree file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libblas3 libbsd0
libcroco3 libdebhelper-perl libelf1 libexpat1
libfile-stripnondeterminism-perl libfreetype6 libgfortran5 libglib2.0-0
libicu63 libimagequant0 libjbig0 libjpeg62-turbo liblapack3 liblcms2-2
libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpng16-16 libpython3-stdlib
libpython3.7-minimal libpython3.7-stdlib libsigsegv2 libssl1.1
libsub-override-perl libsubunit-dev libsubunit0 libtiff5 libtinfo5 libtool
libuchardet0 libwebp6 libwebpdemux2 libwebpmux3 libxml2 m4 man-db
mime-support pkg-config po-debconf python3 python3-biopython
python3-dendropy python3-distutils python3-lib2to3 python3-minimal
python3-nose python3-numpy python3-pil python3-pkg-resources
python3-reportlab python3-reportlab-accel python3-setuptools python3.7
python3.7-minimal raxml sbuild-build-depends-gubbins-dummy sensible-utils
zlib1g-dev
The following packages will be upgraded:
cpp-9 g++-9 gcc-9 gcc-9-base libasan5 libatomic1 libcc1-0 libgcc-9-dev
libgcc1 libgomp1 libstdc++-9-dev libstdc++6 libubsan1
13 upgraded, 79 newly installed, 0 to remove and 16 not upgraded.
Need to get 61.7 MB of archives.
After this operation, 137 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-SV9FF7/apt_archive ./ sbuild-build-depends-gubbins-dummy 0.invalid.0 [936 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20191019-1 [316 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libcc1-0 armhf 9.2.1-21+rpi1 [38.0 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf gcc-9-base armhf 9.2.1-21+rpi1 [195 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libgcc1 armhf 1:9.2.1-21+rpi1 [37.0 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libgomp1 armhf 9.2.1-21+rpi1 [73.8 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libatomic1 armhf 9.2.1-21+rpi1 [8160 B]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libasan5 armhf 9.2.1-21+rpi1 [348 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libubsan1 armhf 9.2.1-21+rpi1 [112 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf g++-9 armhf 9.2.1-21+rpi1 [8207 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libstdc++-9-dev armhf 9.2.1-21+rpi1 [1707 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libgcc-9-dev armhf 9.2.1-21+rpi1 [640 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf gcc-9 armhf 9.2.1-21+rpi1 [7715 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf cpp-9 armhf 9.2.1-21+rpi1 [7458 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libstdc++6 armhf 9.2.1-21+rpi1 [414 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-3 [782 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.1-3 [28.3 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.0-2 [1261 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1d-2 [1268 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-minimal armhf 3.7.5-2 [584 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf python3.7-minimal armhf 3.7.5-2 [1527 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.7.5-1 [36.6 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.64 [37.8 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-stdlib armhf 3.7.5-2 [1668 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf python3.7 armhf 3.7.5-2 [347 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.7.5-1 [20.1 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.7.5-1 [61.5 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.37-6 [253 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.37-6 [111 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.37-6 [66.2 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libsubunit0 armhf 1.3.0-6 [9280 B]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libsubunit-dev armhf 1.3.0-6 [10.3 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf check armhf 0.10.0-3 [178 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-11 [547 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.7.2 [174 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.67-1 [104 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.3-1 [23.6 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.3-1 [14.6 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.3-2 [1137 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-8 [593 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.7.2 [1018 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf python3-lib2to3 all 3.8.0-1 [78.3 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf python3-distutils all 3.8.0-1 [145 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf dh-python all 4.20191017 [94.4 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf fasttree armhf 2.1.11-1 [156 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-1 [108 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libpng16-16 armhf 1.6.37-1 [274 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libfreetype6 armhf 2.10.1-2 [330 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 9.2.1-21+rpi1 [231 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libimagequant0 armhf 2.12.2-1.1 [27.2 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [110 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-1 [1597 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf liblcms2-2 armhf 2.9-3 [116 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libwebp6 armhf 0.6.1-2 [228 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libtiff5 armhf 4.1.0+git191117-1 [250 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libwebpdemux2 armhf 0.6.1-2 [86.7 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libwebpmux3 armhf 0.6.1-2 [94.2 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29-6 [59.8 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf python3-pkg-resources all 41.2.0-1 [154 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf python3-numpy armhf 1:1.16.5-1 [1908 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf python3-reportlab-accel armhf 3.5.31-1 [34.8 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf python3-pil armhf 6.2.0-1 [379 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf python3-reportlab all 3.5.31-1 [548 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf python3-biopython armhf 1.73+dfsg-1 [1265 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf python3-dendropy all 4.4.0-2 [268 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf python3-nose all 1.3.7-4 [132 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf python3-setuptools all 41.2.0-1 [307 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf raxml armhf 8.2.12+dfsg-2 [945 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
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Setting up libstdc++-9-dev:armhf (9.2.1-21+rpi1) ...
Setting up python3 (3.7.5-1) ...
Setting up man-db (2.9.0-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up python3-pil:armhf (6.2.0-1) ...
Setting up python3-reportlab-accel:armhf (3.5.31-1) ...
Setting up g++-9 (9.2.1-21+rpi1) ...
Setting up python3-reportlab (3.5.31-1) ...
Setting up python3-lib2to3 (3.8.0-1) ...
Setting up python3-pkg-resources (41.2.0-1) ...
Setting up python3-distutils (3.8.0-1) ...
Setting up dh-python (4.20191017) ...
Setting up python3-setuptools (41.2.0-1) ...
Setting up po-debconf (1.0.21) ...
Setting up python3-nose (1.3.7-4) ...
Setting up python3-numpy (1:1.16.5-1) ...
Setting up python3-biopython (1.73+dfsg-1) ...
Setting up python3-dendropy (4.4.0-2) ...
Setting up debhelper (12.7.2) ...
Setting up dh-autoreconf (19) ...
Setting up sbuild-build-depends-gubbins-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.29-3+rpi1) ...
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.33.1-5+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-21+rpi1 gcc-9_9.2.1-21+rpi1 libc6-dev_2.29-3+rpi1 libstdc++-9-dev_9.2.1-21+rpi1 libstdc++6_9.2.1-21+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.46 bash_5.0-5 binutils_2.33.1-5+rpi1 binutils-arm-linux-gnueabihf_2.33.1-5+rpi1 binutils-common_2.33.1-5+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 check_0.10.0-3 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.2.1-21+rpi1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.2 debianutils_4.9 dh-autoreconf_19 dh-python_4.20191017 dh-strip-nondeterminism_1.6.3-1 diffutils_1:3.7-3 dirmngr_2.2.17-3+b1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.4-1 fakeroot_1.24-1 fasttree_2.1.11-1 fdisk_2.34-0.1 file_1:5.37-6 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.2.1-21+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-9_9.2.1-21+rpi1 gcc-9-base_9.2.1-21+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.17-3 gnupg-l10n_2.2.17-3 gnupg-utils_2.2.17-3+b1 gpg_2.2.17-3+b1 gpg-agent_2.2.17-3+b1 gpg-wks-client_2.2.17-3+b1 gpg-wks-server_2.2.17-3+b1 gpgconf_2.2.17-3+b1 gpgsm_2.2.17-3+b1 gpgv_2.2.17-3+b1 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-2 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-21+rpi1 libassuan0_2.5.3-7 libatomic1_9.2.1-21+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbinutils_2.33.1-5+rpi1 libblas3_3.9.0-1 libblkid1_2.34-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-3+rpi1 libc-dev-bin_2.29-3+rpi1 libc6_2.29-3+rpi1 libc6-dev_2.29-3+rpi1 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcap2-bin_1:2.27-1 libcc1-0_9.2.1-21+rpi1 libcom-err2_1.45.4-1 libcroco3_0.6.13-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.7.2 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.4-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.3-1 libfreetype6_2.10.1-2 libgcc-9-dev_9.2.1-21+rpi1 libgcc1_1:9.2.1-21+rpi1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran5_9.2.1-21+rpi1 libglib2.0-0_2.62.3-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.10-5 libgomp1_9.2.1-21+rpi1 libgpg-error0_1.36-7 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libimagequant0_2.12.2-1.1 libisl22_0.22-2 libjbig0_2.1-3.1+b2 libjpeg62-turbo_1:1.5.2-2+b1 libksba8_1.3.5-2 liblapack3_3.9.0-1 liblcms2-2_2.9-3 libldap-2.4-2_2.4.48+dfsg-1+b2 libldap-common_2.4.48+dfsg-1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-6 libmagic1_1:5.37-6 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncursesw6_6.1+20191019-1 libnettle7_3.5.1+really3.5.1-2 libnpth0_1.6-1 libp11-kit0_0.23.18.1-2 libpam-cap_1:2.27-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-3 libpcre3_2:8.39-12 libperl5.30_5.30.0-9 libpipeline1_1.5.1-3 libpng16-16_1.6.37-1 libpython3-stdlib_3.7.5-1 libpython3.7-minimal_3.7.5-2 libpython3.7-stdlib_3.7.5-2 libreadline7_7.0-5 libreadline8_8.0-3 libsasl2-2_2.1.27+dfsg-1+b1 libsasl2-modules-db_2.1.27+dfsg-1+b1 libseccomp2_2.4.2-2+rpi1 libselinux1_2.9-3 libsemanage-common_2.9-3 libsemanage1_2.9-3 libsepol1_2.9-2 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.30.1-1 libss2_1.45.4-1 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-21+rpi1 libstdc++6_9.2.1-21+rpi1 libsub-override-perl_0.09-2 libsubunit-dev_1.3.0-6 libsubunit0_1.3.0-6 libsystemd0_243-8+rpi1 libtasn1-6_4.14-3 libtiff5_4.1.0+git191117-1 libtinfo5_6.1+20191019-1 libtinfo6_6.1+20191019-1 libtool_2.4.6-11 libubsan1_9.2.1-21+rpi1 libuchardet0_0.0.6-3 libudev1_243-8+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libwebp6_0.6.1-2 libwebpdemux2_0.6.1-2 libwebpmux3_0.6.1-2 libxml2_2.9.4+dfsg1-8 libzstd1_1.4.4+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.7-2 logsave_1.45.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.3-17 mime-support_3.64 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 netbase_5.7 passwd_1:4.7-2 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 pkg-config_0.29-6 po-debconf_1.0.21 python3_3.7.5-1 python3-biopython_1.73+dfsg-1 python3-dendropy_4.4.0-2 python3-distutils_3.8.0-1 python3-lib2to3_3.8.0-1 python3-minimal_3.7.5-1 python3-nose_1.3.7-4 python3-numpy_1:1.16.5-1 python3-pil_6.2.0-1 python3-pkg-resources_41.2.0-1 python3-reportlab_3.5.31-1 python3-reportlab-accel_3.5.31-1 python3-setuptools_41.2.0-1 python3.7_3.7.5-2 python3.7-minimal_3.7.5-2 raspbian-archive-keyring_20120528.2 raxml_8.2.12+dfsg-2 readline-common_8.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gubbins-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-1 tar_1.30+dfsg-6 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Fri Dec 20 23:22:38 2019 UTC
gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1
gpgv: issuer "moeller@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./gubbins_2.3.5-1.dsc
dpkg-source: info: extracting gubbins in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking gubbins_2.3.5.orig.tar.gz
dpkg-source: info: unpacking gubbins_2.3.5-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying do_not_handle_python_by_upstream_build_system.patch
dpkg-source: info: applying gubbins_exe_in_usr_lib.patch
dpkg-source: info: applying disable_test.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-638f5c9c-6945-4986-bc19-9fc4d5e86a1b
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package gubbins
dpkg-buildpackage: info: source version 2.3.5-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --with python3
debian/rules override_dh_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_clean
rm -rf python/*.egg-info python/build python/Makefile
find . -name "*.pyc" -delete
rm -rf python/output_alignment python/tmp*
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules build-arch
dh build-arch --with python3
dh_update_autotools_config -a
dh_autoreconf -a
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4/libtool.m4'
libtoolize: copying file 'm4/ltoptions.m4'
libtoolize: copying file 'm4/ltsugar.m4'
libtoolize: copying file 'm4/ltversion.m4'
libtoolize: copying file 'm4/lt~obsolete.m4'
configure.ac:20: installing './compile'
configure.ac:10: installing './config.guess'
configure.ac:10: installing './config.sub'
configure.ac:3: installing './install-sh'
configure.ac:3: installing './missing'
src/Makefile.am: installing './depcomp'
parallel-tests: installing './test-driver'
dh_auto_configure -a
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
configure: WARNING: unrecognized options: --disable-maintainer-mode
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking how to create a pax tar archive... gnutar
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking how to print strings... printf
checking whether make supports the include directive... yes (GNU style)
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop
checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) none
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... none
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if compiler needs -Werror to reject unknown flags... no
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for zlib... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking for a Python interpreter with version >= 3.0... python3
checking for python3... /usr/bin/python3
checking for python3 version... 3.7
checking for python3 platform... linux
checking for python3 script directory... ${prefix}/lib/python3.7/site-packages
checking for python3 extension module directory... ${exec_prefix}/lib/python3.7/site-packages
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating release/Makefile
config.status: creating python/Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make all-recursive
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making all in src
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o main.c
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Newickform.lo Newickform.c
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alignment_file.lo alignment_file.c
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o block_tab_file.lo block_tab_file.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c block_tab_file.c -fPIC -DPIC -o .libs/block_tab_file.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c alignment_file.c -fPIC -DPIC -o .libs/alignment_file.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c Newickform.c -fPIC -DPIC -o .libs/Newickform.o
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o branch_sequences.lo branch_sequences.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c block_tab_file.c -o block_tab_file.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c branch_sequences.c -fPIC -DPIC -o .libs/branch_sequences.o
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o string_cat.lo string_cat.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c string_cat.c -fPIC -DPIC -o .libs/string_cat.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c Newickform.c -o Newickform.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c string_cat.c -o string_cat.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fasta_of_snp_sites.lo fasta_of_snp_sites.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c alignment_file.c -o alignment_file.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c fasta_of_snp_sites.c -fPIC -DPIC -o .libs/fasta_of_snp_sites.o
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gff_file.lo gff_file.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c fasta_of_snp_sites.c -o fasta_of_snp_sites.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c gff_file.c -fPIC -DPIC -o .libs/gff_file.o
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gubbins.lo gubbins.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c gff_file.c -o gff_file.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c gubbins.c -fPIC -DPIC -o .libs/gubbins.o
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parse_phylip.lo parse_phylip.c
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parse_vcf.lo parse_vcf.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c parse_phylip.c -fPIC -DPIC -o .libs/parse_phylip.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c gubbins.c -o gubbins.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c parse_vcf.c -fPIC -DPIC -o .libs/parse_vcf.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c branch_sequences.c -o branch_sequences.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylip_of_snp_sites.lo phylip_of_snp_sites.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c phylip_of_snp_sites.c -fPIC -DPIC -o .libs/phylip_of_snp_sites.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c parse_vcf.c -o parse_vcf.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c phylip_of_snp_sites.c -o phylip_of_snp_sites.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o seqUtil.lo seqUtil.c
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snp_searching.lo snp_searching.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c seqUtil.c -fPIC -DPIC -o .libs/seqUtil.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c snp_searching.c -fPIC -DPIC -o .libs/snp_searching.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c seqUtil.c -o seqUtil.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c parse_phylip.c -o parse_phylip.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snp_sites.lo snp_sites.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c snp_searching.c -o snp_searching.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c snp_sites.c -fPIC -DPIC -o .libs/snp_sites.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c snp_sites.c -o snp_sites.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o tree_statistics.lo tree_statistics.c
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o tree_scaling.lo tree_scaling.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c tree_statistics.c -fPIC -DPIC -o .libs/tree_statistics.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c tree_scaling.c -fPIC -DPIC -o .libs/tree_scaling.o
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcf.lo vcf.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c tree_statistics.c -o tree_statistics.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c tree_scaling.c -o tree_scaling.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c vcf.c -fPIC -DPIC -o .libs/vcf.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c vcf.c -o vcf.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:1 -Wl,-z,relro -Wl,-z,now -o libgubbins.la -rpath /usr/lib/arm-linux-gnueabihf Newickform.lo alignment_file.lo block_tab_file.lo branch_sequences.lo string_cat.lo fasta_of_snp_sites.lo gff_file.lo gubbins.lo parse_phylip.lo parse_vcf.lo phylip_of_snp_sites.lo seqUtil.lo snp_searching.lo snp_sites.lo tree_statistics.lo tree_scaling.lo vcf.lo -lm
libtool: link: gcc -shared -fPIC -DPIC .libs/Newickform.o .libs/alignment_file.o .libs/block_tab_file.o .libs/branch_sequences.o .libs/string_cat.o .libs/fasta_of_snp_sites.o .libs/gff_file.o .libs/gubbins.o .libs/parse_phylip.o .libs/parse_vcf.o .libs/phylip_of_snp_sites.o .libs/seqUtil.o .libs/snp_searching.o .libs/snp_sites.o .libs/tree_statistics.o .libs/tree_scaling.o .libs/vcf.o -lm -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libgubbins.so.0 -o .libs/libgubbins.so.0.0.1
libtool: link: (cd ".libs" && rm -f "libgubbins.so.0" && ln -s "libgubbins.so.0.0.1" "libgubbins.so.0")
libtool: link: (cd ".libs" && rm -f "libgubbins.so" && ln -s "libgubbins.so.0.0.1" "libgubbins.so")
libtool: link: ar cru .libs/libgubbins.a Newickform.o alignment_file.o block_tab_file.o branch_sequences.o string_cat.o fasta_of_snp_sites.o gff_file.o gubbins.o parse_phylip.o parse_vcf.o phylip_of_snp_sites.o seqUtil.o snp_searching.o snp_sites.o tree_statistics.o tree_scaling.o vcf.o
ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: ranlib .libs/libgubbins.a
libtool: link: ( cd ".libs" && rm -f "libgubbins.la" && ln -s "../libgubbins.la" "libgubbins.la" )
/bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gubbins main.o libgubbins.la -lz -lm
libtool: link: gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/gubbins main.o ./.libs/libgubbins.so -lz -lm
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
Making all in release
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debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_test
make -j4 check VERBOSE=1
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Making check in src
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make run_all_tests
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gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_branch_sequences.o `test -f '../tests/check_branch_sequences.c' || echo './'`../tests/check_branch_sequences.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_gubbins.o `test -f '../tests/check_gubbins.c' || echo './'`../tests/check_gubbins.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_parse_phylip.o `test -f '../tests/check_parse_phylip.c' || echo './'`../tests/check_parse_phylip.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_snp_searching.o `test -f '../tests/check_snp_searching.c' || echo './'`../tests/check_snp_searching.c
In file included from ../tests/check_gubbins.c:4:
../tests/check_gubbins.c: In function 'check_gubbins_no_recombinations':
../tests/check_gubbins.c:21:15: warning: implicit declaration of function 'number_of_recombinations_in_file' [-Wimplicit-function-declaration]
21 | fail_unless(number_of_recombinations_in_file("../tests/data/no_recombinations.tre.tab") == 0);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/check_branch_sequences.c: In function 'check_copy_and_concat_2d_integer_arrays':
../tests/check_branch_sequences.c:67:16: warning: implicit declaration of function 'copy_and_concat_2d_integer_arrays'; did you mean 'copy_and_concat_integer_arrays'? [-Wimplicit-function-declaration]
67 | output_size = copy_and_concat_2d_integer_arrays(block_coords, 3, block_coords_2, 2, block_coords_out) ;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| copy_and_concat_integer_arrays
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_snp_sites.o `test -f '../tests/check_snp_sites.c' || echo './'`../tests/check_snp_sites.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_vcf_parsing.o `test -f '../tests/check_vcf_parsing.c' || echo './'`../tests/check_vcf_parsing.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-helper_methods.o `test -f '../tests/helper_methods.c' || echo './'`../tests/helper_methods.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-run_all_tests.o `test -f '../tests/run_all_tests.c' || echo './'`../tests/run_all_tests.c
../tests/helper_methods.c: In function 'compare_files':
../tests/helper_methods.c:27:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
27 | fread(expected_buffer, sizeof(char), numbytes, expected_output_fh);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/helper_methods.c:34:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
34 | fread(actual_buffer, sizeof(char), numbytes, actual_output_fh);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/bin/bash ../libtool --tag=CC --mode=link gcc -I../tests -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck libgubbins.la -lz -lm -lrt -lsubunit
libtool: link: gcc -I../tests -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck ./.libs/libgubbins.so -lz -lm -lrt -lsubunit -pthread
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make check-TESTS
make[4]: Entering directory '/<<PKGBUILDDIR>>/src'
make[5]: Entering directory '/<<PKGBUILDDIR>>/src'
PASS: run_all_tests
============================================================================
Testsuite summary for gubbins 2.3.4
============================================================================
# TOTAL: 1
# PASS: 1
# SKIP: 0
# XFAIL: 0
# FAIL: 0
# XPASS: 0
# ERROR: 0
============================================================================
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Making check in release
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cd python && \
python3 setup.py test
running test
running egg_info
creating gubbins.egg-info
writing gubbins.egg-info/PKG-INFO
writing dependency_links to gubbins.egg-info/dependency_links.txt
writing requirements to gubbins.egg-info/requires.txt
writing top-level names to gubbins.egg-info/top_level.txt
writing manifest file 'gubbins.egg-info/SOURCES.txt'
reading manifest file 'gubbins.egg-info/SOURCES.txt'
writing manifest file 'gubbins.egg-info/SOURCES.txt'
running build_ext
/<<PKGBUILDDIR>>/python/gubbins/common.py:536: DeprecationWarning: invalid escape sequence \.
regex_for_file_deletions.append("^RAxML_result."+GubbinsCommon.raxml_base_name(base_filename_without_ext,current_time)+str(file_iteration)+'\.')
/<<PKGBUILDDIR>>/python/gubbins/common.py:550: DeprecationWarning: invalid escape sequence \.
regex_for_file_deletions.append("^"+starting_base_filename+".iteration_"+str(file_iteration)+'[$|\.]')
/<<PKGBUILDDIR>>/python/gubbins/common.py:711: DeprecationWarning: invalid escape sequence \d
elif re.match('^\d', vcf_line) != None :
/<<PKGBUILDDIR>>/python/gubbins/common.py:823: DeprecationWarning: invalid escape sequence \d
searchObj = re.search('misc_feature ([\d]+)..([\d]+)$', line)
/<<PKGBUILDDIR>>/python/gubbins/common.py:830: DeprecationWarning: invalid escape sequence \=
searchTaxa = re.search('taxa\=\"([^"]+)\"', line)
/usr/lib/python3/dist-packages/dendropy/utility/container.py:357: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3,and in 3.9 it will stop working
class CaseInsensitiveDict(collections.MutableMapping):
test_get_sequence_names_from_alignment (test_alignment_python_methods.TestAlignmentPythonMethods) ... ok
test_number_of_sequences_in_alignment (test_alignment_python_methods.TestAlignmentPythonMethods) ... ok
test_reconvert_fasta_file (test_alignment_python_methods.TestAlignmentPythonMethods) ... ok
test_reinsert_gaps_into_fasta_file (test_alignment_python_methods.TestAlignmentPythonMethods) ... ok
test_get_recombination_files (test_converging_recombinations.TestConvergingRecombinations) ... ok
test_multiple_files_have_one_match (test_converging_recombinations.TestConvergingRecombinations) ... ok
test_reading_embl_file (test_converging_recombinations.TestConvergingRecombinations) ... ok
test_two_files_are_different (test_converging_recombinations.TestConvergingRecombinations) ... ok
test_two_files_are_same (test_converging_recombinations.TestConvergingRecombinations) ... ok
test_dont_filter_input_file_with_multiple_duplicate_sequences (test_pre_process_fasta.TestPreProcessFasta) ... ok
test_filter_out_alignments_with_too_much_missing_data (test_pre_process_fasta.TestPreProcessFasta) ... ok
test_input_file_with_all_duplicate_sequences (test_pre_process_fasta.TestPreProcessFasta) ... ok
test_input_file_with_multiple_duplicate_sequences (test_pre_process_fasta.TestPreProcessFasta) ... ok
test_input_file_with_no_duplicate_sequences (test_pre_process_fasta.TestPreProcessFasta) ... ok
test_input_file_with_one_duplicate_sequences (test_pre_process_fasta.TestPreProcessFasta) ... ok
test_add_labels_to_tree (test_raxml_sequence_reconstruction.TestRAxMLSequenceReconstruction) ... ok
test_ancestor_raxml_command_no_verbose (test_raxml_sequence_reconstruction.TestRAxMLSequenceReconstruction) ... ok
test_ancestor_raxml_command_verbose (test_raxml_sequence_reconstruction.TestRAxMLSequenceReconstruction) ... ok
test_convert_raw_ancestral_file_to_fasta (test_raxml_sequence_reconstruction.TestRAxMLSequenceReconstruction) ... ok
test_merging_fasta_files (test_raxml_sequence_reconstruction.TestRAxMLSequenceReconstruction) ... ok
test_more_complex_tree (test_raxml_sequence_reconstruction.TestRAxMLSequenceReconstruction) ... ok
test_root_input_tree (test_raxml_sequence_reconstruction.TestRAxMLSequenceReconstruction) ... ok
test_run_raxml_ancestor_reconstruction (test_raxml_sequence_reconstruction.TestRAxMLSequenceReconstruction) ... ok
test_transfer_internal_labels (test_raxml_sequence_reconstruction.TestRAxMLSequenceReconstruction) ... ok
test_working_directory_construction (test_raxml_sequence_reconstruction.TestRAxMLSequenceReconstruction) ... ok
test_fasttree_current_tree_name (test_string_construction.TestStringConstruction) ... ok
test_fasttree_gubbins_command (test_string_construction.TestStringConstruction) ... ok
test_fasttree_previous_tree_name (test_string_construction.TestStringConstruction) ... ok
test_fasttree_regex_for_file_deletions (test_string_construction.TestStringConstruction) ... ok
test_fasttree_tree_building_command (test_string_construction.TestStringConstruction) ... ok
test_raxml_base_name (test_string_construction.TestStringConstruction) ... ok
test_raxml_current_tree_name (test_string_construction.TestStringConstruction) ... ok
test_raxml_gubbins_command (test_string_construction.TestStringConstruction) ... ok
test_raxml_previous_tree (test_string_construction.TestStringConstruction) ... ok
test_raxml_previous_tree_name (test_string_construction.TestStringConstruction) ... ok
test_raxml_regex_for_file_deletions (test_string_construction.TestStringConstruction) ... ok
test_raxml_regex_for_file_deletions_10 (test_string_construction.TestStringConstruction) ... ok
test_raxml_tree_building_command (test_string_construction.TestStringConstruction) ... ok
test_rename_files (test_string_construction.TestStringConstruction) ... ok
test_starting_files_regex (test_string_construction.TestStringConstruction) ... ok
test_translation_of_fasttree_filenames_to_final_filenames (test_string_construction.TestStringConstruction) ... ok
test_translation_of_raxml_filenames_to_final_filenames (test_string_construction.TestStringConstruction) ... ok
test_filter_out_removed_taxa_from_tree_and_return_new_file (test_tree_python_methods.TestTreePythonMethods) ... ok
test_has_tree_been_seen_before (test_tree_python_methods.TestTreePythonMethods) ... ok
test_internal_node_taxons_removed_when_used_as_starting_tree (test_tree_python_methods.TestTreePythonMethods) ... ok
test_remove_internal_node_labels (test_tree_python_methods.TestTreePythonMethods) ... ok
test_reroot_tree (test_tree_python_methods.TestTreePythonMethods) ... ok
test_reroot_tree_at_midpoint (test_tree_python_methods.TestTreePythonMethods) ... ok
test_reroot_tree_with_outgroup (test_tree_python_methods.TestTreePythonMethods) ... ok
test_reroot_tree_with_outgroups (test_tree_python_methods.TestTreePythonMethods) ... ok
test_reroot_tree_with_outgroups_all_in_different_clade (test_tree_python_methods.TestTreePythonMethods) ... ok
test_reroot_tree_with_outgroups_all_in_one_clade (test_tree_python_methods.TestTreePythonMethods) ... ok
test_reroot_tree_with_outgroups_all_in_one_clade_large (test_tree_python_methods.TestTreePythonMethods) ... ok
test_reroot_tree_with_outgroups_with_two_mixed_clades (test_tree_python_methods.TestTreePythonMethods) ... ok
test_robinson_foulds_distance (test_tree_python_methods.TestTreePythonMethods) ... ok
test_split_all_non_bi_nodes (test_tree_python_methods.TestTreePythonMethods) ... ok
test_are_all_sequence_names_unique (test_validate_fasta_input.TestValidateInputFastaFile) ... ok
test_are_all_sequences_the_same_length (test_validate_fasta_input.TestValidateInputFastaFile) ... ok
test_are_there_enough_sequences_to_build_a_tree (test_validate_fasta_input.TestValidateInputFastaFile) ... ok
test_does_each_sequence_have_a_name (test_validate_fasta_input.TestValidateInputFastaFile) ... ok
test_does_the_sequence_have_sensible_characters (test_validate_fasta_input.TestValidateInputFastaFile) ... ok
test_input_file_exists (test_validate_fasta_input.TestValidateInputFastaFile) ... ok
test_valid_fasta_file (test_validate_fasta_input.TestValidateInputFastaFile) ... ok
test_are_all_names_unique (test_validate_starting_tree.TestValidationOfStartingTree) ... ok
test_do_the_names_match_the_fasta_file (test_validate_starting_tree.TestValidationOfStartingTree) ... ok
test_is_it_a_valid_newick_tree (test_validate_starting_tree.TestValidationOfStartingTree) ... ok
----------------------------------------------------------------------
Ran 66 tests in 3.128s
OK
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --with python3
dh_testroot -a
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_install
make -j1 install DESTDIR=/<<PKGBUILDDIR>>/debian/gubbins AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making install in src
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/gubbins/usr/lib/arm-linux-gnueabihf'
/bin/bash ../libtool --mode=install /usr/bin/install -c libgubbins.la '/<<PKGBUILDDIR>>/debian/gubbins/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/libgubbins.so.0.0.1 /<<PKGBUILDDIR>>/debian/gubbins/usr/lib/arm-linux-gnueabihf/libgubbins.so.0.0.1
libtool: install: (cd /<<PKGBUILDDIR>>/debian/gubbins/usr/lib/arm-linux-gnueabihf && { ln -s -f libgubbins.so.0.0.1 libgubbins.so.0 || { rm -f libgubbins.so.0 && ln -s libgubbins.so.0.0.1 libgubbins.so.0; }; })
libtool: install: (cd /<<PKGBUILDDIR>>/debian/gubbins/usr/lib/arm-linux-gnueabihf && { ln -s -f libgubbins.so.0.0.1 libgubbins.so || { rm -f libgubbins.so && ln -s libgubbins.so.0.0.1 libgubbins.so; }; })
libtool: install: /usr/bin/install -c .libs/libgubbins.lai /<<PKGBUILDDIR>>/debian/gubbins/usr/lib/arm-linux-gnueabihf/libgubbins.la
libtool: install: /usr/bin/install -c .libs/libgubbins.a /<<PKGBUILDDIR>>/debian/gubbins/usr/lib/arm-linux-gnueabihf/libgubbins.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/gubbins/usr/lib/arm-linux-gnueabihf/libgubbins.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/gubbins/usr/lib/arm-linux-gnueabihf/libgubbins.a
libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/gubbins/usr/bin'
/bin/bash ../libtool --mode=install /usr/bin/install -c gubbins '/<<PKGBUILDDIR>>/debian/gubbins/usr/bin'
libtool: warning: 'libgubbins.la' has not been installed in '/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/gubbins /<<PKGBUILDDIR>>/debian/gubbins/usr/bin/gubbins
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
Making install in release
make[3]: Entering directory '/<<PKGBUILDDIR>>/release'
make[4]: Entering directory '/<<PKGBUILDDIR>>/release'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/release'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/release'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[4]: Entering directory '/<<PKGBUILDDIR>>'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
# pybuild --install --system=distutils
cd python && \
python3 setup.py install --root=../debian/gubbins --install-layout=deb --install-lib=/usr/share/gubbins --install-scripts=/usr/share/gubbins
running install
running build
running build_py
creating build
creating build/lib
creating build/lib/gubbins
copying gubbins/PreProcessFasta.py -> build/lib/gubbins
copying gubbins/RAxMLExecutable.py -> build/lib/gubbins
copying gubbins/RAxMLSequenceReconstruction.py -> build/lib/gubbins
copying gubbins/ValidateFastaAlignment.py -> build/lib/gubbins
copying gubbins/__init__.py -> build/lib/gubbins
copying gubbins/common.py -> build/lib/gubbins
running build_scripts
creating build/scripts-3.7
copying and adjusting scripts/run_gubbins.py -> build/scripts-3.7
copying and adjusting scripts/gubbins_drawer.py -> build/scripts-3.7
changing mode of build/scripts-3.7/run_gubbins.py from 664 to 775
changing mode of build/scripts-3.7/gubbins_drawer.py from 664 to 775
running install_lib
creating ../debian/gubbins/usr/share
creating ../debian/gubbins/usr/share/gubbins
creating ../debian/gubbins/usr/share/gubbins/gubbins
copying build/lib/gubbins/PreProcessFasta.py -> ../debian/gubbins/usr/share/gubbins/gubbins
copying build/lib/gubbins/RAxMLExecutable.py -> ../debian/gubbins/usr/share/gubbins/gubbins
copying build/lib/gubbins/RAxMLSequenceReconstruction.py -> ../debian/gubbins/usr/share/gubbins/gubbins
copying build/lib/gubbins/ValidateFastaAlignment.py -> ../debian/gubbins/usr/share/gubbins/gubbins
copying build/lib/gubbins/__init__.py -> ../debian/gubbins/usr/share/gubbins/gubbins
copying build/lib/gubbins/common.py -> ../debian/gubbins/usr/share/gubbins/gubbins
byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/PreProcessFasta.py to PreProcessFasta.cpython-37.pyc
byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/RAxMLExecutable.py to RAxMLExecutable.cpython-37.pyc
byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/RAxMLSequenceReconstruction.py to RAxMLSequenceReconstruction.cpython-37.pyc
byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/ValidateFastaAlignment.py to ValidateFastaAlignment.cpython-37.pyc
byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/__init__.py to __init__.cpython-37.pyc
byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/common.py to common.cpython-37.pyc
running install_egg_info
running egg_info
writing gubbins.egg-info/PKG-INFO
writing dependency_links to gubbins.egg-info/dependency_links.txt
writing requirements to gubbins.egg-info/requires.txt
writing top-level names to gubbins.egg-info/top_level.txt
reading manifest file 'gubbins.egg-info/SOURCES.txt'
writing manifest file 'gubbins.egg-info/SOURCES.txt'
Copying gubbins.egg-info to ../debian/gubbins/usr/share/gubbins/gubbins-2.3.4.egg-info
Skipping SOURCES.txt
running install_scripts
copying build/scripts-3.7/run_gubbins.py -> ../debian/gubbins/usr/share/gubbins
copying build/scripts-3.7/gubbins_drawer.py -> ../debian/gubbins/usr/share/gubbins
changing mode of ../debian/gubbins/usr/share/gubbins/run_gubbins.py to 775
changing mode of ../debian/gubbins/usr/share/gubbins/gubbins_drawer.py to 775
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
find debian -name "*.la" -delete
find debian -name "*.a" -delete
mkdir -p debian/gubbins/usr/lib/gubbins
mv debian/gubbins/usr/bin/gubbins debian/gubbins/usr/lib/gubbins
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_python3 -a
I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/gubbins_drawer.py
I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/run_gubbins.py
dh_lintian -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: symbol gzopen used by debian/gubbins/usr/lib/arm-linux-gnueabihf/libgubbins.so.0.0.1 found in none of the libraries
dpkg-shlibdeps: warning: symbol gzclose used by debian/gubbins/usr/lib/arm-linux-gnueabihf/libgubbins.so.0.0.1 found in none of the libraries
dpkg-shlibdeps: warning: symbol gzread used by debian/gubbins/usr/lib/arm-linux-gnueabihf/libgubbins.so.0.0.1 found in none of the libraries
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/gubbins/usr/lib/gubbins/gubbins was not linked against libz.so.1 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'gubbins-dbgsym' in '../gubbins-dbgsym_2.3.5-1_armhf.deb'.
dpkg-deb: building package 'gubbins' in '../gubbins_2.3.5-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../gubbins_2.3.5-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2019-12-23T05:18:03Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
gubbins_2.3.5-1_armhf.changes:
------------------------------
Format: 1.8
Date: Sat, 21 Dec 2019 00:00:10 +0100
Source: gubbins
Binary: gubbins gubbins-dbgsym
Architecture: armhf
Version: 2.3.5-1
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Steffen Moeller <moeller@debian.org>
Description:
gubbins - phylogenetic analysis of genome sequences
Changes:
gubbins (2.3.5-1) unstable; urgency=medium
.
* Team upload.
* New upstream version
* debhelper-compat 12
* Standards-Version: 4.4.1
* Secure URI in copyright format
* Set upstream metadata fields: Repository, Repository-Browse.
* Cleaner clean
* Reported autogenerated files in source tree to upstream
Checksums-Sha1:
c92211cebeadf7ac0cebb01352166d0a4bc41f78 68196 gubbins-dbgsym_2.3.5-1_armhf.deb
0d3432404b14fac9613620624ca0f13d49114f9d 5817 gubbins_2.3.5-1_armhf.buildinfo
f7c031bc0b588eacada0585abecb8be1773fc67f 47028 gubbins_2.3.5-1_armhf.deb
Checksums-Sha256:
19a5967ed5ccfde6aba54c754cdb824e82fbcafd14a7ac8dd465e4d72efd22b3 68196 gubbins-dbgsym_2.3.5-1_armhf.deb
87391dc9be16b22d514156a9e6e8767dd3549df237f7fd7e9e3ef0643f55c13f 5817 gubbins_2.3.5-1_armhf.buildinfo
0aa1e4b86a4300bae8f7ed38ed259e9070b12df617a0920772cb9d475575b238 47028 gubbins_2.3.5-1_armhf.deb
Files:
a96f27066cfe3d487d76ce028c3b87f6 68196 debug optional gubbins-dbgsym_2.3.5-1_armhf.deb
38b06be40bebb6672a7b02af17ef8c1d 5817 science optional gubbins_2.3.5-1_armhf.buildinfo
fda59a59890bbc054a5bbdf7639895c1 47028 science optional gubbins_2.3.5-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
gubbins-dbgsym_2.3.5-1_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 68196 bytes: control archive=644 bytes.
410 bytes, 12 lines control
299 bytes, 3 lines md5sums
Package: gubbins-dbgsym
Source: gubbins
Version: 2.3.5-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 94
Depends: gubbins (= 2.3.5-1)
Section: debug
Priority: optional
Description: debug symbols for gubbins
Build-Ids: 49c2e783b4eee2fe5a61f733f10c0156104333f2 5e6ea1dcbbcbebd819c8c8bdbc1736898e11ec3b
drwxr-xr-x root/root 0 2019-12-20 23:00 ./
drwxr-xr-x root/root 0 2019-12-20 23:00 ./usr/
drwxr-xr-x root/root 0 2019-12-20 23:00 ./usr/lib/
drwxr-xr-x root/root 0 2019-12-20 23:00 ./usr/lib/debug/
drwxr-xr-x root/root 0 2019-12-20 23:00 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2019-12-20 23:00 ./usr/lib/debug/.build-id/49/
-rw-r--r-- root/root 70416 2019-12-20 23:00 ./usr/lib/debug/.build-id/49/c2e783b4eee2fe5a61f733f10c0156104333f2.debug
drwxr-xr-x root/root 0 2019-12-20 23:00 ./usr/lib/debug/.build-id/5e/
-rw-r--r-- root/root 9400 2019-12-20 23:00 ./usr/lib/debug/.build-id/5e/6ea1dcbbcbebd819c8c8bdbc1736898e11ec3b.debug
drwxr-xr-x root/root 0 2019-12-20 23:00 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2019-12-20 23:00 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 1944 2019-12-20 23:00 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/gubbins.debug
drwxr-xr-x root/root 0 2019-12-20 23:00 ./usr/share/
drwxr-xr-x root/root 0 2019-12-20 23:00 ./usr/share/doc/
lrwxrwxrwx root/root 0 2019-12-20 23:00 ./usr/share/doc/gubbins-dbgsym -> gubbins
gubbins_2.3.5-1_armhf.deb
-------------------------
new Debian package, version 2.0.
size 47028 bytes: control archive=2024 bytes.
1095 bytes, 21 lines control
1614 bytes, 21 lines md5sums
276 bytes, 12 lines * postinst #!/bin/sh
389 bytes, 12 lines * prerm #!/bin/sh
32 bytes, 1 lines shlibs
67 bytes, 2 lines triggers
Package: gubbins
Version: 2.3.5-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 170
Depends: libc6 (>= 2.29), zlib1g (>= 1:1.1.4), python3-biopython, python3-dendropy, python3-nose, python3-reportlab, python3:any, python3, fasttree, raxml
Section: science
Priority: optional
Homepage: https://sanger-pathogens.github.io/gubbins/
Description: phylogenetic analysis of genome sequences
Gubbins supports rapid phylogenetic analysis of large samples of
recombinant bacterial whole genome sequences.
.
Gubbins (Genealogies Unbiased By recomBinations In Nucleotide
Sequences) is an algorithm that iteratively identifies loci containing
elevated densities of base substitutions while concurrently constructing
a phylogeny based on the putative point mutations outside of these
regions. Simulations demonstrate the algorithm generates highly accurate
reconstructions under realistic models of short-term bacterial
evolution, and can be run in only a few hours on alignments of hundreds
of bacterial genome sequences.
drwxr-xr-x root/root 0 2019-12-20 23:00 ./
drwxr-xr-x root/root 0 2019-12-20 23:00 ./usr/
drwxr-xr-x root/root 0 2019-12-20 23:00 ./usr/bin/
lrwxrwxrwx root/root 0 2019-12-20 23:00 ./usr/bin/gubbins_drawer -> ../share/gubbins/gubbins_drawer.py
lrwxrwxrwx root/root 0 2019-12-20 23:00 ./usr/bin/run_gubbins -> ../share/gubbins/run_gubbins.py
drwxr-xr-x root/root 0 2019-12-20 23:00 ./usr/lib/
drwxr-xr-x root/root 0 2019-12-20 23:00 ./usr/lib/arm-linux-gnueabihf/
lrwxrwxrwx root/root 0 2019-12-20 23:00 ./usr/lib/arm-linux-gnueabihf/libgubbins.so -> libgubbins.so.0.0.1
lrwxrwxrwx root/root 0 2019-12-20 23:00 ./usr/lib/arm-linux-gnueabihf/libgubbins.so.0 -> libgubbins.so.0.0.1
-rw-r--r-- root/root 46468 2019-12-20 23:00 ./usr/lib/arm-linux-gnueabihf/libgubbins.so.0.0.1
drwxr-xr-x root/root 0 2019-12-20 23:00 ./usr/lib/gubbins/
-rwxr-xr-x root/root 9964 2019-12-20 23:00 ./usr/lib/gubbins/gubbins
drwxr-xr-x root/root 0 2019-12-20 23:00 ./usr/share/
drwxr-xr-x root/root 0 2019-12-20 23:00 ./usr/share/doc/
drwxr-xr-x root/root 0 2019-12-20 23:00 ./usr/share/doc/gubbins/
-rw-r--r-- root/root 971 2019-12-20 23:00 ./usr/share/doc/gubbins/changelog.Debian.gz
-rw-r--r-- root/root 6617 2019-11-11 18:09 ./usr/share/doc/gubbins/changelog.gz
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| Post Build |
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 12984
Build-Time: 168
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 796
Job: gubbins_2.3.5-1
Machine Architecture: armhf
Package: gubbins
Package-Time: 1014
Source-Version: 2.3.5-1
Space: 12984
Status: successful
Version: 2.3.5-1
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Finished at 2019-12-23T05:18:03Z
Build needed 00:16:54, 12984k disc space