snp-sites →
2.3.1-1 →
armhf → 2016-03-24 07:22:42
sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on bm-wb-02
+==============================================================================+
| snp-sites 2.3.1-1 (armhf) 24 Mar 2016 07:15 |
+==============================================================================+
Package: snp-sites
Version: 2.3.1-1
Source Version: 2.3.1-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/snp-sites-HH4iGH/snp-sites-2.3.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/snp-sites-HH4iGH' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-c0119a94-2b6b-4326-a59f-8f5dcc2d73e6' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [8827 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [10.9 MB]
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+------------------------------------------------------------------------------+
| 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://anonscm.debian.org/git/debian-med/snp-sites.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/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 stretch-staging/main snp-sites 2.3.1-1 (dsc) [2237 B]
Get:2 http://172.17.0.1/private stretch-staging/main snp-sites 2.3.1-1 (tar) [15.6 MB]
Get:3 http://172.17.0.1/private stretch-staging/main snp-sites 2.3.1-1 (diff) [8540 B]
Fetched 15.6 MB in 1s (9231 kB/s)
Download complete and in download only mode
Check architectures
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Check dependencies
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-u_FjMr/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
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Get:3 file:/<<BUILDDIR>>/resolver-u_FjMr/apt_archive ./ Release.gpg [299 B]
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+------------------------------------------------------------------------------+
| Install core build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
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Building dependency tree...
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The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 6 not upgraded.
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Merged Build-Depends: debhelper (>= 9.0.0), autotools-dev, zlib1g-dev, check, pkg-config, dh-autoreconf, d-shlibs, asciidoctor
Filtered Build-Depends: debhelper (>= 9.0.0), autotools-dev, zlib1g-dev, check, pkg-config, dh-autoreconf, d-shlibs, asciidoctor
dpkg-deb: building package 'sbuild-build-depends-snp-sites-dummy' in '/<<BUILDDIR>>/resolver-8yrLtu/apt_archive/sbuild-build-depends-snp-sites-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-8yrLtu/apt_archive ./ InRelease
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Get:2 file:/<<BUILDDIR>>/resolver-8yrLtu/apt_archive ./ Release [2119 B]
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Get:3 file:/<<BUILDDIR>>/resolver-8yrLtu/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-8yrLtu/apt_archive ./ Release.gpg [299 B]
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+------------------------------------------------------------------------------+
| Install snp-sites 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 bsdmainutils
ca-certificates check d-shlibs debhelper dh-autoreconf
dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian
libarchive-zip-perl libbsd0 libcroco3 libffi6
libfile-stripnondeterminism-perl libglib2.0-0 libicu55 libmagic1
libpipeline1 libruby2.3 libsigsegv2 libssl1.0.2 libsubunit-dev libsubunit0
libtool libunistring0 libxml2 libyaml-0-2 m4 man-db openssl pkg-config
po-debconf rake ruby ruby-did-you-mean ruby-minitest ruby-net-telnet
ruby-power-assert ruby-test-unit ruby2.3 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 less www-browser
libmail-box-perl ri ruby-dev bundler
Recommended packages:
curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
libltdl-dev xml-core libmail-sendmail-perl zip fonts-lato libjs-jquery
The following NEW packages will be installed:
asciidoctor autoconf automake autopoint autotools-dev bsdmainutils
ca-certificates check d-shlibs debhelper dh-autoreconf
dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian
libarchive-zip-perl libbsd0 libcroco3 libffi6
libfile-stripnondeterminism-perl libglib2.0-0 libicu55 libmagic1
libpipeline1 libruby2.3 libsigsegv2 libssl1.0.2 libsubunit-dev libsubunit0
libtool libunistring0 libxml2 libyaml-0-2 m4 man-db openssl pkg-config
po-debconf rake ruby ruby-did-you-mean ruby-minitest ruby-net-telnet
ruby-power-assert ruby-test-unit ruby2.3 rubygems-integration
sbuild-build-depends-snp-sites-dummy zlib1g-dev
0 upgraded, 51 newly installed, 0 to remove and 6 not upgraded.
Need to get 24.1 MB/24.1 MB of archives.
After this operation, 83.4 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-8yrLtu/apt_archive ./ sbuild-build-depends-snp-sites-dummy 0.invalid.0 [822 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-7 [1083 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.2-1 [88.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.8 [177 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-4 [28.2 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf libyaml-0-2 armhf 0.1.6-3 [41.5 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf libssl1.0.2 armhf 1.0.2g-1 [886 kB]
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Get:12 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.25-2 [61.2 kB]
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Get:16 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf openssl armhf 1.0.2g-1 [666 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf ca-certificates all 20160104 [200 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf rubygems-integration all 1.10 [4882 B]
Get:20 http://172.17.0.1/private stretch-staging/main armhf rake all 10.5.0-2 [49.4 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf ruby-did-you-mean all 1.0.0-2 [11.2 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf ruby-minitest all 5.8.4-2 [50.3 kB]
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Get:26 http://172.17.0.1/private stretch-staging/main armhf libffi6 armhf 3.2.1-4 [18.5 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libruby2.3 armhf 2.3.0-5 [2834 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf ruby2.3 armhf 2.3.0-5 [167 kB]
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Get:30 http://172.17.0.1/private stretch-staging/main armhf asciidoctor all 1.5.4-1 [163 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-9 [338 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20150820.1 [71.7 kB]
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Get:37 http://172.17.0.1/private stretch-staging/main armhf check armhf 0.10.0-3 [178 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf d-shlibs all 0.66 [16.8 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.46.2-3 [2482 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.7-2 [1400 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.56-2 [94.9 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.016-1 [6998 B]
Get:47 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160313 [808 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-0.1 [200 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 11 [15.7 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf pkg-config armhf 0.29-3 [59.0 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
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Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Selecting previously unselected package sbuild-build-depends-snp-sites-dummy.
Preparing to unpack .../sbuild-build-depends-snp-sites-dummy.deb ...
Unpacking sbuild-build-depends-snp-sites-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.22-3) ...
Setting up groff-base (1.22.3-7) ...
Setting up libbsd0:armhf (0.8.2-1) ...
Setting up bsdmainutils (9.0.8) ...
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 libpipeline1:armhf (1.4.1-2) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libsigsegv2:armhf (2.10-4) ...
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up libyaml-0-2:armhf (0.1.6-3) ...
Setting up libssl1.0.2:armhf (1.0.2g-1) ...
Setting up libmagic1:armhf (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.7-2) ...
Setting up libicu55:armhf (55.1-7) ...
Setting up libxml2:armhf (2.9.3+dfsg1-1) ...
Setting up m4 (1.4.17-5) ...
Setting up openssl (1.0.2g-1) ...
Setting up ca-certificates (20160104) ...
Setting up rubygems-integration (1.10) ...
Setting up ruby-did-you-mean (1.0.0-2) ...
Setting up ruby-minitest (5.8.4-2) ...
Setting up ruby-net-telnet (0.1.1-2) ...
Setting up ruby-power-assert (0.2.7-1) ...
Setting up ruby-test-unit (3.1.7-2) ...
Setting up libffi6:armhf (3.2.1-4) ...
Setting up autoconf (2.69-9) ...
Setting up autotools-dev (20150820.1) ...
Setting up automake (1:1.15-4) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up autopoint (0.19.7-2) ...
Setting up libsubunit0:armhf (1.1.0-3) ...
Setting up libsubunit-dev (1.1.0-3) ...
Setting up check:armhf (0.10.0-3) ...
Setting up d-shlibs (0.66) ...
Setting up libglib2.0-0:armhf (2.46.2-3) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.11-1) ...
Setting up gettext (0.19.7-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.19) ...
Setting up libarchive-zip-perl (1.56-2) ...
Setting up libfile-stripnondeterminism-perl (0.016-1) ...
Setting up libtool (2.4.6-0.1) ...
Setting up pkg-config (0.29-3) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up rake (10.5.0-2) ...
Setting up libruby2.3:armhf (2.3.0-5) ...
Setting up debhelper (9.20160313) ...
Setting up dh-autoreconf (11) ...
Setting up ruby2.3 (2.3.0-5) ...
Setting up ruby (1:2.3.0+1) ...
Setting up asciidoctor (1.5.4-1) ...
Setting up dh-strip-nondeterminism (0.016-1) ...
Setting up sbuild-build-depends-snp-sites-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.22-3) ...
Processing triggers for ca-certificates (20160104) ...
Updating certificates in /etc/ssl/certs...
173 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26-5 dpkg-dev_1.18.4 g++-5_5.3.1-11 gcc-5_5.3.1-11 libc6-dev_2.22-3 libstdc++-4.9-dev_4.9.3-12 libstdc++-5-dev_5.3.1-11 libstdc++6_5.3.1-11 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-3 adduser_3.114 apt_1.2.6 asciidoctor_1.5.4-1 autoconf_2.69-9 automake_1:1.15-4 autopoint_0.19.7-2 autotools-dev_20150820.1 base-files_9.5+rpi1 base-passwd_3.5.39 bash_4.3-14 binutils_2.26-5 bsdmainutils_9.0.8 bsdutils_1:2.27.1-6 build-essential_11.7 bzip2_1.0.6-8 ca-certificates_20160104 check_0.10.0-3 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:5.3.1-1+rpi1 cpp-5_5.3.1-11 d-shlibs_0.66 dash_0.5.8-2.1 debconf_1.5.59 debfoster_2.7-2 debhelper_9.20160313 debianutils_4.7 dh-autoreconf_11 dh-strip-nondeterminism_0.016-1 diffutils_1:3.3-3 dmsetup_2:1.02.116-1 dpkg_1.18.4 dpkg-dev_1.18.4 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.6.0+git+20160126-2 g++_4:5.3.1-1+rpi1 g++-5_5.3.1-11 gcc_4:5.3.1-1+rpi1 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_4.9.3-12 gcc-5_5.3.1-11 gcc-5-base_5.3.1-11 gettext_0.19.7-2 gettext-base_0.19.7-2 gnupg_1.4.20-4 gpgv_1.4.20-4 grep_2.22-1 groff-base_1.22.3-7 gzip_1.6-4 hostname_3.17 init_1.29 init-system-helpers_1.29 initscripts_2.88dsf-59.3 insserv_1.14.0-5.3 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-8+rpi1 kmod_22-1 libacl1_2.2.52-3 libapparmor1_2.10-3 libapt-pkg4.12_1.0.9.10 libapt-pkg5.0_1.2.6 libarchive-zip-perl_1.56-2 libasan1_4.9.3-12 libasan2_5.3.1-11 libatomic1_5.3.1-11 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1 libaudit1_1:2.4.5-1 libblkid1_2.27.1-6 libbsd0_0.8.2-1 libbz2-1.0_1.0.6-8 libc-bin_2.22-3 libc-dev-bin_2.22-3 libc6_2.22-3 libc6-dev_2.22-3 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-11 libcomerr2_1.42.13-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libdb5.3_5.3.28-11 libdbus-1-3_1.10.8-1 libdebconfclient0_0.207 libdevmapper1.02.1_2:1.02.116-1 libdpkg-perl_1.18.4 libdrm2_2.4.67-1 libfakeroot_1.20.2-1 libfdisk1_2.27.1-6 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.016-1 libgc1c2_1:7.4.2-7.3 libgcc-4.9-dev_4.9.3-12 libgcc-5-dev_5.3.1-11 libgcc1_1:5.3.1-11 libgcrypt20_1.6.5-2 libgdbm3_1.8.3-13.1 libglib2.0-0_2.46.2-3 libgmp10_2:6.1.0+dfsg-2 libgomp1_5.3.1-11 libgpg-error0_1.21-2 libicu55_55.1-7 libisl15_0.16.1-1 libklibc_2.0.4-8+rpi1 libkmod2_22-1 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.27.1-6 libmpc3_1.0.3-1 libmpfr4_3.1.4-1 libncurses5_6.0+20160213-1 libncursesw5_6.0+20160213-1 libpam-modules_1.1.8-3.2 libpam-modules-bin_1.1.8-3.2 libpam-runtime_1.1.8-3.2 libpam0g_1.1.8-3.2 libpcre3_2:8.38-3 libperl5.22_5.22.1-9 libpipeline1_1.4.1-2 libpng12-0_1.2.54-4 libprocps3_2:3.3.9-9 libprocps5_2:3.3.11-3 libreadline6_6.3-8+b3 libruby2.3_2.3.0-5 libseccomp2_2.2.3-3 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libsigsegv2_2.10-4 libslang2_2.3.0-2+b1 libsmartcols1_2.27.1-6 libss2_1.42.13-1 libssl1.0.2_1.0.2g-1 libstdc++-4.9-dev_4.9.3-12 libstdc++-5-dev_5.3.1-11 libstdc++6_5.3.1-11 libsubunit-dev_1.1.0-3 libsubunit0_1.1.0-3 libsystemd0_229-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160213-1 libtool_2.4.6-0.1 libubsan0_5.3.1-11 libudev1_229-2 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-28 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-6 libxml2_2.9.3+dfsg1-1 libyaml-0-2_0.1.6-3 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160110+rpi1 m4_1.4.17-5 make_4.1-6 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.04-2 mawk_1.3.3-17 mount_2.27.1-6 multiarch-support_2.22-3 nano_2.5.3-2 ncurses-base_6.0+20160213-1 ncurses-bin_6.0+20160213-1 openssl_1.0.2g-1 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.1-9 perl-base_5.22.1-9 perl-modules-5.22_5.22.1-9 pkg-config_0.29-3 po-debconf_1.0.19 procps_2:3.3.11-3 rake_10.5.0-2 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 ruby_1:2.3.0+1 ruby-did-you-mean_1.0.0-2 ruby-minitest_5.8.4-2 ruby-net-telnet_0.1.1-2 ruby-power-assert_0.2.7-1 ruby-test-unit_3.1.7-2 ruby2.3_2.3.0-5 rubygems-integration_1.10 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-snp-sites-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_229-2 systemd-sysv_229-2 sysv-rc_2.88dsf-59.3 sysvinit-utils_2.88dsf-59.3 tar_1.28-2.1 tzdata_2016a-1 udev_229-2 util-linux_2.27.1-6 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Fri Mar 18 14:50:53 2016 UTC using RSA key ID F09F4872
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./snp-sites_2.3.1-1.dsc
dpkg-source: info: extracting snp-sites in snp-sites-2.3.1
dpkg-source: info: unpacking snp-sites_2.3.1.orig.tar.gz
dpkg-source: info: unpacking snp-sites_2.3.1-1.debian.tar.xz
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-c0119a94-2b6b-4326-a59f-8f5dcc2d73e6
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: source package snp-sites
dpkg-buildpackage: source version 2.3.1-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build snp-sites-2.3.1
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean --with autoreconf
dh_testdir
dh_auto_clean
dh_autoreconf_clean
dh_clean
debian/rules build-arch
dh build-arch --with autoreconf
dh_testdir -a
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 --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 -j1
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 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o alignment-file.lo alignment-file.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -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 -fstack-protector-strong -Wformat -Werror=format-security -c alignment-file.c -fPIE -o alignment-file.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 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o vcf.lo vcf.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -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 -fstack-protector-strong -Wformat -Werror=format-security -c vcf.c -fPIE -o vcf.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 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o phylib-of-snp-sites.lo phylib-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 -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 -fstack-protector-strong -Wformat -Werror=format-security -c phylib-of-snp-sites.c -fPIE -o phylib-of-snp-sites.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -fPIE -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 -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 -fstack-protector-strong -Wformat -Werror=format-security -c snp-sites.c -fPIE -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 -fPIE -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 -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 -fstack-protector-strong -Wformat -Werror=format-security -c fasta-of-snp-sites.c -fPIE -o fasta-of-snp-sites.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -version-info 1:0 -fPIE -pie -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" )
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include --std=c99 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snp_sites-main.o `test -f 'main.c' || echo './'`main.c
/bin/bash ../libtool --tag=CC --mode=link gcc --std=c99 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -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 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -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 -j1 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 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fPIE -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 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fPIE -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 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fPIE -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 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fPIE -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 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -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 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -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 2.3.1
============================================================================
# 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>>'
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>>'
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_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 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 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 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: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: Depends field of package libsnp-sites1-dev: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package libsnp-sites1-dev: unused substitution variable ${devlibs:Depends}
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'snp-sites-dbgsym' in '../snp-sites-dbgsym_2.3.1-1_armhf.deb'.
dpkg-deb: building package 'libsnp-sites1-dbgsym' in '../libsnp-sites1-dbgsym_2.3.1-1_armhf.deb'.
dpkg-deb: building package 'libsnp-sites1-dev' in '../libsnp-sites1-dev_2.3.1-1_armhf.deb'.
dpkg-deb: building package 'snp-sites' in '../snp-sites_2.3.1-1_armhf.deb'.
dpkg-deb: building package 'libsnp-sites1' in '../libsnp-sites1_2.3.1-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../snp-sites_2.3.1-1_armhf.changes
dpkg-genchanges: warning: package libsnp-sites1-dbgsym listed in files list but not in control info
dpkg-genchanges: warning: package snp-sites-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build snp-sites-2.3.1
dpkg-buildpackage: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160324-0722
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
snp-sites_2.3.1-1_armhf.changes:
--------------------------------
Format: 1.8
Date: Fri, 18 Mar 2016 14:46:45 +0000
Source: snp-sites
Binary: snp-sites libsnp-sites1 libsnp-sites1-dev
Architecture: armhf
Version: 2.3.1-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Sascha Steinbiss <sascha@steinbiss.name>
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 (2.3.1-1) unstable; urgency=medium
.
* New upstream version.
Checksums-Sha1:
db7a5c34d37a711ee332f49495b3c9204c7c6aac 16822 libsnp-sites1-dbgsym_2.3.1-1_armhf.deb
b4c43295b8faa4bd51293747c4452de4888a0376 13324 libsnp-sites1-dev_2.3.1-1_armhf.deb
361d4aaf14fa483a82b1d4ce874ba903844914e1 9768 libsnp-sites1_2.3.1-1_armhf.deb
cbbb8d09a8d82c6f9455cb48cbb13e86354cbb9c 5834 snp-sites-dbgsym_2.3.1-1_armhf.deb
ba25715af97b52e9d6e8a2d3702fb05909ae71e7 10252 snp-sites_2.3.1-1_armhf.deb
Checksums-Sha256:
8773e26bf934ce3853490533b070cc12d406c3bf12420789f13b22f73f277c7c 16822 libsnp-sites1-dbgsym_2.3.1-1_armhf.deb
c4956927fbd2a89413c187d89ce23c94a2c3177a84fac64c2a5c2b9c79f4039a 13324 libsnp-sites1-dev_2.3.1-1_armhf.deb
1158090da86ce57454d99336f574c30ed42df0772b0e2efbffc722f1d3964490 9768 libsnp-sites1_2.3.1-1_armhf.deb
f28fede5f472e999fc7bb66e6944ea1fbfcff59154a18da2fb3a7a65dcd830b5 5834 snp-sites-dbgsym_2.3.1-1_armhf.deb
00c56d7804271629330da31e29de2ba91e181d9851270c10a9c1bc6dedce2166 10252 snp-sites_2.3.1-1_armhf.deb
Files:
e35ea83ab7b2d73899f4dfc058fcd33a 16822 debug extra libsnp-sites1-dbgsym_2.3.1-1_armhf.deb
f895251f1b82c4ec48182878689887fa 13324 libdevel optional libsnp-sites1-dev_2.3.1-1_armhf.deb
5c04a7438cada724fb67ba8b61c5b33b 9768 libs optional libsnp-sites1_2.3.1-1_armhf.deb
98da224650635f05abfb6c4c233b1229 5834 debug extra snp-sites-dbgsym_2.3.1-1_armhf.deb
e0dcd73593428a53f1e39026d5537e23 10252 science optional snp-sites_2.3.1-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libsnp-sites1-dbgsym_2.3.1-1_armhf.deb
--------------------------------------
new debian package, version 2.0.
size 16822 bytes: control archive=501 bytes.
442 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: libsnp-sites1-dbgsym
Source: snp-sites
Version: 2.3.1-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 31
Depends: libsnp-sites1 (= 2.3.1-1)
Section: debug
Priority: extra
Homepage: https://github.com/sanger-pathogens/snp-sites
Description: Debug symbols for libsnp-sites1
Auto-Built-Package: debug-symbols
Build-Ids: 2d2897274cce6ca78e62b4afc72394e206fc7db7
drwxr-xr-x root/root 0 2016-03-24 07:22 ./
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/lib/
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/lib/debug/.build-id/2d/
-rw-r--r-- root/root 20936 2016-03-24 07:22 ./usr/lib/debug/.build-id/2d/2897274cce6ca78e62b4afc72394e206fc7db7.debug
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/share/
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-03-24 07:22 ./usr/share/doc/libsnp-sites1-dbgsym -> libsnp-sites1
libsnp-sites1-dev_2.3.1-1_armhf.deb
-----------------------------------
new debian package, version 2.0.
size 13324 bytes: control archive=1072 bytes.
954 bytes, 24 lines control
740 bytes, 10 lines md5sums
Package: libsnp-sites1-dev
Source: snp-sites
Version: 2.3.1-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 56
Depends: libsnp-sites1 (= 2.3.1-1)
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 2016-03-24 07:22 ./
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/include/
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/include/snp-sites/
-rw-r--r-- root/root 1365 2016-03-24 07:22 ./usr/include/snp-sites/alignment-file.h
-rw-r--r-- root/root 1145 2016-03-24 07:22 ./usr/include/snp-sites/fasta-of-snp-sites.h
-rw-r--r-- root/root 8809 2016-03-24 07:22 ./usr/include/snp-sites/kseq.h
-rw-r--r-- root/root 1149 2016-03-24 07:22 ./usr/include/snp-sites/phylib-of-snp-sites.h
-rw-r--r-- root/root 2050 2016-03-24 07:22 ./usr/include/snp-sites/snp-sites.h
-rw-r--r-- root/root 2005 2016-03-24 07:22 ./usr/include/snp-sites/vcf.h
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/lib/
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 19942 2016-03-24 07:22 ./usr/lib/arm-linux-gnueabihf/libsnp-sites.a
lrwxrwxrwx root/root 0 2016-03-24 07:22 ./usr/lib/arm-linux-gnueabihf/libsnp-sites.so -> libsnp-sites.so.1.0.0
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/share/
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/share/doc/libsnp-sites1-dev/
-rw-r--r-- root/root 504 2016-03-11 12:05 ./usr/share/doc/libsnp-sites1-dev/README.Debian
-rw-r--r-- root/root 731 2016-03-18 14:48 ./usr/share/doc/libsnp-sites1-dev/changelog.Debian.gz
-rw-r--r-- root/root 2333 2016-03-11 12:05 ./usr/share/doc/libsnp-sites1-dev/copyright
libsnp-sites1_2.3.1-1_armhf.deb
-------------------------------
new debian package, version 2.0.
size 9768 bytes: control archive=864 bytes.
732 bytes, 19 lines control
238 bytes, 3 lines md5sums
29 bytes, 1 lines shlibs
60 bytes, 2 lines triggers
Package: libsnp-sites1
Source: snp-sites
Version: 2.3.1-1
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 2016-03-24 07:22 ./
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/lib/
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/lib/arm-linux-gnueabihf/
lrwxrwxrwx root/root 0 2016-03-24 07:22 ./usr/lib/arm-linux-gnueabihf/libsnp-sites.so.1 -> libsnp-sites.so.1.0.0
-rw-r--r-- root/root 17708 2016-03-24 07:22 ./usr/lib/arm-linux-gnueabihf/libsnp-sites.so.1.0.0
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/share/
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/share/doc/libsnp-sites1/
-rw-r--r-- root/root 731 2016-03-18 14:48 ./usr/share/doc/libsnp-sites1/changelog.Debian.gz
-rw-r--r-- root/root 2333 2016-03-11 12:05 ./usr/share/doc/libsnp-sites1/copyright
snp-sites-dbgsym_2.3.1-1_armhf.deb
----------------------------------
new debian package, version 2.0.
size 5834 bytes: control archive=493 bytes.
430 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: snp-sites-dbgsym
Source: snp-sites
Version: 2.3.1-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 19
Depends: snp-sites (= 2.3.1-1)
Section: debug
Priority: extra
Homepage: https://github.com/sanger-pathogens/snp-sites
Description: Debug symbols for snp-sites
Auto-Built-Package: debug-symbols
Build-Ids: 5a09322c7bf82a5aa73649bc2ea63cfee245c6c2
drwxr-xr-x root/root 0 2016-03-24 07:22 ./
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/lib/
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/lib/debug/.build-id/5a/
-rw-r--r-- root/root 8928 2016-03-24 07:22 ./usr/lib/debug/.build-id/5a/09322c7bf82a5aa73649bc2ea63cfee245c6c2.debug
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/share/
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-03-24 07:22 ./usr/share/doc/snp-sites-dbgsym -> snp-sites
snp-sites_2.3.1-1_armhf.deb
---------------------------
new debian package, version 2.0.
size 10252 bytes: control archive=1084 bytes.
1159 bytes, 24 lines control
409 bytes, 6 lines md5sums
Package: snp-sites
Version: 2.3.1-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 28
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 2016-03-24 07:22 ./
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/bin/
-rwxr-xr-x root/root 9676 2016-03-24 07:22 ./usr/bin/snp-sites
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/share/
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/share/doc/snp-sites/
-rw-r--r-- root/root 378 2015-12-10 00:16 ./usr/share/doc/snp-sites/README.Debian
-rw-r--r-- root/root 2038 2016-03-18 14:24 ./usr/share/doc/snp-sites/README.md.gz
-rw-r--r-- root/root 731 2016-03-18 14:48 ./usr/share/doc/snp-sites/changelog.Debian.gz
-rw-r--r-- root/root 2333 2016-03-11 12:05 ./usr/share/doc/snp-sites/copyright
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/share/man/
drwxr-xr-x root/root 0 2016-03-24 07:22 ./usr/share/man/man1/
-rw-r--r-- root/root 1377 2016-03-24 07:22 ./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: 21368
Build-Time: 155
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 241
Job: snp-sites_2.3.1-1
Machine Architecture: armhf
Package: snp-sites
Package-Time: 439
Source-Version: 2.3.1-1
Space: 21368
Status: successful
Version: 2.3.1-1
--------------------------------------------------------------------------------
Finished at 20160324-0722
Build needed 00:07:19, 21368k disc space