Package: src:ariba
Version: 2.12.1+ds-1
Severity: serious
ariba fails to build in a clean amd64 sid chroot:
-----------------------------------------------
building 'minimap_ariba' extension
creating build
creating build/temp.linux-amd64-3.7
creating build/temp.linux-amd64-3.7/ariba
creating build/temp.linux-amd64-3.7/ariba/ext
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
-I/usr/include/minimap -I/usr/include/python3.7m -c ariba/ext/minimap_ariba.cpp
-o build/temp.linux-amd64-3.7/ariba/ext/minimap_ariba.o
ariba/ext/minimap_ariba.cpp:15:10: fatal error: Python.h: No such file or
directory
#include "Python.h"
^~~~~~~~~~
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
E: pybuild pybuild:338: build: plugin distutils failed with: exit code=1:
/usr/bin/python3.7 setup.py build
dh_auto_build: pybuild --build --test-nose -i python{version} -p "3.7 3.6"
returned exit code 13
make: *** [debian/rules:10: build] Error 25
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
------------------------------------------------
Full build log attached.
-- dam
sbuild (Debian sbuild) 0.77.0 (06 July 2018) on pc1.creditreform.bg
+==============================================================================+
| ariba 2.12.1+ds-1 (amd64) Tue, 07 Aug 2018 08:12:52 +0000 |
+==============================================================================+
Package: ariba
Version: 2.12.1+ds-1
Source Version: 2.12.1+ds-1
Distribution: sid
Machine Architecture: amd64
Host Architecture: amd64
Build Architecture: amd64
Build Type: binary
I: NOTICE: Log filtering will replace
'var/run/schroot/mount/sid-fa0d2234-8ccc-4429-af64-e6dcf305c240' with
'<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/ariba-HGdlhW/resolver-UgWMEb' with
'<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Hit:1 http://pc1.modsoftsys.net/public sid InRelease
Get:2 http://proxy:9999/debian sid InRelease [233 kB]
Get:3 http://proxy:9999/debian sid/main amd64 Packages.diff/Index [27.9 kB]
Ign:3 http://proxy:9999/debian sid/main amd64 Packages.diff/Index
Get:3 http://proxy:9999/debian sid/main amd64 Packages.diff/Index [27.9 kB]
Ign:3 http://proxy:9999/debian sid/main amd64 Packages.diff/Index
Get:4 http://proxy:9999/debian sid/main amd64 Packages [8191 kB]
Fetched 8452 kB in 2s (5227 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages will be upgraded:
bsdutils fdisk gcc-8-base gzip libblkid1 libfdisk1 libgcc1 libmount1
libpcre3 libsmartcols1 libstdc++6 libuuid1 make mount patch util-linux
16 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 3814 kB of archives.
After this operation, 8192 B of additional disk space will be used.
Get:1 http://proxy:9999/debian sid/main amd64 bsdutils amd64 1:2.32-0.4 [117 kB]
Get:2 http://proxy:9999/debian sid/main amd64 gzip amd64 1.9-2 [119 kB]
Get:3 http://proxy:9999/debian sid/main amd64 libuuid1 amd64 2.32-0.4 [77.6 kB]
Get:4 http://proxy:9999/debian sid/main amd64 libblkid1 amd64 2.32-0.4 [190 kB]
Get:5 http://proxy:9999/debian sid/main amd64 libfdisk1 amd64 2.32-0.4 [229 kB]
Get:6 http://proxy:9999/debian sid/main amd64 libmount1 amd64 2.32-0.4 [201 kB]
Get:7 http://proxy:9999/debian sid/main amd64 libsmartcols1 amd64 2.32-0.4 [146
kB]
Get:8 http://proxy:9999/debian sid/main amd64 fdisk amd64 2.32-0.4 [168 kB]
Get:9 http://proxy:9999/debian sid/main amd64 util-linux amd64 2.32-0.4 [974 kB]
Get:10 http://proxy:9999/debian sid/main amd64 mount amd64 2.32-0.4 [164 kB]
Get:11 http://proxy:9999/debian sid/main amd64 gcc-8-base amd64 8.2.0-3 [186 kB]
Get:12 http://proxy:9999/debian sid/main amd64 libstdc++6 amd64 8.2.0-3 [393 kB]
Get:13 http://proxy:9999/debian sid/main amd64 libgcc1 amd64 1:8.2.0-3 [40.7 kB]
Get:14 http://proxy:9999/debian sid/main amd64 libpcre3 amd64 2:8.39-11 [341 kB]
Get:15 http://proxy:9999/debian sid/main amd64 make amd64 4.2.1-1.2 [341 kB]
Get:16 http://proxy:9999/debian sid/main amd64 patch amd64 2.7.6-3 [126 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 3814 kB in 0s (42.6 MB/s)
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Preparing to unpack .../make_4.2.1-1.2_amd64.deb ...
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Unpacking patch (2.7.6-3) over (2.7.6-2) ...
Processing triggers for ccache (3.4.2-1) ...
Updating symlinks in /usr/lib/ccache ...
Setting up make (4.2.1-1.2) ...
Setting up mount (2.32-0.4) ...
Setting up patch (2.7.6-3) ...
Processing triggers for libc-bin (2.27-5) ...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Local sources
-------------
/tmp/prebuild-ariba-dVRr1vT8em/ariba_2.12.1+ds-1.dsc exists in
/tmp/prebuild-ariba-dVRr1vT8em; copying to chroot
I: NOTICE: Log filtering will replace 'build/ariba-HGdlhW/ariba-2.12.1+ds' with
'<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/ariba-HGdlhW' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11), python3, python3-all, python3-dev,
python3-dendropy (>= 4.2.0), python3-setuptools, python3-pymummer (>= 0.10.2),
python3-pysam (>= 0.9.1), python3-nose (>= 1.3), python3-bs4 (>= 4.1.0),
python3-matplotlib, python3-tk, bowtie2 (>= 2.1.0), cd-hit, mash,
libminimap-dev, libfml-dev (>= 0.1-3), mummer, fastaq (>= 3.12.0), help2man,
asciidoctor, build-essential, fakeroot
Filtered Build-Depends: debhelper (>= 11), python3, python3-all, python3-dev,
python3-dendropy (>= 4.2.0), python3-setuptools, python3-pymummer (>= 0.10.2),
python3-pysam (>= 0.9.1), python3-nose (>= 1.3), python3-bs4 (>= 4.1.0),
python3-matplotlib, python3-tk, bowtie2 (>= 2.1.0), cd-hit, mash,
libminimap-dev, libfml-dev (>= 0.1-3), mummer, fastaq (>= 3.12.0), help2man,
asciidoctor, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in
'/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-main-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [513 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [598 B]
Fetched 2068 B in 0s (199 kB/s)
Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
asciidoctor autoconf automake autopoint autotools-dev blt bowtie2
bsdmainutils build-essential ca-certificates cd-hit cpp cpp-8 debhelper
dh-autoreconf dh-python dh-strip-nondeterminism dwz fakeroot fastaq file
fontconfig-config fonts-lyx g++ g++-8 gawk gcc gcc-8 gettext gettext-base
groff-base help2man intltool-debian libarchive-zip-perl libasan5 libatomic1
libblas3 libbsd0 libc-dev-bin libc6-dev libcapnp-0.6.1 libcc1-0 libcroco3
libcurl3-gnutls libelf1 libexpat1 libexpat1-dev libfakeroot
libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig1
libfreetype6 libgcc-8-dev libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3
libgsl23 libgslcblas0 libgssapi-krb5-2 libharfbuzz0b libhts2 libicu-le-hb0
libicu60 libisl19 libitm1 libjs-jquery libjs-jquery-ui libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2
libldap-common liblocale-gettext-perl liblsan0 libmagic-mgc libmagic1
libminimap-dev libminimap0 libmpc3 libmpdec2 libmpfr6 libmpx2 libncurses6
libnghttp2-14 libpipeline1 libpng16-16 libpsl5 libpython-stdlib
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-dev
libpython3-stdlib libpython3.6 libpython3.6-dev libpython3.6-minimal
libpython3.6-stdlib libpython3.7-minimal libpython3.7-stdlib libquadmath0
libreadline7 librtmp1 libruby2.5 libsasl2-2 libsasl2-modules-db libsigsegv2
libsqlite3-0 libssh2-1 libssl1.1 libstdc++-8-dev libtbb2 libtcl8.6
libtimedate-perl libtk8.6 libtool libtsan0 libubsan1 libx11-6 libx11-data
libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1
libyaml-0-2 linux-libc-dev m4 man-db mash mime-support mummer openssl
po-debconf python python-matplotlib-data python-minimal python2
python2-minimal python2.7 python2.7-minimal python3 python3-all python3-bs4
python3-cycler python3-dateutil python3-dendropy python3-dev
python3-distutils python3-kiwisolver python3-lib2to3 python3-matplotlib
python3-minimal python3-nose python3-numpy python3-pkg-resources
python3-pymummer python3-pyparsing python3-pysam python3-setuptools
python3-six python3-tk python3-tz python3.6 python3.6-dev python3.6-minimal
python3.7 python3.7-minimal rake readline-common ruby ruby-asciidoctor
ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert
ruby-test-unit ruby-xmlrpc ruby2.5 rubygems-integration samtools
tk8.6-blt2.5 ttf-bitstream-vera ucf x11-common zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc blt-demo bowtie2-examples
wamerican | wordlist whois vacation cpp-doc gcc-8-locales dh-make
g++-multilib g++-8-multilib gcc-8-doc libstdc++6-8-dbg gawk-doc gcc-multilib
manpages-dev flex bison gdb gcc-doc gcc-8-multilib libgcc1-dbg libgomp1-dbg
libitm1-dbg libatomic1-dbg libasan5-dbg liblsan0-dbg libtsan0-dbg
libubsan1-dbg libmpx2-dbg libquadmath0-dbg gettext-doc libasprintf-dev
libgettextpo-dev groff glibc-doc gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info
| gsl-ref-html krb5-doc krb5-user libjs-jquery-ui-docs libstdc++-8-doc
tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc
apparmor less www-browser libmail-box-perl python-doc python-tk python2-doc
python2.7-doc binfmt-support python3-doc python3-venv python-cycler-doc
dvipng ffmpeg gir1.2-gtk-3.0 ghostscript inkscape ipython3 librsvg2-common
python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo
python3-gobject python3-pyqt4 python3-scipy python3-sip python3-tornado
texlive-extra-utils texlive-latex-extra ttf-staypuft python-nose-doc
gfortran python-numpy-doc python3-numpy-dbg python-pyparsing-doc
python-setuptools-doc tix python3-tk-dbg python3.6-venv python3.6-doc
python3.7-venv python3.7-doc readline-doc ri ruby-dev bundler
Recommended packages:
curl | wget | lynx manpages manpages-dev libarchive-cpio-perl
libglib2.0-data shared-mime-info xdg-user-dirs javascript-common
krb5-locales libgpm2 publicsuffix libsasl2-modules libltdl-dev
libmail-sendmail-perl python3-chardet python3-lxml python3-pil zip
fonts-lato cwltool
The following NEW packages will be installed:
asciidoctor autoconf automake autopoint autotools-dev blt bowtie2
bsdmainutils build-essential ca-certificates cd-hit cpp cpp-8 debhelper
dh-autoreconf dh-python dh-strip-nondeterminism dwz fakeroot fastaq file
fontconfig-config fonts-lyx g++ g++-8 gawk gcc gcc-8 gettext gettext-base
groff-base help2man intltool-debian libarchive-zip-perl libasan5 libatomic1
libblas3 libbsd0 libc-dev-bin libc6-dev libcapnp-0.6.1 libcc1-0 libcroco3
libcurl3-gnutls libelf1 libexpat1 libexpat1-dev libfakeroot
libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig1
libfreetype6 libgcc-8-dev libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3
libgsl23 libgslcblas0 libgssapi-krb5-2 libharfbuzz0b libhts2 libicu-le-hb0
libicu60 libisl19 libitm1 libjs-jquery libjs-jquery-ui libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2
libldap-common liblocale-gettext-perl liblsan0 libmagic-mgc libmagic1
libminimap-dev libminimap0 libmpc3 libmpdec2 libmpfr6 libmpx2 libncurses6
libnghttp2-14 libpipeline1 libpng16-16 libpsl5 libpython-stdlib
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-dev
libpython3-stdlib libpython3.6 libpython3.6-dev libpython3.6-minimal
libpython3.6-stdlib libpython3.7-minimal libpython3.7-stdlib libquadmath0
libreadline7 librtmp1 libruby2.5 libsasl2-2 libsasl2-modules-db libsigsegv2
libsqlite3-0 libssh2-1 libssl1.1 libstdc++-8-dev libtbb2 libtcl8.6
libtimedate-perl libtk8.6 libtool libtsan0 libubsan1 libx11-6 libx11-data
libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1
libyaml-0-2 linux-libc-dev m4 man-db mash mime-support mummer openssl
po-debconf python python-matplotlib-data python-minimal python2
python2-minimal python2.7 python2.7-minimal python3 python3-all python3-bs4
python3-cycler python3-dateutil python3-dendropy python3-dev
python3-distutils python3-kiwisolver python3-lib2to3 python3-matplotlib
python3-minimal python3-nose python3-numpy python3-pkg-resources
python3-pymummer python3-pyparsing python3-pysam python3-setuptools
python3-six python3-tk python3-tz python3.6 python3.6-dev python3.6-minimal
python3.7 python3.7-minimal rake readline-common ruby ruby-asciidoctor
ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert
ruby-test-unit ruby-xmlrpc ruby2.5 rubygems-integration samtools
sbuild-build-depends-main-dummy tk8.6-blt2.5 ttf-bitstream-vera ucf
x11-common zlib1g-dev
0 upgraded, 193 newly installed, 0 to remove and 0 not upgraded.
Need to get 155 MB of archives.
After this operation, 499 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy
0.invalid.0 [1016 B]
Get:2 http://proxy:9999/debian sid/main amd64 libbsd0 amd64 0.9.1-1 [99.3 kB]
Get:3 http://proxy:9999/debian sid/main amd64 bsdmainutils amd64 11.1.2+b1 [191
kB]
Get:4 http://proxy:9999/debian sid/main amd64 groff-base amd64 1.22.3-10 [1176
kB]
Get:5 http://proxy:9999/debian sid/main amd64 libpipeline1 amd64 1.5.0-1 [29.0
kB]
Get:6 http://proxy:9999/debian sid/main amd64 man-db amd64 2.8.4-2 [1194 kB]
Get:7 http://proxy:9999/debian sid/main amd64 libpython2.7-minimal amd64
2.7.15-3 [393 kB]
Get:8 http://proxy:9999/debian sid/main amd64 python2.7-minimal amd64 2.7.15-3
[1358 kB]
Get:9 http://proxy:9999/debian sid/main amd64 python2-minimal amd64 2.7.15-3
[41.3 kB]
Get:10 http://proxy:9999/debian sid/main amd64 python-minimal amd64 2.7.15-3
[20.9 kB]
Get:11 http://proxy:9999/debian sid/main amd64 mime-support all 3.61 [37.1 kB]
Get:12 http://proxy:9999/debian sid/main amd64 libexpat1 amd64 2.2.5-3 [96.8 kB]
Get:13 http://proxy:9999/debian sid/main amd64 readline-common all 7.0-5 [70.6
kB]
Get:14 http://proxy:9999/debian sid/main amd64 libreadline7 amd64 7.0-5 [151 kB]
Get:15 http://proxy:9999/debian sid/main amd64 libsqlite3-0 amd64 3.24.0-1 [608
kB]
Get:16 http://proxy:9999/debian sid/main amd64 libssl1.1 amd64 1.1.0h-4 [1352
kB]
Get:17 http://proxy:9999/debian sid/main amd64 libpython2.7-stdlib amd64
2.7.15-3 [1904 kB]
Get:18 http://proxy:9999/debian sid/main amd64 python2.7 amd64 2.7.15-3 [298 kB]
Get:19 http://proxy:9999/debian sid/main amd64 libpython2-stdlib amd64 2.7.15-3
[20.7 kB]
Get:20 http://proxy:9999/debian sid/main amd64 libpython-stdlib amd64 2.7.15-3
[20.7 kB]
Get:21 http://proxy:9999/debian sid/main amd64 python2 amd64 2.7.15-3 [41.5 kB]
Get:22 http://proxy:9999/debian sid/main amd64 python amd64 2.7.15-3 [22.7 kB]
Get:23 http://proxy:9999/debian sid/main amd64 libmpfr6 amd64 4.0.1-1 [764 kB]
Get:24 http://proxy:9999/debian sid/main amd64 libsigsegv2 amd64 2.12-2 [32.8
kB]
Get:25 http://proxy:9999/debian sid/main amd64 gawk amd64 1:4.1.4+dfsg-1+b1
[571 kB]
Get:26 http://proxy:9999/debian sid/main amd64 liblocale-gettext-perl amd64
1.07-3+b3 [18.7 kB]
Get:27 http://proxy:9999/debian sid/main amd64 libpython3.6-minimal amd64
3.6.6-1 [572 kB]
Get:28 http://proxy:9999/debian sid/main amd64 python3.6-minimal amd64 3.6.6-1
[1649 kB]
Get:29 http://proxy:9999/debian sid/main amd64 python3-minimal amd64 3.6.6-1
[36.4 kB]
Get:30 http://proxy:9999/debian sid/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB]
Get:31 http://proxy:9999/debian sid/main amd64 libpython3.6-stdlib amd64
3.6.6-1 [1709 kB]
Get:32 http://proxy:9999/debian sid/main amd64 python3.6 amd64 3.6.6-1 [234 kB]
Get:33 http://proxy:9999/debian sid/main amd64 libpython3-stdlib amd64 3.6.6-1
[19.8 kB]
Get:34 http://proxy:9999/debian sid/main amd64 python3 amd64 3.6.6-1 [47.5 kB]
Get:35 http://proxy:9999/debian sid/main amd64 libpython3.7-minimal amd64
3.7.0-4 [590 kB]
Get:36 http://proxy:9999/debian sid/main amd64 python3.7-minimal amd64 3.7.0-4
[1727 kB]
Get:37 http://proxy:9999/debian sid/main amd64 libmagic-mgc amd64 1:5.34-2 [239
kB]
Get:38 http://proxy:9999/debian sid/main amd64 libmagic1 amd64 1:5.34-2 [116 kB]
Get:39 http://proxy:9999/debian sid/main amd64 file amd64 1:5.34-2 [65.8 kB]
Get:40 http://proxy:9999/debian sid/main amd64 gettext-base amd64 0.19.8.1-6+b1
[122 kB]
Get:41 http://proxy:9999/debian sid/main amd64 ucf all 3.0038 [67.8 kB]
Get:42 http://proxy:9999/debian sid/main amd64 openssl amd64 1.1.0h-4 [744 kB]
Get:43 http://proxy:9999/debian sid/main amd64 ca-certificates all 20180409
[161 kB]
Get:44 http://proxy:9999/debian sid/main amd64 rubygems-integration all 1.11
[4994 B]
Get:45 http://proxy:9999/debian sid/main amd64 rake all 12.3.1-3 [66.9 kB]
Get:46 http://proxy:9999/debian sid/main amd64 ruby-did-you-mean all 1.2.1-1
[14.4 kB]
Get:47 http://proxy:9999/debian sid/main amd64 ruby-minitest all 5.10.3-1 [53.5
kB]
Get:48 http://proxy:9999/debian sid/main amd64 ruby-net-telnet all 0.1.1-2
[12.5 kB]
Get:49 http://proxy:9999/debian sid/main amd64 ruby-power-assert all 1.1.1-1
[10.9 kB]
Get:50 http://proxy:9999/debian sid/main amd64 ruby-test-unit all 3.2.7-1 [72.3
kB]
Get:51 http://proxy:9999/debian sid/main amd64 ruby-xmlrpc all 0.3.0-2 [23.7 kB]
Get:52 http://proxy:9999/debian sid/main amd64 libncurses6 amd64 6.1+20180714-1
[102 kB]
Get:53 http://proxy:9999/debian sid/main amd64 libyaml-0-2 amd64 0.2.1-1 [47.2
kB]
Get:54 http://proxy:9999/debian sid/main amd64 libruby2.5 amd64 2.5.1-5 [3419
kB]
Get:55 http://proxy:9999/debian sid/main amd64 ruby2.5 amd64 2.5.1-5 [385 kB]
Get:56 http://proxy:9999/debian sid/main amd64 ruby amd64 1:2.5.1 [11.3 kB]
Get:57 http://proxy:9999/debian sid/main amd64 ruby-asciidoctor all 1.5.7.1-1
[183 kB]
Get:58 http://proxy:9999/debian sid/main amd64 asciidoctor amd64 1.5.7.1-1
[63.9 kB]
Get:59 http://proxy:9999/debian sid/main amd64 m4 amd64 1.4.18-1 [202 kB]
Get:60 http://proxy:9999/debian sid/main amd64 autoconf all 2.69-11 [341 kB]
Get:61 http://proxy:9999/debian sid/main amd64 autotools-dev all 20180224.1
[77.0 kB]
Get:62 http://proxy:9999/debian sid/main amd64 automake all 1:1.16.1-1 [771 kB]
Get:63 http://proxy:9999/debian sid/main amd64 autopoint all 0.19.8.1-6 [434 kB]
Get:64 http://proxy:9999/debian sid/main amd64 libtcl8.6 amd64 8.6.8+dfsg-4
[988 kB]
Get:65 http://proxy:9999/debian sid/main amd64 libpng16-16 amd64 1.6.34-2 [288
kB]
Get:66 http://proxy:9999/debian sid/main amd64 libfreetype6 amd64 2.8.1-2 [461
kB]
Get:67 http://proxy:9999/debian sid/main amd64 ttf-bitstream-vera all 1.10-8
[352 kB]
Get:68 http://proxy:9999/debian sid/main amd64 fontconfig-config all 2.13.0-5
[280 kB]
Get:69 http://proxy:9999/debian sid/main amd64 libfontconfig1 amd64 2.13.0-5
[343 kB]
Get:70 http://proxy:9999/debian sid/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9
kB]
Get:71 http://proxy:9999/debian sid/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3
kB]
Get:72 http://proxy:9999/debian sid/main amd64 libxcb1 amd64 1.13-2 [136 kB]
Get:73 http://proxy:9999/debian sid/main amd64 libx11-data all 2:1.6.5-1 [292
kB]
Get:74 http://proxy:9999/debian sid/main amd64 libx11-6 amd64 2:1.6.5-1 [749 kB]
Get:75 http://proxy:9999/debian sid/main amd64 libxext6 amd64 2:1.3.3-1+b2
[52.5 kB]
Get:76 http://proxy:9999/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1
[33.0 kB]
Get:77 http://proxy:9999/debian sid/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB]
Get:78 http://proxy:9999/debian sid/main amd64 x11-common all 1:7.7+19 [251 kB]
Get:79 http://proxy:9999/debian sid/main amd64 libxss1 amd64 1:1.2.2-1+b2 [16.5
kB]
Get:80 http://proxy:9999/debian sid/main amd64 libtk8.6 amd64 8.6.8-4 [752 kB]
Get:81 http://proxy:9999/debian sid/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-4
[587 kB]
Get:82 http://proxy:9999/debian sid/main amd64 blt amd64 2.5.3+dfsg-4 [14.8 kB]
Get:83 http://proxy:9999/debian sid/main amd64 libatomic1 amd64 8.2.0-3 [8892 B]
Get:84 http://proxy:9999/debian sid/main amd64 libtbb2 amd64 2017~U7-8 [140 kB]
Get:85 http://proxy:9999/debian sid/main amd64 bowtie2 amd64 2.3.4.1-2 [1180 kB]
Get:86 http://proxy:9999/debian sid/main amd64 libc-dev-bin amd64 2.27-5 [271
kB]
Get:87 http://proxy:9999/debian sid/main amd64 linux-libc-dev amd64 4.17.8-1
[1479 kB]
Get:88 http://proxy:9999/debian sid/main amd64 libc6-dev amd64 2.27-5 [2666 kB]
Get:89 http://proxy:9999/debian sid/main amd64 libisl19 amd64 0.20-1 [587 kB]
Get:90 http://proxy:9999/debian sid/main amd64 libmpc3 amd64 1.1.0-1 [41.3 kB]
Get:91 http://proxy:9999/debian sid/main amd64 cpp-8 amd64 8.2.0-3 [7193 kB]
Get:92 http://proxy:9999/debian sid/main amd64 cpp amd64 4:8.1.0-1 [19.2 kB]
Get:93 http://proxy:9999/debian sid/main amd64 libcc1-0 amd64 8.2.0-3 [38.6 kB]
Get:94 http://proxy:9999/debian sid/main amd64 libgomp1 amd64 8.2.0-3 [75.6 kB]
Get:95 http://proxy:9999/debian sid/main amd64 libitm1 amd64 8.2.0-3 [27.8 kB]
Get:96 http://proxy:9999/debian sid/main amd64 libasan5 amd64 8.2.0-3 [360 kB]
Get:97 http://proxy:9999/debian sid/main amd64 liblsan0 amd64 8.2.0-3 [130 kB]
Get:98 http://proxy:9999/debian sid/main amd64 libtsan0 amd64 8.2.0-3 [283 kB]
Get:99 http://proxy:9999/debian sid/main amd64 libubsan1 amd64 8.2.0-3 [119 kB]
Get:100 http://proxy:9999/debian sid/main amd64 libmpx2 amd64 8.2.0-3 [11.4 kB]
Get:101 http://proxy:9999/debian sid/main amd64 libquadmath0 amd64 8.2.0-3 [133
kB]
Get:102 http://proxy:9999/debian sid/main amd64 libgcc-8-dev amd64 8.2.0-3
[2295 kB]
Get:103 http://proxy:9999/debian sid/main amd64 gcc-8 amd64 8.2.0-3 [7627 kB]
Get:104 http://proxy:9999/debian sid/main amd64 gcc amd64 4:8.1.0-1 [5192 B]
Get:105 http://proxy:9999/debian sid/main amd64 libstdc++-8-dev amd64 8.2.0-3
[1525 kB]
Get:106 http://proxy:9999/debian sid/main amd64 g++-8 amd64 8.2.0-3 [7767 kB]
Get:107 http://proxy:9999/debian sid/main amd64 g++ amd64 4:8.1.0-1 [1636 B]
Get:108 http://proxy:9999/debian sid/main amd64 build-essential amd64 12.5
[7556 B]
Get:109 http://proxy:9999/debian sid/main amd64 cd-hit amd64 4.6.8-1 [517 kB]
Get:110 http://proxy:9999/debian sid/main amd64 libtool all 2.4.6-2.1 [547 kB]
Get:111 http://proxy:9999/debian sid/main amd64 dh-autoreconf all 19 [16.9 kB]
Get:112 http://proxy:9999/debian sid/main amd64 libarchive-zip-perl all 1.60-1
[95.6 kB]
Get:113 http://proxy:9999/debian sid/main amd64
libfile-stripnondeterminism-perl all 0.042-1 [20.1 kB]
Get:114 http://proxy:9999/debian sid/main amd64 libtimedate-perl all 2.3000-2
[42.2 kB]
Get:115 http://proxy:9999/debian sid/main amd64 dh-strip-nondeterminism all
0.042-1 [12.1 kB]
Get:116 http://proxy:9999/debian sid/main amd64 libelf1 amd64 0.170-0.5 [162 kB]
Get:117 http://proxy:9999/debian sid/main amd64 dwz amd64 0.12-2 [77.5 kB]
Get:118 http://proxy:9999/debian sid/main amd64 libglib2.0-0 amd64 2.56.1-2
[2928 kB]
Get:119 http://proxy:9999/debian sid/main amd64 libgraphite2-3 amd64 1.3.11-2
[85.2 kB]
Get:120 http://proxy:9999/debian sid/main amd64 libharfbuzz0b amd64 1.8.5-1
[893 kB]
Get:121 http://proxy:9999/debian sid/main amd64 libicu-le-hb0 amd64
1.0.3+git161113-5 [14.6 kB]
Get:122 http://proxy:9999/debian sid/main amd64 libicu60 amd64 60.2-6 [8073 kB]
Get:123 http://proxy:9999/debian sid/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b1
[725 kB]
Get:124 http://proxy:9999/debian sid/main amd64 libcroco3 amd64 0.6.12-2 [144
kB]
Get:125 http://proxy:9999/debian sid/main amd64 gettext amd64 0.19.8.1-6+b1
[1302 kB]
Get:126 http://proxy:9999/debian sid/main amd64 intltool-debian all
0.35.0+20060710.4 [26.3 kB]
Get:127 http://proxy:9999/debian sid/main amd64 po-debconf all 1.0.20 [247 kB]
Get:128 http://proxy:9999/debian sid/main amd64 debhelper all 11.3.5 [981 kB]
Get:129 http://proxy:9999/debian sid/main amd64 python3-lib2to3 all 3.6.6-1
[79.1 kB]
Get:130 http://proxy:9999/debian sid/main amd64 python3-distutils all 3.6.6-1
[144 kB]
Get:131 http://proxy:9999/debian sid/main amd64 dh-python all 3.20180723 [94.2
kB]
Get:132 http://proxy:9999/debian sid/main amd64 libfakeroot amd64 1.23-1 [45.9
kB]
Get:133 http://proxy:9999/debian sid/main amd64 fakeroot amd64 1.23-1 [85.8 kB]
Get:134 http://proxy:9999/debian sid/main amd64 python3-pkg-resources all
39.2.0-1 [142 kB]
Get:135 http://proxy:9999/debian sid/main amd64 libkeyutils1 amd64 1.5.9-9.3
[13.0 kB]
Get:136 http://proxy:9999/debian sid/main amd64 libkrb5support0 amd64 1.16-2
[62.8 kB]
Get:137 http://proxy:9999/debian sid/main amd64 libk5crypto3 amd64 1.16-2 [121
kB]
Get:138 http://proxy:9999/debian sid/main amd64 libkrb5-3 amd64 1.16-2 [316 kB]
Get:139 http://proxy:9999/debian sid/main amd64 libgssapi-krb5-2 amd64 1.16-2
[158 kB]
Get:140 http://proxy:9999/debian sid/main amd64 libsasl2-modules-db amd64
2.1.27~101-g0780600+dfsg-3.1 [68.6 kB]
Get:141 http://proxy:9999/debian sid/main amd64 libsasl2-2 amd64
2.1.27~101-g0780600+dfsg-3.1 [105 kB]
Get:142 http://proxy:9999/debian sid/main amd64 libldap-common all
2.4.46+dfsg-5 [88.3 kB]
Get:143 http://proxy:9999/debian sid/main amd64 libldap-2.4-2 amd64
2.4.46+dfsg-5 [223 kB]
Get:144 http://proxy:9999/debian sid/main amd64 libnghttp2-14 amd64 1.32.0-1
[83.0 kB]
Get:145 http://proxy:9999/debian sid/main amd64 libpsl5 amd64 0.20.2-1 [53.7 kB]
Get:146 http://proxy:9999/debian sid/main amd64 librtmp1 amd64
2.4+20151223.gitfa8646d.1-2 [60.5 kB]
Get:147 http://proxy:9999/debian sid/main amd64 libssh2-1 amd64 1.8.0-2 [138 kB]
Get:148 http://proxy:9999/debian sid/main amd64 libcurl3-gnutls amd64 7.60.0-2
[314 kB]
Get:149 http://proxy:9999/debian sid/main amd64 libhts2 amd64 1.7-2 [311 kB]
Get:150 http://proxy:9999/debian sid/main amd64 samtools amd64 1.7-2+b1 [410 kB]
Get:151 http://proxy:9999/debian sid/main amd64 fastaq all 3.17.0-2 [47.8 kB]
Get:152 http://proxy:9999/debian sid/main amd64 fonts-lyx all 2.3.0-2 [198 kB]
Get:153 http://proxy:9999/debian sid/main amd64 help2man amd64 1.47.6 [169 kB]
Get:154 http://proxy:9999/debian sid/main amd64 libgfortran5 amd64 8.2.0-3 [583
kB]
Get:155 http://proxy:9999/debian sid/main amd64 libblas3 amd64 3.8.0-1+b1 [148
kB]
Get:156 http://proxy:9999/debian sid/main amd64 libcapnp-0.6.1 amd64 0.6.1-1
[661 kB]
Get:157 http://proxy:9999/debian sid/main amd64 libexpat1-dev amd64 2.2.5-3
[140 kB]
Get:158 http://proxy:9999/debian sid/main amd64 libfml0 amd64 0.1-5 [69.3 kB]
Get:159 http://proxy:9999/debian sid/main amd64 zlib1g-dev amd64
1:1.2.11.dfsg-1 [214 kB]
Get:160 http://proxy:9999/debian sid/main amd64 libfml-dev amd64 0.1-5 [81.4 kB]
Get:161 http://proxy:9999/debian sid/main amd64 libgslcblas0 amd64 2.5+dfsg-4
[96.8 kB]
Get:162 http://proxy:9999/debian sid/main amd64 libgsl23 amd64 2.5+dfsg-4 [878
kB]
Get:163 http://proxy:9999/debian sid/main amd64 libjs-jquery all 3.2.1-1 [154
kB]
Get:164 http://proxy:9999/debian sid/main amd64 libjs-jquery-ui all
1.12.1+dfsg-5 [232 kB]
Get:165 http://proxy:9999/debian sid/main amd64 liblapack3 amd64 3.8.0-1+b1
[2112 kB]
Get:166 http://proxy:9999/debian sid/main amd64 libminimap0 amd64 0.2-4 [23.0
kB]
Get:167 http://proxy:9999/debian sid/main amd64 libminimap-dev amd64 0.2-4
[33.8 kB]
Get:168 http://proxy:9999/debian sid/main amd64 libpython3.6 amd64 3.6.6-1
[1415 kB]
Get:169 http://proxy:9999/debian sid/main amd64 libpython3.6-dev amd64 3.6.6-1
[44.8 MB]
Get:170 http://proxy:9999/debian sid/main amd64 libpython3-dev amd64 3.6.6-1
[19.9 kB]
Get:171 http://proxy:9999/debian sid/main amd64 libpython3.7-stdlib amd64
3.7.0-4 [1733 kB]
Get:172 http://proxy:9999/debian sid/main amd64 mash amd64 2.0-2 [142 kB]
Get:173 http://proxy:9999/debian sid/main amd64 mummer amd64 3.23+dfsg-4 [809
kB]
Get:174 http://proxy:9999/debian sid/main amd64 python-matplotlib-data all
2.2.2-4 [4123 kB]
Get:175 http://proxy:9999/debian sid/main amd64 python3.7 amd64 3.7.0-4 [309 kB]
Get:176 http://proxy:9999/debian sid/main amd64 python3-all amd64 3.6.6-1 [1060
B]
Get:177 http://proxy:9999/debian sid/main amd64 python3-bs4 all 4.6.0-1 [88.1
kB]
Get:178 http://proxy:9999/debian sid/main amd64 python3-six all 1.11.0-2 [15.2
kB]
Get:179 http://proxy:9999/debian sid/main amd64 python3-cycler all 0.10.0-1
[7556 B]
Get:180 http://proxy:9999/debian sid/main amd64 python3-dateutil all 2.6.1-1
[52.8 kB]
Get:181 http://proxy:9999/debian sid/main amd64 python3-dendropy all 4.4.0-1
[265 kB]
Get:182 http://proxy:9999/debian sid/main amd64 python3.6-dev amd64 3.6.6-1
[507 kB]
Get:183 http://proxy:9999/debian sid/main amd64 python3-dev amd64 3.6.6-1 [1260
B]
Get:184 http://proxy:9999/debian sid/main amd64 python3-kiwisolver amd64
1.0.1-2+b1 [65.4 kB]
Get:185 http://proxy:9999/debian sid/main amd64 python3-pyparsing all
2.2.0+dfsg1-2 [89.6 kB]
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Setting up python3-pyparsing (2.2.0+dfsg1-2) ...
Setting up python3-cycler (0.10.0-1) ...
Setting up python3-pkg-resources (39.2.0-1) ...
Setting up python3-bs4 (4.6.0-1) ...
Setting up libpython3.6-dev:amd64 (3.6.6-1) ...
Setting up python2 (2.7.15-3) ...
Setting up gcc-8 (8.2.0-3) ...
Setting up g++-8 (8.2.0-3) ...
Setting up libpython-stdlib:amd64 (2.7.15-3) ...
Setting up python3-nose (1.3.7-4) ...
Setting up libxrender1:amd64 (1:0.9.10-1) ...
Setting up libkrb5-3:amd64 (1.16-2) ...
Setting up libxft2:amd64 (2.3.2-2) ...
Setting up python3-dendropy (4.4.0-1) ...
Setting up python3.6-dev (3.6.6-1) ...
Setting up python3-lib2to3 (3.6.6-1) ...
Setting up python3-tz (2018.5-1) ...
Setting up python3-distutils (3.6.6-1) ...
Setting up python (2.7.15-3) ...
Setting up python3-dateutil (2.6.1-1) ...
Setting up libpython3-dev:amd64 (3.6.6-1) ...
Setting up libtool (2.4.6-2.1) ...
Setting up python3-kiwisolver (1.0.1-2+b1) ...
Setting up libxext6:amd64 (2:1.3.3-1+b2) ...
Setting up python3-numpy (1:1.14.5-1+b1) ...
Setting up libxss1:amd64 (1:1.2.2-1+b2) ...
Setting up gcc (4:8.1.0-1) ...
Setting up bowtie2 (2.3.4.1-2) ...
Setting up libgssapi-krb5-2:amd64 (1.16-2) ...
Setting up g++ (4:8.1.0-1) ...
update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto
mode
Setting up python3-setuptools (39.2.0-1) ...
Setting up python3-matplotlib (2.2.2-4+b1) ...
Setting up dh-python (3.20180723) ...
Setting up build-essential (12.5) ...
Setting up libcurl3-gnutls:amd64 (7.60.0-2) ...
Setting up libtk8.6:amd64 (8.6.8-4) ...
Setting up python3-dev (3.6.6-1) ...
Setting up tk8.6-blt2.5 (2.5.3+dfsg-4) ...
Setting up python3-all (3.6.6-1) ...
Setting up libhts2:amd64 (1.7-2) ...
Setting up blt (2.5.3+dfsg-4) ...
Setting up python3-pysam (0.14+ds-2+b1) ...
Setting up python3-tk:amd64 (3.6.6-1) ...
Setting up samtools (1.7-2+b1) ...
Setting up fastaq (3.17.0-2) ...
Setting up python3-pymummer (0.10.3-1) ...
Setting up dh-autoreconf (19) ...
Setting up rake (12.3.1-3) ...
Setting up libicu-le-hb0:amd64 (1.0.3+git161113-5) ...
Setting up libruby2.5:amd64 (2.5.1-5) ...
Setting up libicu60:amd64 (60.2-6) ...
Setting up libxml2:amd64 (2.9.4+dfsg1-7+b1) ...
Setting up libcroco3:amd64 (0.6.12-2) ...
Setting up ruby2.5 (2.5.1-5) ...
Setting up gettext (0.19.8.1-6+b1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up ruby (1:2.5.1) ...
Setting up po-debconf (1.0.20) ...
Setting up ruby-asciidoctor (1.5.7.1-1) ...
Setting up debhelper (11.3.5) ...
Setting up asciidoctor (1.5.7.1-1) ...
Setting up dh-strip-nondeterminism (0.042-1) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-5) ...
Processing triggers for ca-certificates (20180409) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (amd64 included in any)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.17.0-1-amd64 #1 SMP Debian 4.17.8-1 (2018-07-20) amd64 (x86_64)
Toolchain package versions: binutils_2.31.1-2 dpkg-dev_1.19.0.5 g++-8_8.2.0-3
gcc-8_8.2.0-3 libc6-dev_2.27-5 libstdc++-8-dev_8.2.0-3 libstdc++6_8.2.0-3
linux-libc-dev_4.17.8-1
Package versions: adduser_3.117 apt_1.6.3 asciidoctor_1.5.7.1-1
autoconf_2.69-11 automake_1:1.16.1-1 autopoint_0.19.8.1-6
autotools-dev_20180224.1 base-files_10.1 base-passwd_3.5.45 bash_4.4.18-3.1
binutils_2.31.1-2 binutils-common_2.31.1-2 binutils-x86-64-linux-gnu_2.31.1-2
blt_2.5.3+dfsg-4 bowtie2_2.3.4.1-2 bsdmainutils_11.1.2+b1 bsdutils_1:2.32-0.4
build-essential_12.5 bzip2_1.0.6-8.1 ca-certificates_20180409 ccache_3.4.2-1
cd-hit_4.6.8-1 coreutils_8.28-1 cpp_4:8.1.0-1 cpp-8_8.2.0-3 dash_0.5.8-2.10
debconf_1.5.69 debhelper_11.3.5 debian-archive-keyring_2017.7 debianutils_4.8.6
dh-autoreconf_19 dh-python_3.20180723 dh-strip-nondeterminism_0.042-1
diffutils_1:3.6-1 dpkg_1.19.0.5+b1 dpkg-dev_1.19.0.5 dwz_0.12-2
e2fslibs_1.44.3-1 e2fsprogs_1.44.3-1 fakeroot_1.23-1 fastaq_3.17.0-2
fdisk_2.32-0.4 file_1:5.34-2 findutils_4.6.0+git+20171230-2
fontconfig-config_2.13.0-5 fonts-lyx_2.3.0-2 g++_4:8.1.0-1 g++-8_8.2.0-3
gawk_1:4.1.4+dfsg-1+b1 gcc_4:8.1.0-1 gcc-8_8.2.0-3 gcc-8-base_8.2.0-3
gettext_0.19.8.1-6+b1 gettext-base_0.19.8.1-6+b1 gpgv_2.2.9-1 grep_3.1-2
groff-base_1.22.3-10 gzip_1.9-2 help2man_1.47.6 hostname_3.20 init_1.51
init-system-helpers_1.51 initscripts_2.88dsf-59.10 insserv_1.14.0-5.4+b1
intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3+b1 libapt-pkg5.0_1.6.3
libarchive-zip-perl_1.60-1 libasan5_8.2.0-3 libatomic1_8.2.0-3
libattr1_1:2.4.47-2+b2 libaudit-common_1:2.8.3-1 libaudit1_1:2.8.3-1+b1
libbinutils_2.31.1-2 libblas3_3.8.0-1+b1 libblkid1_2.32-0.4 libbsd0_0.9.1-1
libbz2-1.0_1.0.6-8.1 libc-bin_2.27-5 libc-dev-bin_2.27-5 libc6_2.27-5
libc6-dev_2.27-5 libcap-ng0_0.7.9-1 libcapnp-0.6.1_0.6.1-1 libcc1-0_8.2.0-3
libcom-err2_1.44.3-1 libcroco3_0.6.12-2 libcurl3-gnutls_7.60.0-2
libdb5.3_5.3.28-13.1+b1 libdebconfclient0_0.244 libdpkg-perl_1.19.0.5
libelf1_0.170-0.5 libexpat1_2.2.5-3 libexpat1-dev_2.2.5-3 libext2fs2_1.44.3-1
libfakeroot_1.23-1 libfdisk1_2.32-0.4 libffi6_3.2.1-8
libfile-stripnondeterminism-perl_0.042-1 libfml-dev_0.1-5 libfml0_0.1-5
libfontconfig1_2.13.0-5 libfreetype6_2.8.1-2 libgcc-8-dev_8.2.0-3
libgcc1_1:8.2.0-3 libgcrypt20_1.8.3-1 libgdbm-compat4_1.14.1-6+b1
libgdbm5_1.14.1-6+b1 libgfortran5_8.2.0-3 libglib2.0-0_2.56.1-2
libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.19-1 libgomp1_8.2.0-3
libgpg-error0_1.32-1 libgraphite2-3_1.3.11-2 libgsl23_2.5+dfsg-4
libgslcblas0_2.5+dfsg-4 libgssapi-krb5-2_1.16-2 libharfbuzz0b_1.8.5-1
libhogweed4_3.4-1 libhts2_1.7-2 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6
libidn2-0_2.0.4-2.2 libisl19_0.20-1 libitm1_8.2.0-3 libjs-jquery_3.2.1-1
libjs-jquery-ui_1.12.1+dfsg-5 libk5crypto3_1.16-2 libkeyutils1_1.5.9-9.3
libkrb5-3_1.16-2 libkrb5support0_1.16-2 liblapack3_3.8.0-1+b1
libldap-2.4-2_2.4.46+dfsg-5 libldap-common_2.4.46+dfsg-5
liblocale-gettext-perl_1.07-3+b3 liblsan0_8.2.0-3 liblz4-1_1.8.2-1
liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2
libminimap-dev_0.2-4 libminimap0_0.2-4 libmount1_2.32-0.4 libmpc3_1.1.0-1
libmpdec2_2.4.2-2 libmpfr6_4.0.1-1 libmpx2_8.2.0-3 libncurses6_6.1+20180714-1
libncursesw6_6.1+20180714-1 libnettle6_3.4-1 libnghttp2-14_1.32.0-1
libp11-kit0_0.23.12-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7
libpam-runtime_1.1.8-3.7 libpam0g_1.1.8-3.7 libpcre3_2:8.39-11
libperl5.26_5.26.2-6 libpipeline1_1.5.0-1 libpng16-16_1.6.34-2 libpsl5_0.20.2-1
libpython-stdlib_2.7.15-3 libpython2-stdlib_2.7.15-3
libpython2.7-minimal_2.7.15-3 libpython2.7-stdlib_2.7.15-3
libpython3-dev_3.6.6-1 libpython3-stdlib_3.6.6-1 libpython3.6_3.6.6-1
libpython3.6-dev_3.6.6-1 libpython3.6-minimal_3.6.6-1
libpython3.6-stdlib_3.6.6-1 libpython3.7-minimal_3.7.0-4
libpython3.7-stdlib_3.7.0-4 libquadmath0_8.2.0-3 libreadline7_7.0-5
librtmp1_2.4+20151223.gitfa8646d.1-2 libruby2.5_2.5.1-5
libsasl2-2_2.1.27~101-g0780600+dfsg-3.1
libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-3
libselinux1_2.8-1+b1 libsemanage-common_2.8-1 libsemanage1_2.8-1+b1
libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.32-0.4 libsqlite3-0_3.24.0-1
libss2_1.44.3-1 libssh2-1_1.8.0-2 libssl1.1_1.1.0h-4 libstdc++-8-dev_8.2.0-3
libstdc++6_8.2.0-3 libsystemd0_239-7 libtasn1-6_4.13-3 libtbb2_2017~U7-8
libtcl8.6_8.6.8+dfsg-4 libtimedate-perl_2.3000-2 libtinfo6_6.1+20180714-1
libtk8.6_8.6.8-4 libtool_2.4.6-2.1 libtsan0_8.2.0-3 libubsan1_8.2.0-3
libudev1_239-7 libunistring2_0.9.10-1 libuuid1_2.32-0.4 libx11-6_2:1.6.5-1
libx11-data_2:1.6.5-1 libxau6_1:1.0.8-1+b2 libxcb1_1.13-2 libxdmcp6_1:1.1.2-3
libxext6_2:1.3.3-1+b2 libxft2_2.3.2-2 libxml2_2.9.4+dfsg1-7+b1
libxrender1_1:0.9.10-1 libxss1_1:1.2.2-1+b2 libyaml-0-2_0.2.1-1
libzstd1_1.3.4+dfsg-3 linux-libc-dev_4.17.8-1 login_1:4.5-1.1
lsb-base_9.20170808 m4_1.4.18-1 make_4.2.1-1.2 man-db_2.8.4-2 mash_2.0-2
mawk_1.3.3-17+b3 mime-support_3.61 mount_2.32-0.4 mummer_3.23+dfsg-4
ncurses-base_6.1+20180714-1 ncurses-bin_6.1+20180714-1 openssl_1.1.0h-4
passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.26.2-6 perl-base_5.26.2-6
perl-modules-5.26_5.26.2-6 po-debconf_1.0.20 python_2.7.15-3
python-matplotlib-data_2.2.2-4 python-minimal_2.7.15-3 python2_2.7.15-3
python2-minimal_2.7.15-3 python2.7_2.7.15-3 python2.7-minimal_2.7.15-3
python3_3.6.6-1 python3-all_3.6.6-1 python3-bs4_4.6.0-1 python3-cycler_0.10.0-1
python3-dateutil_2.6.1-1 python3-dendropy_4.4.0-1 python3-dev_3.6.6-1
python3-distutils_3.6.6-1 python3-kiwisolver_1.0.1-2+b1 python3-lib2to3_3.6.6-1
python3-matplotlib_2.2.2-4+b1 python3-minimal_3.6.6-1 python3-nose_1.3.7-4
python3-numpy_1:1.14.5-1+b1 python3-pkg-resources_39.2.0-1
python3-pymummer_0.10.3-1 python3-pyparsing_2.2.0+dfsg1-2
python3-pysam_0.14+ds-2+b1 python3-setuptools_39.2.0-1 python3-six_1.11.0-2
python3-tk_3.6.6-1 python3-tz_2018.5-1 python3.6_3.6.6-1 python3.6-dev_3.6.6-1
python3.6-minimal_3.6.6-1 python3.7_3.7.0-4 python3.7-minimal_3.7.0-4
rake_12.3.1-3 readline-common_7.0-5 ruby_1:2.5.1 ruby-asciidoctor_1.5.7.1-1
ruby-did-you-mean_1.2.1-1 ruby-minitest_5.10.3-1 ruby-net-telnet_0.1.1-2
ruby-power-assert_1.1.1-1 ruby-test-unit_3.2.7-1 ruby-xmlrpc_0.3.0-2
ruby2.5_2.5.1-5 rubygems-integration_1.11 samtools_1.7-2+b1
sbuild-build-depends-main-dummy_0.invalid.0 sed_4.5-1 sensible-utils_0.0.12
startpar_0.59-4 sysv-rc_2.88dsf-59.10 sysvinit-core_2.88dsf-59.10
sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-2 tk8.6-blt2.5_2.5.3+dfsg-4
ttf-bitstream-vera_1.10-8 tzdata_2018e-1 ucf_3.0038 util-linux_2.32-0.4
x11-common_1:7.7+19 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1
zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: ariba
Binary: ariba
Architecture: any
Version: 2.12.1+ds-1
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Uploaders: Sascha Steinbiss <sa...@debian.org>
Homepage: https://github.com/sanger-pathogens/ariba
Standards-Version: 4.1.4
Vcs-Browser: https://salsa.debian.org/med-team/ariba
Vcs-Git: https://salsa.debian.org/med-team/ariba.git
Testsuite: autopkgtest
Build-Depends: debhelper (>= 11), python3, python3-all, python3-dev,
python3-dendropy (>= 4.2.0), python3-setuptools, python3-pymummer (>= 0.10.2),
python3-pysam (>= 0.9.1), python3-nose (>= 1.3), python3-bs4 (>= 4.1.0),
python3-matplotlib, python3-tk, bowtie2 (>= 2.1.0), cd-hit, mash,
libminimap-dev, libfml-dev (>= 0.1-3), mummer, fastaq (>= 3.12.0), help2man,
asciidoctor
Package-List:
ariba deb science optional arch=any
Checksums-Sha1:
824b7e8cd2a63ad82ddd862400a767b004f3e19e 350652 ariba_2.12.1+ds.orig.tar.xz
7af4e63ae5e0094d32020c16ca4826caf927ea7c 6088 ariba_2.12.1+ds-1.debian.tar.xz
Checksums-Sha256:
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ariba_2.12.1+ds.orig.tar.xz
cbb9d3388b85088cddd49ba0d7b2fcf06c2fa29bfab11da9281ab785442a9e88 6088
ariba_2.12.1+ds-1.debian.tar.xz
Files:
d51e0a4cc0f3df3992a3bd4556f2dc66 350652 ariba_2.12.1+ds.orig.tar.xz
8289473254a3ccdebd237760edcdd386 6088 ariba_2.12.1+ds-1.debian.tar.xz
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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General
error
gpgv: Signature made Wed Jun 20 11:04:53 2018 UTC
gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./ariba_2.12.1+ds-1.dsc
dpkg-source: info: extracting ariba in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking ariba_2.12.1+ds.orig.tar.xz
dpkg-source: info: unpacking ariba_2.12.1+ds-1.debian.tar.xz
dpkg-source: info: applying use_debian_packaged_libs_for_extension.patch
dpkg-source: info: applying use_bwa_compatible_fermi-lite.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
CCACHE_COMPRESS=1
CCACHE_DIR=/var/cache/ccache-sbuild
CCACHE_UMASK=002
HOME=/sbuild-nonexistent
LANG=bg_BG.UTF-8
LC_ALL=POSIX
LC_MEASUREMENT=bg_BG.UTF-8
LC_MONETARY=bg_BG.UTF-8
LC_NUMERIC=bg_BG.UTF-8
LC_PAPER=bg_BG.UTF-8
LC_TIME=bg_BG.UTF-8
LOGNAME=dam
PATH=/usr/lib/ccache:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/<<PKGBUILDDIR>>
SCHROOT_ALIAS_NAME=sid
SCHROOT_CHROOT_NAME=sid
SCHROOT_COMMAND=env
SCHROOT_GID=1000
SCHROOT_GROUP=dam
SCHROOT_SESSION_ID=sid-fa0d2234-8ccc-4429-af64-e6dcf305c240
SCHROOT_UID=1000
SCHROOT_USER=dam
SHELL=/bin/sh
USER=dam
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package ariba
dpkg-buildpackage: info: source version 2.12.1+ds-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Sascha Steinbiss <sa...@debian.org>
dpkg-source --before-build ariba-2.12.1+ds
dpkg-buildpackage: info: host architecture amd64
fakeroot debian/rules clean
dh clean --with python3 --buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -rf /<<PKGBUILDDIR>>/debian/man
dh_auto_clean --
I: pybuild base:217: python3.7 setup.py clean
running clean
removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build' (and everything
under it)
'build/bdist.linux-amd64' does not exist -- can't clean it
'build/scripts-3.7' does not exist -- can't clean it
I: pybuild base:217: python3.6 setup.py clean
running clean
removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.6_ariba/build' (and everything
under it)
'build/bdist.linux-amd64' does not exist -- can't clean it
'build/scripts-3.6' does not exist -- can't clean it
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean -O--buildsystem=pybuild
debian/rules build
dh build --with python3 --buildsystem=pybuild
dh_update_autotools_config -O--buildsystem=pybuild
dh_autoreconf -O--buildsystem=pybuild
dh_auto_configure -O--buildsystem=pybuild
I: pybuild base:217: python3.7 setup.py config
running config
I: pybuild base:217: python3.6 setup.py config
running config
dh_auto_build -O--buildsystem=pybuild
I: pybuild base:217: /usr/bin/python3.7 setup.py build
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/samtools_variants.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/ref_seq_chooser.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/sequence_metadata.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/pubmlst_ref_preparer.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/common.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/summary.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/ref_preparer.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/refdata_query.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/vfdb_parser.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/megares_data_finder.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/assembly.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/external_progs.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/report.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/bam_parse.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/read_filter.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/ref_genes_getter.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/mic_plotter.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/histogram.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/versions.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/card_record.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/read_store.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/flag.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/mlst_profile.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/faidx.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/megares_zip_parser.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/summary_cluster_variant.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/summary_cluster.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/cdhit.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/report_flag_expander.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/assembly_compare.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/sequence_variant.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/clusters.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/summary_sample.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/aln_to_metadata.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/mapping.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/assembly_variants.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/scaffold_graph.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/reference_data.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/link.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/cluster.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/mlst_reporter.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/report_filter.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
copying ariba/pubmlst_getter.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
copying ariba/tasks/getref.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
copying ariba/tasks/summary.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
copying ariba/tasks/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
copying ariba/tasks/prepareref.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
copying ariba/tasks/aln2meta.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
copying ariba/tasks/test.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
copying ariba/tasks/micplot.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
copying ariba/tasks/refquery.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
copying ariba/tasks/flag.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
copying ariba/tasks/version.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
copying ariba/tasks/run.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
copying ariba/tasks/pubmlstget.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
copying ariba/tasks/reportfilter.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
copying ariba/tasks/expandflag.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
copying ariba/tasks/pubmlstspecies.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/test_run_data
copying ariba/test_run_data/ref_seqs.fa ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/test_run_data
copying ariba/test_run_data/reads_1.fq ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/test_run_data
copying ariba/test_run_data/reads_2.fq ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/test_run_data
copying ariba/test_run_data/metadata.tsv ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/test_run_data
copying ariba/test_run_data/ref_fasta_to_make_reads_from.fa ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/test_run_data
running build_ext
building 'minimap_ariba' extension
creating build
creating build/temp.linux-amd64-3.7
creating build/temp.linux-amd64-3.7/ariba
creating build/temp.linux-amd64-3.7/ariba/ext
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
-I/usr/include/minimap -I/usr/include/python3.7m -c ariba/ext/minimap_ariba.cpp
-o build/temp.linux-amd64-3.7/ariba/ext/minimap_ariba.o
ariba/ext/minimap_ariba.cpp:15:10: fatal error: Python.h: No such file or
directory
#include "Python.h"
^~~~~~~~~~
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
E: pybuild pybuild:338: build: plugin distutils failed with: exit code=1:
/usr/bin/python3.7 setup.py build
dh_auto_build: pybuild --build --test-nose -i python{version} -p "3.7 3.6"
returned exit code 13
make: *** [debian/rules:10: build] Error 25
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2018-08-07T08:13:50Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: amd64
Build Type: binary
Build-Space: 6420
Build-Time: 4
Distribution: sid
Fail-Stage: build
Host Architecture: amd64
Install-Time: 43
Job: /tmp/prebuild-ariba-dVRr1vT8em/ariba_2.12.1+ds-1.dsc
Machine Architecture: amd64
Package: ariba
Package-Time: 58
Source-Version: 2.12.1+ds-1
Space: 6420
Status: attempted
Version: 2.12.1+ds-1
--------------------------------------------------------------------------------
Finished at 2018-08-07T08:13:50Z
Build needed 00:00:58, 6420k disk space
