snp-sites →
2.4.0-1 →
armhf → 2018-06-17 05:18:42
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01
+==============================================================================+
| snp-sites 2.4.0-1 (armhf) Sun, 17 Jun 2018 05:07:38 +0000 |
+==============================================================================+
Package: snp-sites
Version: 2.4.0-1
Source Version: 2.4.0-1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/buster-staging-armhf-sbuild-c2d1cc80-7efc-4dc5-9d73-f47ec36af124' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.8 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.6 MB]
Fetched 23.4 MB in 29s (821 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'snp-sites' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/snp-sites.git
Please use:
git clone https://salsa.debian.org/med-team/snp-sites.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 15.6 MB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main snp-sites 2.4.0-1 (dsc) [1945 B]
Get:2 http://172.17.0.1/private buster-staging/main snp-sites 2.4.0-1 (tar) [15.6 MB]
Get:3 http://172.17.0.1/private buster-staging/main snp-sites 2.4.0-1 (diff) [7888 B]
Fetched 15.6 MB in 4s (4035 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/snp-sites-UpNCQ7/snp-sites-2.4.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/snp-sites-UpNCQ7' 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-lXmMJT/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-lXmMJT/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-lXmMJT/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-lXmMJT/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-lXmMJT/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-lXmMJT/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-lXmMJT/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-lXmMJT/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-lXmMJT/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2966 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-lXmMJT/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-lXmMJT/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:
ca-certificates e2fsprogs-l10n libsasl2-modules libssl1.1 openssl
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 51 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-lXmMJT/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15544 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 (>= 11), zlib1g-dev, check, pkg-config, d-shlibs, asciidoctor
Filtered Build-Depends: debhelper (>= 11), zlib1g-dev, check, pkg-config, d-shlibs, asciidoctor
dpkg-deb: building package 'sbuild-build-depends-snp-sites-dummy' in '/<<BUILDDIR>>/resolver-lXmMJT/apt_archive/sbuild-build-depends-snp-sites-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-snp-sites-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-lXmMJT/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-lXmMJT/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-lXmMJT/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-lXmMJT/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-lXmMJT/apt_archive ./ Sources [527 B]
Get:5 copy:/<<BUILDDIR>>/resolver-lXmMJT/apt_archive ./ Packages [606 B]
Fetched 2466 B in 1s (3811 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-lXmMJT/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-lXmMJT/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install snp-sites 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:
e2fsprogs-l10n libsasl2-modules
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
asciidoctor autoconf automake autopoint autotools-dev bsdmainutils check
d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
libcroco3 libelf1 libfile-stripnondeterminism-perl libfreetype6 libglib2.0-0
libgraphite2-3 libharfbuzz0b libicu-le-hb0 libicu60 libmagic-mgc libmagic1
libpipeline1 libruby2.5 libsigsegv2 libsubunit-dev libsubunit0
libtimedate-perl libtool libxml2 libyaml-0-2 m4 man-db pkg-config po-debconf
rake ruby ruby-asciidoctor ruby-did-you-mean ruby-minitest ruby-net-telnet
ruby-power-assert ruby-test-unit ruby-xmlrpc ruby2.5 rubygems-integration
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
www-browser libmail-box-perl ri ruby-dev bundler
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libmail-sendmail-perl zip fonts-lato libjs-jquery
The following NEW packages will be installed:
asciidoctor autoconf automake autopoint autotools-dev bsdmainutils check
d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
libcroco3 libelf1 libfile-stripnondeterminism-perl libfreetype6 libglib2.0-0
libgraphite2-3 libharfbuzz0b libicu-le-hb0 libicu60 libmagic-mgc libmagic1
libpipeline1 libruby2.5 libsigsegv2 libsubunit-dev libsubunit0
libtimedate-perl libtool libxml2 libyaml-0-2 m4 man-db pkg-config po-debconf
rake ruby ruby-asciidoctor ruby-did-you-mean ruby-minitest ruby-net-telnet
ruby-power-assert ruby-test-unit ruby-xmlrpc ruby2.5 rubygems-integration
sbuild-build-depends-snp-sites-dummy zlib1g-dev
0 upgraded, 56 newly installed, 0 to remove and 51 not upgraded.
Need to get 25.3 MB of archives.
After this operation, 86.0 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-lXmMJT/apt_archive ./ sbuild-build-depends-snp-sites-dummy 0.invalid.0 [892 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.3-2 [1146 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.33-3 [234 kB]
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Get:9 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.33-3 [64.7 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-6 [117 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf rubygems-integration all 1.11 [4994 B]
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Get:16 http://172.17.0.1/private buster-staging/main armhf ruby-power-assert all 1.1.1-1 [10.9 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf ruby-test-unit all 3.2.7-1 [72.3 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf ruby-xmlrpc all 0.3.0-1 [23.5 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libyaml-0-2 armhf 0.1.7-2 [39.9 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libruby2.5 armhf 2.5.1-3 [3125 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf ruby2.5 armhf 2.5.1-3 [384 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf ruby armhf 1:2.5.1 [11.3 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf ruby-asciidoctor all 1.5.7.1-1 [183 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf asciidoctor armhf 1.5.7.1-1 [63.9 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3.1 [736 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-6 [434 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libsubunit0 armhf 1.1.0-5 [8912 B]
Get:32 http://172.17.0.1/private buster-staging/main armhf libsubunit-dev armhf 1.1.0-5 [9836 B]
Get:33 http://172.17.0.1/private buster-staging/main armhf check armhf 0.10.0-3 [178 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf d-shlibs all 0.82 [18.8 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2.1 [547 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.042-1 [20.1 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.042-1 [12.1 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.4 [160 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.56.1-2 [2754 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libfreetype6 armhf 2.8.1-2 [402 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libgraphite2-3 armhf 1.3.11-2 [73.5 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.7.6-1+b1 [799 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb0 armhf 1.0.3+git161113-5 [12.8 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libicu60 armhf 60.2-6 [7789 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7 [602 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-2 [132 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-6 [1218 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.3.2 [994 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf pkg-config armhf 0.29-4 [59.2 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
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Unpacking sbuild-build-depends-snp-sites-dummy (0.invalid.0) ...
Setting up ruby-xmlrpc (0.3.0-1) ...
Setting up libarchive-zip-perl (1.60-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libelf1:armhf (0.170-0.4) ...
Setting up groff-base (1.22.3-10) ...
Setting up libglib2.0-0:armhf (2.56.1-2) ...
No schema files found: doing nothing.
Setting up libsubunit0:armhf (1.1.0-5) ...
Setting up d-shlibs (0.82) ...
Setting up gettext-base (0.19.8.1-6) ...
Setting up libpipeline1:armhf (1.5.0-1) ...
Setting up m4 (1.4.18-1) ...
Setting up libbsd0:armhf (0.9.1-1) ...
Setting up libfreetype6:armhf (2.8.1-2) ...
Setting up libmagic-mgc (1:5.33-3) ...
Setting up libmagic1:armhf (1:5.33-3) ...
Setting up libgraphite2-3:armhf (1.3.11-2) ...
Setting up libsubunit-dev:armhf (1.1.0-5) ...
Setting up pkg-config (0.29-4) ...
Setting up ruby-did-you-mean (1.2.1-1) ...
Setting up libyaml-0-2:armhf (0.1.7-2) ...
Processing triggers for libc-bin (2.27-3+rpi1) ...
Setting up dwz (0.12-2) ...
Setting up autotools-dev (20180224.1) ...
Setting up ruby-net-telnet (0.1.1-2) ...
Setting up check:armhf (0.10.0-3) ...
Setting up rubygems-integration (1.11) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up ruby-minitest (5.10.3-1) ...
Setting up autopoint (0.19.8.1-6) ...
Setting up ruby-power-assert (1.1.1-1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up libfile-stripnondeterminism-perl (0.042-1) ...
Setting up ruby-test-unit (3.2.7-1) ...
Setting up libharfbuzz0b:armhf (1.7.6-1+b1) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.33-3) ...
Setting up automake (1:1.15.1-3.1) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-2.1) ...
Setting up rake (12.3.1-3) ...
Setting up libicu-le-hb0:armhf (1.0.3+git161113-5) ...
Setting up dh-strip-nondeterminism (0.042-1) ...
Setting up libruby2.5:armhf (2.5.1-3) ...
Setting up libicu60:armhf (60.2-6) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up ruby2.5 (2.5.1-3) ...
Setting up gettext (0.19.8.1-6) ...
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 (11.3.2) ...
Setting up dh-autoreconf (19) ...
Setting up asciidoctor (1.5.7.1-1) ...
Setting up sbuild-build-depends-snp-sites-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-3+rpi1) ...
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.30-15+rpi1 dpkg-dev_1.19.0.5 g++-7_7.3.0-12 gcc-7_7.3.0-12 libc6-dev_2.27-3+rpi1 libstdc++-7-dev_7.3.0-12 libstdc++6_8.1.0-3+rpi1 linux-libc-dev_4.16.5-1+rpi1
Package versions: adduser_3.117 apt_1.6.1 asciidoctor_1.5.7.1-1 autoconf_2.69-11 automake_1:1.15.1-3.1 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-2+b1 binutils_2.30-15+rpi1 binutils-arm-linux-gnueabihf_2.30-15+rpi1 binutils-common_2.30-15+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.32-0.1 build-essential_12.4+b1 bzip2_1.0.6-8.1 ca-certificates_20170717 check_0.10.0-3 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.3.0-12 d-shlibs_0.82 dash_0.5.8-2.10 debconf_1.5.66 debhelper_11.3.2 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.042-1 diffutils_1:3.6-1 dirmngr_2.2.5-1 dmsetup_2:1.02.145-4.1+b4 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.2-1 e2fsprogs_1.44.2-1 e2fsprogs-l10n_1.44.2-1 fakeroot_1.22-2 fdisk_2.31.1-0.5 file_1:5.33-3 findutils_4.6.0+git+20171230-2 g++_4:7.2.0-1d1 g++-7_7.3.0-12 gcc_4:7.2.0-1d1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1 gcc-5-base_5.5.0-8 gcc-7_7.3.0-12 gcc-7-base_7.3.0-12 gcc-8-base_8.1.0-3+rpi1 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gnupg_2.2.5-1 gnupg-agent_2.2.5-1 gnupg-l10n_2.2.5-1 gnupg-utils_2.2.5-1 gpg_2.2.5-1 gpg-agent_2.2.5-1 gpg-wks-client_2.2.5-1 gpg-wks-server_2.2.5-1 gpgconf_2.2.5-1 gpgsm_2.2.5-1 gpgv_2.2.5-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5 hostname_3.20 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-11+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.12-4 libapt-pkg5.0_1.6.1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-2 libasan4_7.3.0-12 libassuan0_2.5.1-2 libatomic1_8.1.0-3+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.3-1 libaudit1_1:2.8.3-1 libbinutils_2.30-15+rpi1 libblkid1_2.32-0.1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-3+rpi1 libc-dev-bin_2.27-3+rpi1 libc6_2.27-3+rpi1 libc6-dev_2.27-3+rpi1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.1.0-3+rpi1 libcilkrts5_7.3.0-12 libcom-err2_1.44.2-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.8-2 libdebconfclient0_0.243 libdevmapper1.02.1_2:1.02.145-4.1+b4 libdpkg-perl_1.19.0.5 libdrm-common_2.4.91-2+rpi1 libdrm2_2.4.91-2+rpi1 libelf1_0.170-0.4 libext2fs2_1.44.2-1 libfakeroot_1.22-2 libfdisk1_2.32-0.1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.042-1 libfreetype6_2.8.1-2 libgcc-7-dev_7.3.0-12 libgcc1_1:8.1.0-3+rpi1 libgcrypt20_1.8.2-2 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libglib2.0-0_2.56.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1 libgomp1_8.1.0-3+rpi1 libgpg-error0_1.31-1 libgraphite2-3_1.3.11-2 libharfbuzz0b_1.7.6-1+b1 libhogweed4_3.4-1 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.4-1.1 libip4tc0_1.6.2-1 libisl15_0.18-4 libjson-c3_0.12.1-1.3 libklibc_2.0.4-11+rpi1 libkmod2_25-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.46+dfsg-5+rpi1 libldap-common_2.4.46+dfsg-5+rpi1 liblz4-1_1.8.2-1+rpi1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.33-3 libmagic1_1:5.33-3 libmount1_2.32-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1+20180210-4 libncurses6_6.1+20180210-4 libncursesw5_6.1+20180210-4 libncursesw6_6.1+20180210-4 libnettle6_3.4-1 libnpth0_1.5-3 libp11-kit0_0.23.10-2 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_2:8.39-9 libperl5.24_5.24.1-7 libperl5.26_5.26.2-5 libpipeline1_1.5.0-1 libplymouth4_0.9.3-3 libpng16-16_1.6.34-1 libprocps7_2:3.3.15-1 libreadline7_7.0-3 libruby2.5_2.5.1-3 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-2 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-2 libsigsegv2_2.12-2 libsmartcols1_2.32-0.1 libsqlite3-0_3.23.1-1 libss2_1.44.2-1 libssl1.1_1.1.0h-4 libstdc++-7-dev_7.3.0-12 libstdc++6_8.1.0-3+rpi1 libsubunit-dev_1.1.0-5 libsubunit0_1.1.0-5 libsystemd0_238-4 libtasn1-6_4.13-3 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180210-4 libtinfo6_6.1+20180210-4 libtool_2.4.6-2.1 libubsan0_7.3.0-12 libudev1_238-4 libunistring2_0.9.8-1 libustr-1.0-1_1.0.4-6 libuuid1_2.32-0.1 libxml2_2.9.4+dfsg1-7 libyaml-0-2_0.1.7-2 libzstd1_1.3.4+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.16.5-1+rpi1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.8.3-2 mawk_1.3.3-17 mount_2.32-0.1 multiarch-support_2.27-3+rpi1 nano_2.9.5-1 ncurses-base_6.1+20180210-4 ncurses-bin_6.1-1 netbase_5.4 openssl_1.1.0h-4 passwd_1:4.5-1 patch_2.7.6-2 perl_5.26.2-5 perl-base_5.26.2-5 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-5 pinentry-curses_1.1.0-1 pkg-config_0.29-4 plymouth_0.9.3-3 po-debconf_1.0.20 procps_2:3.3.15-1 rake_12.3.1-3 raspbian-archive-keyring_20120528.2 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_0.3.0-1 ruby2.5_2.5.1-3 rubygems-integration_1.11 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-snp-sites-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_238-4 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-2 tzdata_2018e-1 udev_238-4 util-linux_2.31.1-0.5 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
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Thu Jun 14 22:12:42 2018 UTC
gpgv: using RSA key 8451F9178172E7E2DC73F79551F84A8FECCA7E09
gpgv: issuer "satta@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./snp-sites_2.4.0-1.dsc
dpkg-source: info: extracting snp-sites in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking snp-sites_2.4.0.orig.tar.gz
dpkg-source: info: unpacking snp-sites_2.4.0-1.debian.tar.xz
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=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-c2d1cc80-7efc-4dc5-9d73-f47ec36af124
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package snp-sites
dpkg-buildpackage: info: source version 2.4.0-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build snp-sites-2.4.0
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --with autoreconf
dh_clean
debian/rules build-arch
dh build-arch --with autoreconf
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:13: installing './compile'
configure.ac:7: installing './config.guess'
configure.ac:7: installing './config.sub'
configure.ac:2: installing './install-sh'
configure.ac:2: 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 --libexecdir=\${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 build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for CHECK... yes
checking for style of include used by make... GNU
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 how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking 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 getopt.h usability... yes
checking getopt.h presence... yes
checking for getopt.h... yes
checking for floor in -lm... yes
checking if zlib is wanted... yes
checking for inflateEnd in -lz... yes
checking for zlib.h... (cached) yes
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
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... mt
checking if mt is a manifest tool... no
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 that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/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'
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -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 -I/usr/include -I/usr/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcf.lo vcf.c
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylib-of-snp-sites.lo phylib-of-snp-sites.c
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -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 -I/usr/include -I/usr/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c phylib-of-snp-sites.c -fPIC -DPIC -o .libs/phylib-of-snp-sites.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -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 -I/usr/include -I/usr/include -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 -I/usr/include -I/usr/include -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 -I/usr/include -I/usr/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c phylib-of-snp-sites.c -o phylib-of-snp-sites.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -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 -I/usr/include -I/usr/include -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 -I/usr/include -I/usr/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c vcf.c -o vcf.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -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
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -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
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include --std=c99 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snp_sites-main.o `test -f 'main.c' || echo './'`main.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -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
/bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 1:0 -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib -o libsnp-sites.la -rpath /usr/lib/arm-linux-gnueabihf alignment-file.lo vcf.lo phylib-of-snp-sites.lo snp-sites.lo fasta-of-snp-sites.lo -lz -lm
libtool: link: gcc -shared -fPIC -DPIC .libs/alignment-file.o .libs/vcf.o .libs/phylib-of-snp-sites.o .libs/snp-sites.o .libs/fasta-of-snp-sites.o -L/usr/lib -lz -lm -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libsnp-sites.so.1 -o .libs/libsnp-sites.so.1.0.0
libtool: link: (cd ".libs" && rm -f "libsnp-sites.so.1" && ln -s "libsnp-sites.so.1.0.0" "libsnp-sites.so.1")
libtool: link: (cd ".libs" && rm -f "libsnp-sites.so" && ln -s "libsnp-sites.so.1.0.0" "libsnp-sites.so")
libtool: link: ar cru .libs/libsnp-sites.a alignment-file.o vcf.o phylib-of-snp-sites.o snp-sites.o fasta-of-snp-sites.o
ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: ranlib .libs/libsnp-sites.a
libtool: link: ( cd ".libs" && rm -f "libsnp-sites.la" && ln -s "../libsnp-sites.la" "libsnp-sites.la" )
/bin/bash ../libtool --tag=CC --mode=link gcc --std=c99 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib -o snp-sites snp_sites-main.o libsnp-sites.la -lpthread -lz -lm
libtool: link: gcc --std=c99 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/snp-sites snp_sites-main.o -L/usr/lib ./.libs/libsnp-sites.so -lpthread -lz -lm
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
make -j4 check VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making check in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make run-all-tests
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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/usr/include -I/usr/include -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check-vcf.o `test -f '../tests/check-vcf.c' || echo './'`../tests/check-vcf.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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/usr/include -I/usr/include -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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
/bin/bash ../libtool --tag=CC --mode=link gcc -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib -o run-all-tests ../tests/run_all_tests-check-snp-sites.o ../tests/run_all_tests-check-vcf.o ../tests/run_all_tests-helper-methods.o ../tests/run_all_tests-run-all-tests.o libsnp-sites.la -lpthread -lcheck_pic -pthread -lrt -lm -lsubunit -lz -lm
libtool: link: gcc -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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-snp-sites.o ../tests/run_all_tests-check-vcf.o ../tests/run_all_tests-helper-methods.o ../tests/run_all_tests-run-all-tests.o -pthread -L/usr/lib ./.libs/libsnp-sites.so -lpthread -lcheck_pic -lrt -lsubunit -lz -lm -pthread
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make check-TESTS
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src'
PASS: run-all-tests
============================================================================
Testsuite summary for snp-sites 2.4.0
============================================================================
# TOTAL: 1
# PASS: 1
# SKIP: 0
# XFAIL: 0
# FAIL: 0
# XPASS: 0
# ERROR: 0
============================================================================
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --with autoreconf
dh_testroot -a
dh_prep -a
dh_auto_install -a
make -j1 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making install in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf'
/bin/bash ../libtool --mode=install /usr/bin/install -c libsnp-sites.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/libsnp-sites.so.1.0.0 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.so.1.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libsnp-sites.so.1.0.0 libsnp-sites.so.1 || { rm -f libsnp-sites.so.1 && ln -s libsnp-sites.so.1.0.0 libsnp-sites.so.1; }; })
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libsnp-sites.so.1.0.0 libsnp-sites.so || { rm -f libsnp-sites.so && ln -s libsnp-sites.so.1.0.0 libsnp-sites.so; }; })
libtool: install: /usr/bin/install -c .libs/libsnp-sites.lai /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.la
libtool: install: /usr/bin/install -c .libs/libsnp-sites.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.a
libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/bin/bash ../libtool --mode=install /usr/bin/install -c snp-sites '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
libtool: warning: 'libsnp-sites.la' has not been installed in '/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/snp-sites /<<PKGBUILDDIR>>/debian/tmp/usr/bin/snp-sites
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/include/snp-sites'
/usr/bin/install -c -m 644 alignment-file.h vcf.h phylib-of-snp-sites.h snp-sites.h fasta-of-snp-sites.h kseq.h '/<<PKGBUILDDIR>>/debian/tmp/usr/include/snp-sites'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
ls -ARl
.:
total 1720
-rw-r--r-- 1 root root 397 Jan 29 16:18 .gitignore
drwxr-xr-x 1 root root 100 Jun 17 05:15 .pc
-rw-r--r-- 1 root root 177 Jan 29 16:18 .travis.yml
-rw-r--r-- 1 root root 109 Jan 29 16:18 AUTHORS
-rw-r--r-- 1 root root 224 Jan 29 16:18 Dockerfile
-rw-r--r-- 1 root root 1742 Jan 29 16:18 INSTALL
-rw-r--r-- 1 root root 33565 Jan 29 16:18 LICENSE
-rw-rw-r-- 1 root root 26197 Jun 17 05:17 Makefile
-rw-r--r-- 1 root root 36 Jan 29 16:18 Makefile.am
-rw-rw-r-- 1 root root 25607 Jun 17 05:16 Makefile.in
-rw-r--r-- 1 root root 6158 Jan 29 16:18 README.md
-rw-r--r-- 1 root root 6 Jan 29 16:18 VERSION
-rw-rw-r-- 1 root root 52578 Jun 17 05:16 aclocal.m4
drwxr-xr-x 1 root root 112 Jun 17 05:16 autom4te.cache
-rwxr-xr-x 1 root root 7333 Jun 17 05:16 compile
-rwxr-xr-x 1 root root 44283 Jun 17 05:16 config.guess
-rw-rw-r-- 1 root root 2181 Jun 17 05:17 config.h
-rw-rw-r-- 1 root root 1980 Jun 17 05:16 config.h.in
-rw-rw-r-- 1 root root 40989 Jun 17 05:17 config.log
-rwxrwxr-x 1 root root 69548 Jun 17 05:17 config.status
-rwxr-xr-x 1 root root 36136 Jun 17 05:16 config.sub
-rwxrwxr-x 1 root root 609847 Jun 17 05:16 configure
-rw-r--r-- 1 root root 569 Jan 29 16:18 configure.ac
drwxr-xr-x 1 root root 498 Jun 17 05:17 debian
-rwxr-xr-x 1 root root 23567 Jun 17 05:16 depcomp
drwxr-xr-x 1 root root 92 Jan 29 16:18 example_data
-rwxr-xr-x 1 root root 15155 Jun 17 05:16 install-sh
-rwxrwxr-x 1 root root 351151 Jun 17 05:17 libtool
-rw-r--r-- 1 root root 330179 Jun 17 05:16 ltmain.sh
drwxr-xr-x 1 root root 162 Jun 17 05:16 m4
-rwxr-xr-x 1 root root 6872 Jun 17 05:16 missing
drwxr-xr-x 1 root root 62 Jan 29 16:18 paper_supporting_material
-rw-r--r-- 1 root root 1971 Jan 29 16:18 snp-sites.txt
drwxr-xr-x 1 root root 890 Jun 17 05:17 src
-rw-rw-r-- 1 root root 23 Jun 17 05:17 stamp-h1
-rwxr-xr-x 1 root root 4640 Jun 17 05:16 test-driver
drwxr-xr-x 1 root root 472 Jun 17 05:17 tests
./.pc:
total 12
-rw-r--r-- 1 root root 15 Jun 17 05:15 .quilt_patches
-rw-r--r-- 1 root root 7 Jun 17 05:15 .quilt_series
-rw-r--r-- 1 root root 2 Jun 17 05:15 .version
-rw-r--r-- 1 root root 0 Jun 17 05:15 applied-patches
./autom4te.cache:
total 2064
-rw-rw-r-- 1 root root 612826 Jun 17 05:16 output.0
-rw-rw-r-- 1 root root 612826 Jun 17 05:16 output.1
-rw-rw-r-- 1 root root 612826 Jun 17 05:16 output.2
-rw-rw-r-- 1 root root 23978 Jun 17 05:16 requests
-rw-rw-r-- 1 root root 100543 Jun 17 05:16 traces.0
-rw-rw-r-- 1 root root 39708 Jun 17 05:16 traces.1
-rw-rw-r-- 1 root root 98399 Jun 17 05:16 traces.2
./debian:
total 60
-rw-rw-r-- 1 root root 5308 Jun 17 05:16 autoreconf.after
-rw-rw-r-- 1 root root 4020 Jun 17 05:15 autoreconf.before
-rw-r--r-- 1 root root 3135 Jun 14 15:29 changelog
-rw-r--r-- 1 root root 3 Jun 14 15:29 compat
-rw-r--r-- 1 root root 2926 Jun 14 15:29 control
-rw-r--r-- 1 root root 2334 Jun 14 15:29 copyright
-rw-rw-r-- 1 root root 42 Jun 17 05:17 debhelper-build-stamp
-rw-r--r-- 1 root root 10 Jun 14 15:29 docs
drwxrwxr-x 1 root root 0 Jun 17 05:17 libsnp-sites1
drwxrwxr-x 1 root root 0 Jun 17 05:17 libsnp-sites1-dev
-rw-r--r-- 1 root root 504 Jun 14 15:29 libsnp-sites1-dev.README.Debian
-rwxr-xr-x 1 root root 635 Jun 14 15:29 rules
drwxrwxr-x 1 root root 0 Jun 17 05:17 snp-sites
-rw-r--r-- 1 root root 378 Jun 14 15:29 snp-sites.README.Debian
-rw-r--r-- 1 root root 18 Jun 14 15:29 snp-sites.install
-rw-r--r-- 1 root root 12 Jun 14 15:29 snp-sites.manpages
drwxr-xr-x 1 root root 44 Jun 14 15:29 source
drwxr-xr-x 1 root root 118 Jun 14 15:29 tests
drwxr-xr-x 1 root root 6 Jun 17 05:17 tmp
drwxr-xr-x 1 root root 24 Jun 14 15:29 upstream
-rw-r--r-- 1 root root 122 Jun 14 15:29 watch
./debian/libsnp-sites1:
total 0
./debian/libsnp-sites1-dev:
total 0
./debian/snp-sites:
total 0
./debian/source:
total 8
-rwxr-xr-x 1 root root 12 Jun 14 15:29 format
-rwxr-xr-x 1 root root 57 Jun 14 15:29 include-binaries
./debian/tests:
total 12
-rw-r--r-- 1 root root 3447 Jun 14 15:29 alignment_file_one_line_per_sequence.aln.gz
-rw-r--r-- 1 root root 747 Jun 14 15:29 build-lib
-rw-r--r-- 1 root root 99 Jun 14 15:29 control
./debian/tmp:
total 0
drwxrwxr-x 1 root root 26 Jun 17 05:17 usr
./debian/tmp/usr:
total 0
drwxrwxr-x 1 root root 18 Jun 17 05:17 bin
drwxrwxr-x 1 root root 18 Jun 17 05:17 include
drwxrwxr-x 1 root root 38 Jun 17 05:17 lib
./debian/tmp/usr/bin:
total 24
-rwxr-xr-x 1 root root 23728 Jun 17 05:17 snp-sites
./debian/tmp/usr/include:
total 0
drwxrwxr-x 1 root root 158 Jun 17 05:17 snp-sites
./debian/tmp/usr/include/snp-sites:
total 32
-rw-r--r-- 1 root root 1365 Jun 17 05:17 alignment-file.h
-rw-r--r-- 1 root root 1145 Jun 17 05:17 fasta-of-snp-sites.h
-rw-r--r-- 1 root root 8809 Jun 17 05:17 kseq.h
-rw-r--r-- 1 root root 1149 Jun 17 05:17 phylib-of-snp-sites.h
-rw-r--r-- 1 root root 2050 Jun 17 05:17 snp-sites.h
-rw-r--r-- 1 root root 2005 Jun 17 05:17 vcf.h
./debian/tmp/usr/lib:
total 0
drwxrwxr-x 1 root root 164 Jun 17 05:17 arm-linux-gnueabihf
./debian/tmp/usr/lib/arm-linux-gnueabihf:
total 148
-rw-r--r-- 1 root root 76856 Jun 17 05:17 libsnp-sites.a
-rwxr-xr-x 1 root root 1001 Jun 17 05:17 libsnp-sites.la
lrwxrwxrwx 1 root root 21 Jun 17 05:17 libsnp-sites.so -> libsnp-sites.so.1.0.0
lrwxrwxrwx 1 root root 21 Jun 17 05:17 libsnp-sites.so.1 -> libsnp-sites.so.1.0.0
-rwxr-xr-x 1 root root 59264 Jun 17 05:17 libsnp-sites.so.1.0.0
./debian/upstream:
total 8
-rwxr-xr-x 1 root root 334 Jun 14 15:29 edam
-rw-r--r-- 1 root root 724 Jun 14 15:29 metadata
./example_data:
total 15164
-rw-r--r-- 1 root root 768 Jan 29 16:18 Readme.md
-rw-r--r-- 1 root root 15521067 Jan 29 16:18 salmonella_serovars_core_genes.aln.gz
./m4:
total 344
-rw-r--r-- 1 root root 306297 Jun 17 05:16 libtool.m4
-rw-r--r-- 1 root root 14514 Jun 17 05:16 ltoptions.m4
-rw-r--r-- 1 root root 4384 Jun 17 05:16 ltsugar.m4
-rw-r--r-- 1 root root 699 Jun 17 05:16 ltversion.m4
-rw-r--r-- 1 root root 6140 Jun 17 05:16 lt~obsolete.m4
-rw-r--r-- 1 root root 5416 Jan 29 16:18 m4_ax_check_zlib.m4
-rw-r--r-- 1 root root 0 Jan 29 16:18 test
./paper_supporting_material:
total 4
-rwxr-xr-x 1 root root 2658 Jan 29 16:18 snp_sites_create_simulated_data
./src:
total 332
drwxrwxr-x 1 root root 386 Jun 17 05:17 .libs
-rw-rw-r-- 1 root root 49724 Jun 17 05:17 Makefile
-rw-r--r-- 1 root root 820 Jan 29 16:18 Makefile.am
-rw-rw-r-- 1 root root 51839 Jun 17 05:16 Makefile.in
-rw-r--r-- 1 root root 5399 Jan 29 16:18 alignment-file.c
-rw-r--r-- 1 root root 1365 Jan 29 16:18 alignment-file.h
-rw-rw-r-- 1 root root 311 Jun 17 05:17 alignment-file.lo
-rw-rw-r-- 1 root root 23564 Jun 17 05:17 alignment-file.o
-rw-r--r-- 1 root root 1978 Jan 29 16:18 fasta-of-snp-sites.c
-rw-r--r-- 1 root root 1145 Jan 29 16:18 fasta-of-snp-sites.h
-rw-rw-r-- 1 root root 323 Jun 17 05:17 fasta-of-snp-sites.lo
-rw-rw-r-- 1 root root 7432 Jun 17 05:17 fasta-of-snp-sites.o
-rw-r--r-- 1 root root 8809 Jan 29 16:18 kseq.h
-rw-rw-r-- 1 root root 1000 Jun 17 05:17 libsnp-sites.la
-rw-r--r-- 1 root root 4744 Jan 29 16:18 main.c
-rw-r--r-- 1 root root 2277 Jan 29 16:18 phylib-of-snp-sites.c
-rw-r--r-- 1 root root 1149 Jan 29 16:18 phylib-of-snp-sites.h
-rw-rw-r-- 1 root root 326 Jun 17 05:17 phylib-of-snp-sites.lo
-rw-rw-r-- 1 root root 7808 Jun 17 05:17 phylib-of-snp-sites.o
-rwxrwxr-x 1 root root 6330 Jun 17 05:17 run-all-tests
-rw-rw-r-- 1 root root 340 Jun 17 05:17 run-all-tests.log
-rw-rw-r-- 1 root root 82 Jun 17 05:17 run-all-tests.trs
-rwxrwxr-x 1 root root 6290 Jun 17 05:17 snp-sites
-rw-r--r-- 1 root root 6305 Jan 29 16:18 snp-sites.c
-rw-r--r-- 1 root root 2050 Jan 29 16:18 snp-sites.h
-rw-rw-r-- 1 root root 296 Jun 17 05:17 snp-sites.lo
-rw-rw-r-- 1 root root 15152 Jun 17 05:17 snp-sites.o
-rw-rw-r-- 1 root root 18704 Jun 17 05:17 snp_sites-main.o
-rw-rw-r-- 1 root root 227 Jun 17 05:17 test-suite.log
-rw-r--r-- 1 root root 6713 Jan 29 16:18 vcf.c
-rw-r--r-- 1 root root 2005 Jan 29 16:18 vcf.h
-rw-rw-r-- 1 root root 278 Jun 17 05:17 vcf.lo
-rw-rw-r-- 1 root root 21624 Jun 17 05:17 vcf.o
./src/.libs:
total 348
-rw-rw-r-- 1 root root 23232 Jun 17 05:17 alignment-file.o
-rw-rw-r-- 1 root root 7484 Jun 17 05:17 fasta-of-snp-sites.o
-rw-rw-r-- 1 root root 76856 Jun 17 05:17 libsnp-sites.a
lrwxrwxrwx 1 root root 18 Jun 17 05:17 libsnp-sites.la -> ../libsnp-sites.la
-rw-rw-r-- 1 root root 1001 Jun 17 05:17 libsnp-sites.lai
lrwxrwxrwx 1 root root 21 Jun 17 05:17 libsnp-sites.so -> libsnp-sites.so.1.0.0
lrwxrwxrwx 1 root root 21 Jun 17 05:17 libsnp-sites.so.1 -> libsnp-sites.so.1.0.0
-rwxrwxr-x 1 root root 59264 Jun 17 05:17 libsnp-sites.so.1.0.0
-rw-rw-r-- 1 root root 7864 Jun 17 05:17 phylib-of-snp-sites.o
-rwxrwxr-x 1 root root 92036 Jun 17 05:17 run-all-tests
-rwxrwxr-x 1 root root 23728 Jun 17 05:17 snp-sites
-rw-rw-r-- 1 root root 15072 Jun 17 05:17 snp-sites.o
-rw-rw-r-- 1 root root 21260 Jun 17 05:17 vcf.o
./tests:
total 120
drwxrwxr-x 1 root root 18 Jun 17 05:17 .deps
-rw-rw-r-- 1 root root 0 Jun 17 05:17 .dirstamp
-rw-r--r-- 1 root root 15128 Jan 29 16:18 check-snp-sites.c
-rw-r--r-- 1 root root 938 Jan 29 16:18 check-snp-sites.h
-rw-r--r-- 1 root root 3112 Jan 29 16:18 check-vcf.c
-rw-r--r-- 1 root root 1090 Jan 29 16:18 check-vcf.h
drwxr-xr-x 1 root root 1674 Jan 29 16:18 data
-rw-r--r-- 1 root root 2190 Jan 29 16:18 helper-methods.c
-rw-r--r-- 1 root root 985 Jan 29 16:18 helper-methods.h
-rw-r--r-- 1 root root 1409 Jan 29 16:18 run-all-tests.c
-rw-rw-r-- 1 root root 48040 Jun 17 05:17 run_all_tests-check-snp-sites.o
-rw-rw-r-- 1 root root 13584 Jun 17 05:17 run_all_tests-check-vcf.o
-rw-rw-r-- 1 root root 7792 Jun 17 05:17 run_all_tests-helper-methods.o
-rw-rw-r-- 1 root root 6324 Jun 17 05:17 run_all_tests-run-all-tests.o
./tests/.deps:
total 0
-rw-rw-r-- 1 root root 0 Jun 17 05:17 .dirstamp
./tests/data:
total 724
-rw-r--r-- 1 root root 219249 Jan 29 16:18 alignment_file_multiple_lines_per_sequence.aln
-rw-r--r-- 1 root root 219240 Jan 29 16:18 alignment_file_one_line_per_sequence.aln
-rw-r--r-- 1 root root 3447 Jan 29 16:18 alignment_file_one_line_per_sequence.aln.gz
-rw-r--r-- 1 root root 1683 Jan 29 16:18 alignment_file_one_line_per_sequence.aln.phylip
-rw-r--r-- 1 root root 1786 Jan 29 16:18 alignment_file_one_line_per_sequence.aln.snp_sites.aln
-rw-r--r-- 1 root root 2388 Jan 29 16:18 alignment_file_one_line_per_sequence.aln.vcf
-rw-r--r-- 1 root root 1715 Jan 29 16:18 alignment_file_one_line_per_sequence_reference.aln.phylip
-rw-r--r-- 1 root root 1819 Jan 29 16:18 alignment_file_one_line_per_sequence_reference.snp_sites.aln
-rw-r--r-- 1 root root 219241 Jan 29 16:18 alignment_file_with_n.aln
-rw-r--r-- 1 root root 1683 Jan 29 16:18 alignment_file_with_n.aln.phylip
-rw-r--r-- 1 root root 1786 Jan 29 16:18 alignment_file_with_n.aln.snp_sites.aln
-rw-r--r-- 1 root root 2388 Jan 29 16:18 alignment_file_with_n.aln.vcf
-rw-r--r-- 1 root root 53 Jan 29 16:18 pure_mode_alignment.aln
-rw-r--r-- 1 root root 37 Jan 29 16:18 pure_mode_alignment.aln.phylip
-rw-r--r-- 1 root root 36 Jan 29 16:18 pure_mode_alignment.aln.snp_sites.aln
-rw-r--r-- 1 root root 227 Jan 29 16:18 pure_mode_alignment.aln.vcf
-rw-r--r-- 1 root root 45 Jan 29 16:18 pure_mode_monomorphic_alignment.aln
-rw-r--r-- 1 root root 40 Jan 29 16:18 pure_mode_monomorphic_alignment.aln.phylip
-rw-r--r-- 1 root root 39 Jan 29 16:18 pure_mode_monomorphic_alignment.aln.snp_sites.aln
-rw-r--r-- 1 root root 252 Jan 29 16:18 pure_mode_monomorphic_alignment.aln.vcf
-rw-r--r-- 1 root root 96 Jan 29 16:18 small_alignment.aln
-rw-r--r-- 1 root root 100 Jan 29 16:18 uneven_alignment.aln
dh_install
d-shlibmove --commit \
--multiarch \
--exclude-la \
--movedev "debian/tmp/usr/include/snp-sites/*.h" usr/include/snp-sites \
debian/tmp/usr/lib/*/libsnp-sites.so
Library package automatic movement utility
--> zlib1g-dev package exists.
set -e
install -d -m 755 debian/libsnp-sites1-dev/usr/lib/arm-linux-gnueabihf
install -d -m 755 debian/libsnp-sites1/usr/lib/arm-linux-gnueabihf
mv debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.a debian/libsnp-sites1-dev/usr/lib/arm-linux-gnueabihf
mv debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.so debian/libsnp-sites1-dev/usr/lib/arm-linux-gnueabihf
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.so.1 debian/libsnp-sites1/usr/lib/arm-linux-gnueabihf
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.so.1.0.0 debian/libsnp-sites1/usr/lib/arm-linux-gnueabihf
PKGDEV=libsnp-sites1-dev
PKGSHL=libsnp-sites1
install -d -m 755 debian/libsnp-sites1-dev/usr/include/snp-sites
mv debian/tmp/usr/include/snp-sites/*.h debian/libsnp-sites1-dev/usr/include/snp-sites
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
debian/rules override_dh_installman
make[1]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p /<<PKGBUILDDIR>>/debian/man
asciidoctor -a docdate='' -b manpage /<<PKGBUILDDIR>>/snp-sites.txt
mv /<<PKGBUILDDIR>>/snp-sites.1 /<<PKGBUILDDIR>>/debian/man
dh_installman --
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/snp-sites/usr/bin/snp-sites was not linked against libpthread.so.0 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/snp-sites/usr/bin/snp-sites was not linked against libz.so.1 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/snp-sites/usr/bin/snp-sites was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/snp-sites/usr/bin/snp-sites was not linked against libm.so.6 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libsnp-sites1/usr/lib/arm-linux-gnueabihf/libsnp-sites.so.1.0.0 was not linked against libm.so.6 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: Depends field of package libsnp-sites1-dev: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: package libsnp-sites1-dev: unused substitution variable ${devlibs:Depends}
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'libsnp-sites1' in '../libsnp-sites1_2.4.0-1_armhf.deb'.
dpkg-deb: building package 'snp-sites' in '../snp-sites_2.4.0-1_armhf.deb'.
dpkg-deb: building package 'libsnp-sites1-dev' in '../libsnp-sites1-dev_2.4.0-1_armhf.deb'.
dpkg-deb: building package 'snp-sites-dbgsym' in '../snp-sites-dbgsym_2.4.0-1_armhf.deb'.
dpkg-deb: building package 'libsnp-sites1-dbgsym' in '../libsnp-sites1-dbgsym_2.4.0-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../snp-sites_2.4.0-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build snp-sites-2.4.0
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-06-17T05:17:57Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
snp-sites_2.4.0-1_armhf.changes:
--------------------------------
Format: 1.8
Date: Thu, 14 Jun 2018 17:29:53 +0200
Source: snp-sites
Binary: snp-sites libsnp-sites1 libsnp-sites1-dev
Architecture: armhf
Version: 2.4.0-1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Sascha Steinbiss <satta@debian.org>
Description:
libsnp-sites1 - Shared libraries of the package snp-sites
libsnp-sites1-dev - Static libraries and header files for the package snp-sites
snp-sites - Binary code for the package snp-sites
Changes:
snp-sites (2.4.0-1) unstable; urgency=medium
.
* New upstream version.
* Adjust watchfile to allow 'v' in version tags.
* Update upstream metadata (thanks Steffen Moeller).
* Remove obsolete autotools Build-Depends.
* Use debhelper 11.
* Bump Standards-Version.
* Use secure copyright format URL.
Checksums-Sha1:
c6b7ded35a08f1a20f1b87dbbf9b7eb89adb19e9 17452 libsnp-sites1-dbgsym_2.4.0-1_armhf.deb
cb9b27665a2734154327b54e50377ef0a22f97e7 13296 libsnp-sites1-dev_2.4.0-1_armhf.deb
c6dfe7ea2f856b5b086fae776be28c8b329d37be 10108 libsnp-sites1_2.4.0-1_armhf.deb
c3f126c0c8ea08ce484496d9d98f520a8e7dcd52 6012 snp-sites-dbgsym_2.4.0-1_armhf.deb
c65c9e0cd5247d93853db06b07da1e452407053e 7091 snp-sites_2.4.0-1_armhf.buildinfo
10a6cbe9c464e65395f90eb821fde0f417bf5404 10916 snp-sites_2.4.0-1_armhf.deb
Checksums-Sha256:
eacd0426679aa2fb8e5148eb87ef7615740f575483f1a8fd8c440a59775e7c56 17452 libsnp-sites1-dbgsym_2.4.0-1_armhf.deb
57ad5dca16ebab67aa29405e01481a968c670dfb13ba68df67fa18757604e3bc 13296 libsnp-sites1-dev_2.4.0-1_armhf.deb
d067317988a5fcd04945344be0a24c69db48b3a36caad71d39e79277515a9d99 10108 libsnp-sites1_2.4.0-1_armhf.deb
ceeda9ac5f87781dee4060a9ec40bc5e2837f3a4492a33bf321f5e38d49342a5 6012 snp-sites-dbgsym_2.4.0-1_armhf.deb
8b5e2af1e0adabeddaabb9150659a20591a4bfc3528a76bb40101e418c1e4e55 7091 snp-sites_2.4.0-1_armhf.buildinfo
f72168d11b9060ac72e81accdfce0908d95fe57d700787228c7608e9bcc76ce3 10916 snp-sites_2.4.0-1_armhf.deb
Files:
0a41e4a87d0bfea828325999da9197e9 17452 debug optional libsnp-sites1-dbgsym_2.4.0-1_armhf.deb
ebc4205ab6bab20c50f90b5430e93e3a 13296 libdevel optional libsnp-sites1-dev_2.4.0-1_armhf.deb
ebc6aedb87321b64c1d009a4c21c476b 10108 libs optional libsnp-sites1_2.4.0-1_armhf.deb
f17e7f3cd3d8d52119e296ccc04ffef9 6012 debug optional snp-sites-dbgsym_2.4.0-1_armhf.deb
1aeabed245d936a58682bb85317b7030 7091 science optional snp-sites_2.4.0-1_armhf.buildinfo
3ef01d7ce69c8fe30000a3c14fcbe5ce 10916 science optional snp-sites_2.4.0-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libsnp-sites1-dbgsym_2.4.0-1_armhf.deb
--------------------------------------
new Debian package, version 2.0.
size 17452 bytes: control archive=540 bytes.
389 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: libsnp-sites1-dbgsym
Source: snp-sites
Version: 2.4.0-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 31
Depends: libsnp-sites1 (= 2.4.0-1)
Section: debug
Priority: optional
Description: debug symbols for libsnp-sites1
Build-Ids: 4eddb585a5e9e73aad9c83d406b63cc21fdc5ecd
drwxr-xr-x root/root 0 2018-06-14 15:29 ./
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/lib/
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/lib/debug/.build-id/4e/
-rw-r--r-- root/root 21328 2018-06-14 15:29 ./usr/lib/debug/.build-id/4e/ddb585a5e9e73aad9c83d406b63cc21fdc5ecd.debug
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/share/
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-06-14 15:29 ./usr/share/doc/libsnp-sites1-dbgsym -> libsnp-sites1
libsnp-sites1-dev_2.4.0-1_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 13296 bytes: control archive=1152 bytes.
954 bytes, 24 lines control
740 bytes, 10 lines md5sums
Package: libsnp-sites1-dev
Source: snp-sites
Version: 2.4.0-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 55
Depends: libsnp-sites1 (= 2.4.0-1)
Conflicts: libsnp-sites-dev
Provides: libsnp-sites-dev
Section: libdevel
Priority: optional
Homepage: https://github.com/sanger-pathogens/snp-sites
Description: Static libraries and header files for the package snp-sites
Snp-sites finds single nucleotide polymorphism (SNP) sites from
multi-fasta alignment input files (which might be compressed). Its
output can be in various widely used formats (Multi Fasta Alignment,
Vcf, phylip).
.
The software has been developed at the Wellcome Trust Sanger Institute.
.
This package contains the development files to include snp-sites
into your own code. The library enables Python developers to make
snp-sites function calls (Python bindings) through the Boost Python
Library.
drwxr-xr-x root/root 0 2018-06-14 15:29 ./
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/include/
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/include/snp-sites/
-rw-r--r-- root/root 1365 2018-06-14 15:29 ./usr/include/snp-sites/alignment-file.h
-rw-r--r-- root/root 1145 2018-06-14 15:29 ./usr/include/snp-sites/fasta-of-snp-sites.h
-rw-r--r-- root/root 8809 2018-06-14 15:29 ./usr/include/snp-sites/kseq.h
-rw-r--r-- root/root 1149 2018-06-14 15:29 ./usr/include/snp-sites/phylib-of-snp-sites.h
-rw-r--r-- root/root 2050 2018-06-14 15:29 ./usr/include/snp-sites/snp-sites.h
-rw-r--r-- root/root 2005 2018-06-14 15:29 ./usr/include/snp-sites/vcf.h
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/lib/
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 19096 2018-06-14 15:29 ./usr/lib/arm-linux-gnueabihf/libsnp-sites.a
lrwxrwxrwx root/root 0 2018-06-14 15:29 ./usr/lib/arm-linux-gnueabihf/libsnp-sites.so -> libsnp-sites.so.1.0.0
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/share/
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/share/doc/libsnp-sites1-dev/
-rw-r--r-- root/root 504 2018-06-14 15:29 ./usr/share/doc/libsnp-sites1-dev/README.Debian
-rw-r--r-- root/root 977 2018-06-14 15:29 ./usr/share/doc/libsnp-sites1-dev/changelog.Debian.gz
-rw-r--r-- root/root 2334 2018-06-14 15:29 ./usr/share/doc/libsnp-sites1-dev/copyright
libsnp-sites1_2.4.0-1_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 10108 bytes: control archive=940 bytes.
732 bytes, 19 lines control
238 bytes, 3 lines md5sums
29 bytes, 1 lines shlibs
67 bytes, 2 lines triggers
Package: libsnp-sites1
Source: snp-sites
Version: 2.4.0-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 33
Depends: libc6 (>= 2.4), zlib1g (>= 1:1.1.4)
Section: libs
Priority: optional
Homepage: https://github.com/sanger-pathogens/snp-sites
Description: Shared libraries of the package snp-sites
Snp-sites finds single nucleotide polymorphism (SNP) sites from
multi-fasta alignment input files (which might be compressed). Its
output can be in various widely used formats (Multi Fasta Alignment,
Vcf, phylip).
.
The software has been developed at the Wellcome Trust Sanger Institute.
.
This package contains the dynamic library uses by snp-sites.
drwxr-xr-x root/root 0 2018-06-14 15:29 ./
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/lib/
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/lib/arm-linux-gnueabihf/
lrwxrwxrwx root/root 0 2018-06-14 15:29 ./usr/lib/arm-linux-gnueabihf/libsnp-sites.so.1 -> libsnp-sites.so.1.0.0
-rw-r--r-- root/root 17668 2018-06-14 15:29 ./usr/lib/arm-linux-gnueabihf/libsnp-sites.so.1.0.0
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/share/
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/share/doc/libsnp-sites1/
-rw-r--r-- root/root 977 2018-06-14 15:29 ./usr/share/doc/libsnp-sites1/changelog.Debian.gz
-rw-r--r-- root/root 2334 2018-06-14 15:29 ./usr/share/doc/libsnp-sites1/copyright
snp-sites-dbgsym_2.4.0-1_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 6012 bytes: control archive=536 bytes.
377 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: snp-sites-dbgsym
Source: snp-sites
Version: 2.4.0-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 19
Depends: snp-sites (= 2.4.0-1)
Section: debug
Priority: optional
Description: debug symbols for snp-sites
Build-Ids: 4437dc66b3f29f705dab1777f474e1090c59959c
drwxr-xr-x root/root 0 2018-06-14 15:29 ./
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/lib/
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/lib/debug/.build-id/44/
-rw-r--r-- root/root 8940 2018-06-14 15:29 ./usr/lib/debug/.build-id/44/37dc66b3f29f705dab1777f474e1090c59959c.debug
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/share/
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-06-14 15:29 ./usr/share/doc/snp-sites-dbgsym -> snp-sites
snp-sites_2.4.0-1_armhf.deb
---------------------------
new Debian package, version 2.0.
size 10916 bytes: control archive=1160 bytes.
1159 bytes, 24 lines control
409 bytes, 6 lines md5sums
Package: snp-sites
Version: 2.4.0-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 33
Depends: libc6 (>= 2.4), libsnp-sites1, zlib1g (>= 1:1.1.4)
Section: science
Priority: optional
Homepage: https://github.com/sanger-pathogens/snp-sites
Description: Binary code for the package snp-sites
This program finds single nucleotide polymorphism (SNP) sites from
multi-fasta alignment input files (which might be compressed). Its
output can be in various widely used formats (Multi Fasta Alignment,
Vcf, phylip).
.
The software has been developed at the Wellcome Trust Sanger Institute.
.
A Single Nucleotide - polymorphism (SNP, pronounced snip; plural snips)
is a DNA sequence variation occurring when a Single Nucleotide — A, T, C
or G — in the genome (or other shared sequence) differs between members
of a biological species or paired chromosomes. For example, two
sequenced DNA fragments from different individuals, AAGCCTA to AAGCTTA,
contain a difference in a single nucleotide. In this case there are two
alleles. Almost all common SNPs have only two alleles.
drwxr-xr-x root/root 0 2018-06-14 15:29 ./
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/bin/
-rwxr-xr-x root/root 13780 2018-06-14 15:29 ./usr/bin/snp-sites
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/share/
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/share/doc/snp-sites/
-rw-r--r-- root/root 378 2018-06-14 15:29 ./usr/share/doc/snp-sites/README.Debian
-rw-r--r-- root/root 2449 2018-01-29 16:18 ./usr/share/doc/snp-sites/README.md.gz
-rw-r--r-- root/root 977 2018-06-14 15:29 ./usr/share/doc/snp-sites/changelog.Debian.gz
-rw-r--r-- root/root 2334 2018-06-14 15:29 ./usr/share/doc/snp-sites/copyright
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/share/man/
drwxr-xr-x root/root 0 2018-06-14 15:29 ./usr/share/man/man1/
-rw-r--r-- root/root 1396 2018-06-14 15:29 ./usr/share/man/man1/snp-sites.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 21312
Build-Time: 128
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 427
Job: snp-sites_2.4.0-1
Machine Architecture: armhf
Package: snp-sites
Package-Time: 619
Source-Version: 2.4.0-1
Space: 21312
Status: successful
Version: 2.4.0-1
--------------------------------------------------------------------------------
Finished at 2018-06-17T05:17:57Z
Build needed 00:10:19, 21312k disc space