snp-sites →
2.0.2-2 →
armhf → 2015-12-04 11:44:35
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bm-wb-02
╔══════════════════════════════════════════════════════════════════════════════╗
║ snp-sites 2.0.2-2 (armhf) 04 Dec 2015 11:33 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: snp-sites
Version: 2.0.2-2
Source Version: 2.0.2-2
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/snp-sites-3Ipjla/snp-sites-2.0.2' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/snp-sites-3Ipjla' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-f502698f-0190-47ba-97c3-4343ca29a25f' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 stretch-staging/main Sources [8506 kB]
Get:3 http://172.17.0.1 stretch-staging/main armhf Packages [10.5 MB]
Ign http://172.17.0.1 stretch-staging/main Translation-en
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
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Check APT
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Download source files with APT
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NOTICE: 'snp-sites' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/snp-sites.git
Need to get 49.7 kB of source archives.
Get:1 http://172.17.0.1/private/ stretch-staging/main snp-sites 2.0.2-2 (dsc) [2265 B]
Get:2 http://172.17.0.1/private/ stretch-staging/main snp-sites 2.0.2-2 (tar) [43.1 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main snp-sites 2.0.2-2 (diff) [4384 B]
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Download complete and in download only mode
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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-1T9Ksu/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
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Ign file: ./ Translation-en
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
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The following NEW packages will be installed:
sbuild-build-depends-core-dummy
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Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9.0.0), autotools-dev, zlib1g-dev, check, dh-autoreconf, d-shlibs, libxml2-utils, docbook, docbook-xsl, xsltproc, asciidoc, libsubunit-dev
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9.0.0), autotools-dev, zlib1g-dev, check, dh-autoreconf, d-shlibs, libxml2-utils, docbook, docbook-xsl, xsltproc, asciidoc, libsubunit-dev
dpkg-deb: building package 'sbuild-build-depends-snp-sites-dummy' in '/«BUILDDIR»/resolver-1UcZSY/apt_archive/sbuild-build-depends-snp-sites-dummy.deb'.
OK
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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 extra packages will be installed:
asciidoc autoconf automake autopoint autotools-dev bsdmainutils check
d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism docbook docbook-xsl
file gettext gettext-base groff-base intltool-debian libarchive-zip-perl
libcroco3 libexpat1 libffi6 libfile-stripnondeterminism-perl libglib2.0-0
libicu55 libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib libsigsegv2 libsqlite3-0 libssl1.0.2 libsubunit-dev
libsubunit0 libtool libunistring0 libxml2 libxml2-utils libxslt1.1 m4 man-db
mime-support po-debconf python python-minimal python2.7 python2.7-minimal
sgml-base sgml-data xml-core xsltproc zlib1g-dev
Suggested packages:
source-highlight vim-addon-manager autoconf-archive gnu-standards
autoconf-doc wamerican wordlist whois vacation dh-make docbook-defguide
docbook-dsssl docbook-xml psgml dbtoepub docbook-xsl-doc-html
docbook-xsl-doc-pdf docbook-xsl-doc-text docbook-xsl-doc docbook-xsl-saxon
fop libsaxon-java libxalan2-java libxslthl-java xalan gettext-doc
libasprintf-dev libgettextpo-dev groff libtool-doc automaken gfortran
fortran95-compiler gcj-jdk less www-browser libmail-box-perl python-doc
python-tk python2.7-doc binfmt-support sgml-base-doc perlsgml w3-recs opensp
Recommended packages:
dblatex docbook-utils xmlto curl wget lynx-cur libglib2.0-data
shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
asciidoc autoconf automake autopoint autotools-dev bsdmainutils check
d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism docbook docbook-xsl
file gettext gettext-base groff-base intltool-debian libarchive-zip-perl
libcroco3 libexpat1 libffi6 libfile-stripnondeterminism-perl libglib2.0-0
libicu55 libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib libsigsegv2 libsqlite3-0 libssl1.0.2 libsubunit-dev
libsubunit0 libtool libunistring0 libxml2 libxml2-utils libxslt1.1 m4 man-db
mime-support po-debconf python python-minimal python2.7 python2.7-minimal
sbuild-build-depends-snp-sites-dummy sgml-base sgml-data xml-core xsltproc
zlib1g-dev
0 upgraded, 54 newly installed, 0 to remove and 24 not upgraded.
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Get:4 http://172.17.0.1/private/ stretch-staging/main man-db armhf 2.7.5-1 [975 kB]
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Get:46 http://172.17.0.1/private/ stretch-staging/main xml-core all 0.13+nmu2 [24.2 kB]
Get:47 http://172.17.0.1/private/ stretch-staging/main sgml-data all 2.0.10 [181 kB]
Get:48 http://172.17.0.1/private/ stretch-staging/main docbook all 4.5-5.1 [453 kB]
Get:49 http://172.17.0.1/private/ stretch-staging/main docbook-xsl all 1.78.1+dfsg-1 [2339 kB]
Get:50 http://172.17.0.1/private/ stretch-staging/main libxml2-utils armhf 2.9.2+zdfsg1-4 [101 kB]
Get:51 http://172.17.0.1/private/ stretch-staging/main libxslt1.1 armhf 1.1.28-2.1 [211 kB]
Get:52 http://172.17.0.1/private/ stretch-staging/main xsltproc armhf 1.1.28-2.1 [118 kB]
Get:53 http://172.17.0.1/private/ stretch-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
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Selecting previously unselected package sgml-data.
Preparing to unpack .../sgml-data_2.0.10_all.deb ...
Unpacking sgml-data (2.0.10) ...
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Unpacking docbook (4.5-5.1) ...
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Unpacking docbook-xsl (1.78.1+dfsg-1) ...
Selecting previously unselected package libxml2-utils.
Preparing to unpack .../libxml2-utils_2.9.2+zdfsg1-4_armhf.deb ...
Unpacking libxml2-utils (2.9.2+zdfsg1-4) ...
Selecting previously unselected package libxslt1.1:armhf.
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Unpacking libxslt1.1:armhf (1.1.28-2.1) ...
Selecting previously unselected package xsltproc.
Preparing to unpack .../xsltproc_1.1.28-2.1_armhf.deb ...
Unpacking xsltproc (1.1.28-2.1) ...
Selecting previously unselected package zlib1g-dev:armhf.
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 (2.19-22) ...
Setting up groff-base (1.22.3-4) ...
Setting up bsdmainutils (9.0.6) ...
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 (1.4.1-1) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up mime-support (3.59) ...
Setting up libexpat1:armhf (2.1.0-7) ...
Setting up libffi6:armhf (3.2.1-3) ...
Setting up libsqlite3-0:armhf (3.9.2-1) ...
Setting up libssl1.0.2:armhf (1.0.2d-3) ...
Setting up libpython2.7-stdlib:armhf (2.7.10-5+b1) ...
Setting up python2.7 (2.7.10-5+b1) ...
Setting up libpython-stdlib:armhf (2.7.9-1) ...
Setting up python (2.7.9-1) ...
Setting up libsigsegv2:armhf (2.10-4) ...
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up sgml-base (1.26+nmu4) ...
Setting up libmagic1:armhf (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.6-1) ...
Setting up libicu55:armhf (55.1-6) ...
Setting up libxml2:armhf (2.9.2+zdfsg1-4) ...
Setting up m4 (1.4.17-4) ...
Setting up asciidoc (8.6.9-3) ...
Setting up autoconf (2.69-9) ...
Setting up autotools-dev (20150820.1) ...
Setting up automake (1:1.15-3) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up autopoint (0.19.6-1) ...
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 (0.62) ...
Setting up libglib2.0-0:armhf (2.46.2-1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.9-1) ...
Setting up gettext (0.19.6-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.18) ...
Setting up libarchive-zip-perl (1.53-1) ...
Setting up libfile-stripnondeterminism-perl (0.014-1) ...
Setting up libtool (2.4.2-1.11) ...
Setting up xml-core (0.13+nmu2) ...
Setting up libxml2-utils (2.9.2+zdfsg1-4) ...
Setting up libxslt1.1:armhf (1.1.28-2.1) ...
Setting up xsltproc (1.1.28-2.1) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Processing triggers for sgml-base (1.26+nmu4) ...
Setting up sgml-data (2.0.10) ...
Setting up docbook-xsl (1.78.1+dfsg-1) ...
Processing triggers for sgml-base (1.26+nmu4) ...
Setting up docbook (4.5-5.1) ...
Processing triggers for sgml-base (1.26+nmu4) ...
Setting up dh-strip-nondeterminism (0.014-1) ...
Setting up debhelper (9.20151005) ...
Setting up dh-autoreconf (10) ...
Setting up sbuild-build-depends-snp-sites-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.19-22) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25.1-7 dpkg-dev_1.18.3 g++-5_5.2.1-23+rpi1 gcc-5_5.2.1-23+rpi1 libc6-dev_2.19-22 libstdc++-4.9-dev_4.9.3-5 libstdc++-5-dev_5.2.1-23+rpi1 libstdc++6_5.2.1-23+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.10.2 asciidoc_8.6.9-3 autoconf_2.69-9 automake_1:1.15-3 autopoint_0.19.6-1 autotools-dev_20150820.1 base-files_9.4+rpi1 base-passwd_3.5.38 bash_4.3-14 binutils_2.25.1-7 bsdmainutils_9.0.6 bsdutils_1:2.27.1-1 build-essential_11.7 bzip2_1.0.6-8 check_0.10.0-3 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:5.2.1-4+rpi2 cpp-5_5.2.1-23+rpi1 d-shlibs_0.62 dash_0.5.7-4 debconf_1.5.58 debfoster_2.7-2 debhelper_9.20151005 debianutils_4.5.1 dh-autoreconf_10 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-2 dmsetup_2:1.02.110-1+rpi1 docbook_4.5-5.1 docbook-xsl_1.78.1+dfsg-1 dpkg_1.18.3 dpkg-dev_1.18.3 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.4.2-10 g++_4:5.2.1-4+rpi2 g++-5_5.2.1-23+rpi1 gcc_4:5.2.1-4+rpi2 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-1 gcc-4.9-base_4.9.3-5 gcc-5_5.2.1-23+rpi1 gcc-5-base_5.2.1-23+rpi1 gettext_0.19.6-1 gettext-base_0.19.6-1 gnupg_1.4.19-6 gpgv_1.4.19-6 grep_2.22-1 groff-base_1.22.3-4 gzip_1.6-4 hostname_3.16 init_1.24 init-system-helpers_1.24 initramfs-tools_0.120 initscripts_2.88dsf-59.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-2+rpi1 kmod_21-1 libacl1_2.2.52-2 libapparmor1_2.10-2+b2 libapt-pkg4.12_1.0.9.10 libapt-pkg4.16_1.0.10.2 libarchive-zip-perl_1.53-1 libasan1_4.9.3-5 libasan2_5.2.1-23+rpi1 libatomic1_5.2.1-23+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.4-4 libaudit1_1:2.4.4-4 libblkid1_2.27.1-1 libbz2-1.0_1.0.6-8 libc-bin_2.19-22 libc-dev-bin_2.19-22 libc6_2.19-22 libc6-dev_2.19-22 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.2.1-23+rpi1 libcomerr2_1.42.13-1 libcroco3_0.6.9-1 libcryptsetup4_2:1.6.6-5 libdb5.3_5.3.28-11 libdbus-1-3_1.10.4-1 libdebconfclient0_0.197 libdevmapper1.02.1_2:1.02.110-1+rpi1 libdpkg-perl_1.18.3 libdrm2_2.4.65-3 libexpat1_2.1.0-7 libfakeroot_1.20.2-1 libfdisk1_2.27.1-1 libffi6_3.2.1-3 libfile-stripnondeterminism-perl_0.014-1 libgc1c2_1:7.4.2-7 libgcc-4.9-dev_4.9.3-5 libgcc-5-dev_5.2.1-23+rpi1 libgcc1_1:5.2.1-23+rpi1 libgcrypt20_1.6.4-3 libgdbm3_1.8.3-13.1 libglib2.0-0_2.46.2-1 libgmp10_2:6.1.0+dfsg-2 libgomp1_5.2.1-23+rpi1 libgpg-error0_1.20-1 libicu55_55.1-6 libisl13_0.14-2 libklibc_2.0.4-2+rpi1 libkmod2_21-1 liblocale-gettext-perl_1.07-1 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.27.1-1 libmpc3_1.0.3-1 libmpfr4_3.1.3-1 libncurses5_6.0+20151024-2 libncursesw5_6.0+20151024-2 libnih-dbus1_1.0.3-4.3 libnih1_1.0.3-4.3 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpcre3_2:8.35-7.4 libpipeline1_1.4.1-1 libpng12-0_1.2.54-1 libprocps3_2:3.3.9-9 libprocps4_2:3.3.10-2 libpython-stdlib_2.7.9-1 libpython2.7-minimal_2.7.10-5+b1 libpython2.7-stdlib_2.7.10-5+b1 libreadline6_6.3-8+b3 libseccomp2_2.2.3-2 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_2.27.1-1 libsqlite3-0_3.9.2-1 libss2_1.42.13-1 libssl1.0.2_1.0.2d-3 libstdc++-4.9-dev_4.9.3-5 libstdc++-5-dev_5.2.1-23+rpi1 libstdc++6_5.2.1-23+rpi1 libsubunit-dev_1.1.0-3 libsubunit0_1.1.0-3 libsystemd0_228-2 libtext-charwidth-perl_0.04-7+b4 libtext-iconv-perl_1.7-5+b5 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20151024-2 libtool_2.4.2-1.11 libubsan0_5.2.1-23+rpi1 libudev1_228-2 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-27 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-1 libxml2_2.9.2+zdfsg1-4 libxml2-utils_2.9.2+zdfsg1-4 libxslt1.1_1.1.28-2.1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_4.1+Debian13+rpi1+nmu1 m4_1.4.17-4 make_4.0-8.2 makedev_2.3.1-93 man-db_2.7.5-1 mawk_1.3.3-17 mime-support_3.59 mount_2.27.1-1 multiarch-support_2.19-22 nano_2.4.2-1 ncurses-base_6.0+20151024-2 ncurses-bin_6.0+20151024-2 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.20.2-6 perl-base_5.20.2-6 perl-modules_5.20.2-6 po-debconf_1.0.18 procps_2:3.3.10-2 python_2.7.9-1 python-minimal_2.7.9-1 python2.7_2.7.10-5+b1 python2.7-minimal_2.7.10-5+b1 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-snp-sites-dummy_0.invalid.0 sed_4.2.2-6.1 sensible-utils_0.0.9 sgml-base_1.26+nmu4 sgml-data_2.0.10 startpar_0.59-3 systemd_228-2 systemd-sysv_228-2 sysv-rc_2.88dsf-59.2 sysvinit-utils_2.88dsf-59.2 tar_1.28-2.1 tzdata_2015g-1 udev_228-2 util-linux_2.27.1-1 xml-core_0.13+nmu2 xsltproc_1.1.28-2.1 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 Sun Nov 29 07:37:30 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./snp-sites_2.0.2-2.dsc
dpkg-source: info: extracting snp-sites in snp-sites-2.0.2
dpkg-source: info: unpacking snp-sites_2.0.2.orig.tar.gz
dpkg-source: info: unpacking snp-sites_2.0.2-2.debian.tar.xz
dpkg-source: info: applying fix_manpage.patch
dpkg-source: info: applying add_lib_subunit.patch
dpkg-source: info: applying reproducible-build.patch
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-f502698f-0190-47ba-97c3-4343ca29a25f
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 2.0.2-2
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build snp-sites-2.0.2
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_autoreconf -a
libtoolize: putting auxiliary files in `.'.
libtoolize: copying file `./ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIR, `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:7: 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:26: warning: source file '../tests/check-snp-sites.c' is in a subdirectory,
src/Makefile.am:26: but option 'subdir-objects' is disabled
automake: warning: possible forward-incompatibility.
automake: At least a source file is in a subdirectory, but the 'subdir-objects'
automake: automake option hasn't been enabled. For now, the corresponding output
automake: object file(s) will be placed in the top-level directory. However,
automake: this behaviour will change in future Automake versions: they will
automake: unconditionally cause object files to be placed in the same subdirectory
automake: of the corresponding sources.
automake: You are advised to start using 'subdir-objects' option throughout your
automake: project, to avoid future incompatibilities.
src/Makefile.am:26: warning: source file '../tests/check-vcf.c' is in a subdirectory,
src/Makefile.am:26: but option 'subdir-objects' is disabled
src/Makefile.am:26: warning: source file '../tests/helper-methods.c' is in a subdirectory,
src/Makefile.am:26: but option 'subdir-objects' is disabled
src/Makefile.am:26: warning: source file '../tests/run-all-tests.c' is in a subdirectory,
src/Makefile.am:26: but option 'subdir-objects' is disabled
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 how to print strings... printf
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 for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
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 mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) none
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... none
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking 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
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
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.. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o alignment-file.lo alignment-file.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c alignment-file.c -fPIC -DPIC -o .libs/alignment-file.o
alignment-file.c: In function 'read_line':
alignment-file.c:229:8: warning: implicit declaration of function 'size_of_string' [-Wimplicit-function-declaration]
if(size_of_string(sequence) > 0)
^
alignment-file.c:233:5: warning: implicit declaration of function 'concat_strings_created_with_malloc' [-Wimplicit-function-declaration]
concat_strings_created_with_malloc(sequence,current_line_buffer);
^
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -g -O2 -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=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o vcf.lo vcf.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -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.. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c vcf.c -o vcf.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -g -O2 -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.. -D_FORTIFY_SOURCE=2 -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.. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c phylib-of-snp-sites.c -o phylib-of-snp-sites.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o snp-sites.lo snp-sites.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c snp-sites.c -fPIC -DPIC -o .libs/snp-sites.o
snp-sites.c: In function 'generate_snp_sites':
snp-sites.c:139:4: warning: implicit declaration of function 'create_fasta_of_snp_sites' [-Wimplicit-function-declaration]
create_fasta_of_snp_sites(multi_fasta_output_filename, number_of_snps, bases_for_snps, sequence_names, number_of_samples);
^
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -g -O2 -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.. -D_FORTIFY_SOURCE=2 -g -O2 -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.. -D_FORTIFY_SOURCE=2 -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.. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c fasta-of-snp-sites.c -o fasta-of-snp-sites.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o parse-phylip.lo parse-phylip.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c parse-phylip.c -fPIC -DPIC -o .libs/parse-phylip.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c parse-phylip.c -o parse-phylip.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o string-cat.lo string-cat.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c string-cat.c -fPIC -DPIC -o .libs/string-cat.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c string-cat.c -o string-cat.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -version-info 1:0 -Wl,-z,relro -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 parse-phylip.lo string-cat.lo
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 .libs/parse-phylip.o .libs/string-cat.o -O2 -Wl,-z -Wl,relro -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 parse-phylip.o string-cat.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.. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o main.c
/bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -o snp-sites main.o -lm libsnp-sites.la -lz -lpthread -lrt
libtool: link: gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -o .libs/snp-sites main.o -lm ./.libs/libsnp-sites.so -lz -lpthread -lrt
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
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.. -D_FORTIFY_SOURCE=2 -I../tests -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o 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.. -D_FORTIFY_SOURCE=2 -I../tests -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o run_all_tests-check-vcf.o `test -f '../tests/check-vcf.c' || echo './'`../tests/check-vcf.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -I../tests -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o run_all_tests-helper-methods.o `test -f '../tests/helper-methods.c' || echo './'`../tests/helper-methods.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -I../tests -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o 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 -I../tests -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -o run-all-tests run_all_tests-check-snp-sites.o run_all_tests-check-vcf.o run_all_tests-helper-methods.o run_all_tests-run-all-tests.o -lm -lcheck -lsubunit libsnp-sites.la -lz -lpthread -lrt
libtool: link: gcc -I../tests -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -o .libs/run-all-tests run_all_tests-check-snp-sites.o run_all_tests-check-vcf.o run_all_tests-helper-methods.o run_all_tests-run-all-tests.o -lm -lcheck -lsubunit ./.libs/libsnp-sites.so -lz -lpthread -lrt
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 1
============================================================================
# TOTAL: 1
# PASS: 1
# SKIP: 0
# XFAIL: 0
# FAIL: 0
# XPASS: 0
# ERROR: 0
============================================================================
make[4]: Leaving directory '/«PKGBUILDDIR»/src'
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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: install: 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: install: 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 parse-phylip.h string-cat.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 \
--movedev "debian/tmp/usr/include/snp-sites/*.h" usr/include/snp-sites \
debian/tmp/usr/lib/*/libsnp-sites.so
Library package automatic movement utility
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.la debian/libsnp-sites1-dev/usr/lib/arm-linux-gnueabihf || true
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
a2x --no-xmllint --doctype manpage --format 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/snp-sites/usr/bin/snp-sites was not linked against librt.so.1 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: symbol gzclose used by debian/libsnp-sites1/usr/lib/arm-linux-gnueabihf/libsnp-sites.so.1.0.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol gzread used by debian/libsnp-sites1/usr/lib/arm-linux-gnueabihf/libsnp-sites.so.1.0.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol gzopen used by debian/libsnp-sites1/usr/lib/arm-linux-gnueabihf/libsnp-sites.so.1.0.0 found in none of the libraries
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: 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
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'libsnp-sites1' in '../libsnp-sites1_2.0.2-2_armhf.deb'.
dpkg-deb: building package 'libsnp-sites1-dev' in '../libsnp-sites1-dev_2.0.2-2_armhf.deb'.
dpkg-deb: building package 'snp-sites' in '../snp-sites_2.0.2-2_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../snp-sites_2.0.2-2_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build snp-sites-2.0.2
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20151204-1143
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
snp-sites_2.0.2-2_armhf.changes:
────────────────────────────────
Format: 1.8
Date: Sun, 29 Nov 2015 01:58:03 +0000
Source: snp-sites
Binary: snp-sites libsnp-sites1 libsnp-sites1-dev
Architecture: armhf
Version: 2.0.2-2
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
Closes: 806568
Changes:
snp-sites (2.0.2-2) unstable; urgency=medium
.
* Make build reproducible
Closes: #806568
Thanks to Reiner Herrmann for the patch
* Cosmetics in man page
Checksums-Sha1:
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13a450f7ddb44e7e23021c73cd5ca0e7e9f334e8 9654 libsnp-sites1_2.0.2-2_armhf.deb
b08de394884da0ab13f33ced60ce85a370a2167b 7092 snp-sites_2.0.2-2_armhf.deb
Checksums-Sha256:
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1b50f26492eaaba414b0e00545cf39b72faf4bdea371892dc968c2221030c894 9654 libsnp-sites1_2.0.2-2_armhf.deb
8eb09ce79aa5ecf3862cb4a75fba5353e3c3f6f824777cdc16ce055aa59d8c57 7092 snp-sites_2.0.2-2_armhf.deb
Files:
fe70485c8579803febff8b4db26370d5 13808 libdevel optional libsnp-sites1-dev_2.0.2-2_armhf.deb
adf3f03281cb5ad93fd083b91eefaa9a 9654 libs optional libsnp-sites1_2.0.2-2_armhf.deb
1f7dbc8f3caf3c14c71fab99015cdf22 7092 science optional snp-sites_2.0.2-2_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
libsnp-sites1-dev_2.0.2-2_armhf.deb
───────────────────────────────────
new debian package, version 2.0.
size 13808 bytes: control archive=1164 bytes.
954 bytes, 24 lines control
958 bytes, 13 lines md5sums
Package: libsnp-sites1-dev
Source: snp-sites
Version: 2.0.2-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 60
Depends: libsnp-sites1 (= 2.0.2-2)
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 2015-12-04 11:43 ./
drwxr-xr-x root/root 0 2015-12-04 11:43 ./usr/
drwxr-xr-x root/root 0 2015-12-04 11:43 ./usr/include/
drwxr-xr-x root/root 0 2015-12-04 11:43 ./usr/include/snp-sites/
-rw-r--r-- root/root 1845 2015-12-04 11:43 ./usr/include/snp-sites/alignment-file.h
-rw-r--r-- root/root 1076 2015-12-04 11:43 ./usr/include/snp-sites/fasta-of-snp-sites.h
-rw-r--r-- root/root 8809 2015-12-04 11:43 ./usr/include/snp-sites/kseq.h
-rw-r--r-- root/root 1035 2015-12-04 11:43 ./usr/include/snp-sites/parse-phylip.h
-rw-r--r-- root/root 1080 2015-12-04 11:43 ./usr/include/snp-sites/phylib-of-snp-sites.h
-rw-r--r-- root/root 1527 2015-12-04 11:43 ./usr/include/snp-sites/snp-sites.h
-rw-r--r-- root/root 1021 2015-12-04 11:43 ./usr/include/snp-sites/string-cat.h
-rw-r--r-- root/root 1912 2015-12-04 11:43 ./usr/include/snp-sites/vcf.h
drwxr-xr-x root/root 0 2015-12-04 11:43 ./usr/lib/
drwxr-xr-x root/root 0 2015-12-04 11:43 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 21168 2015-12-04 11:43 ./usr/lib/arm-linux-gnueabihf/libsnp-sites.a
-rw-r--r-- root/root 984 2015-12-04 11:43 ./usr/lib/arm-linux-gnueabihf/libsnp-sites.la
lrwxrwxrwx root/root 0 2015-12-04 11:43 ./usr/lib/arm-linux-gnueabihf/libsnp-sites.so -> libsnp-sites.so.1.0.0
drwxr-xr-x root/root 0 2015-12-04 11:43 ./usr/share/
drwxr-xr-x root/root 0 2015-12-04 11:43 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-12-04 11:43 ./usr/share/doc/libsnp-sites1-dev/
-rw-r--r-- root/root 552 2015-11-29 07:36 ./usr/share/doc/libsnp-sites1-dev/README.Debian
-rw-r--r-- root/root 435 2015-11-29 07:36 ./usr/share/doc/libsnp-sites1-dev/changelog.Debian.gz
-rw-r--r-- root/root 2178 2015-11-29 07:36 ./usr/share/doc/libsnp-sites1-dev/copyright
libsnp-sites1_2.0.2-2_armhf.deb
───────────────────────────────
new debian package, version 2.0.
size 9654 bytes: control archive=853 bytes.
711 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: 2.0.2-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 33
Depends: libc6 (>= 2.4)
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 2015-12-04 11:43 ./
drwxr-xr-x root/root 0 2015-12-04 11:43 ./usr/
drwxr-xr-x root/root 0 2015-12-04 11:43 ./usr/lib/
drwxr-xr-x root/root 0 2015-12-04 11:43 ./usr/lib/arm-linux-gnueabihf/
lrwxrwxrwx root/root 0 2015-12-04 11:43 ./usr/lib/arm-linux-gnueabihf/libsnp-sites.so.1 -> libsnp-sites.so.1.0.0
-rw-r--r-- root/root 17880 2015-12-04 11:43 ./usr/lib/arm-linux-gnueabihf/libsnp-sites.so.1.0.0
drwxr-xr-x root/root 0 2015-12-04 11:43 ./usr/share/
drwxr-xr-x root/root 0 2015-12-04 11:43 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-12-04 11:43 ./usr/share/doc/libsnp-sites1/
-rw-r--r-- root/root 435 2015-11-29 07:36 ./usr/share/doc/libsnp-sites1/changelog.Debian.gz
-rw-r--r-- root/root 2178 2015-11-29 07:36 ./usr/share/doc/libsnp-sites1/copyright
snp-sites_2.0.2-2_armhf.deb
───────────────────────────
new debian package, version 2.0.
size 7092 bytes: control archive=1092 bytes.
1159 bytes, 24 lines control
406 bytes, 6 lines md5sums
Package: snp-sites
Version: 2.0.2-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 24
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.
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drwxr-xr-x root/root 0 2015-12-04 11:43 ./usr/
drwxr-xr-x root/root 0 2015-12-04 11:43 ./usr/bin/
-rwxr-xr-x root/root 5532 2015-12-04 11:43 ./usr/bin/snp-sites
drwxr-xr-x root/root 0 2015-12-04 11:43 ./usr/share/
drwxr-xr-x root/root 0 2015-12-04 11:43 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-12-04 11:43 ./usr/share/doc/snp-sites/
-rw-r--r-- root/root 378 2015-11-29 07:36 ./usr/share/doc/snp-sites/README.Debian
-rw-r--r-- root/root 1214 2015-09-03 10:15 ./usr/share/doc/snp-sites/README.md
-rw-r--r-- root/root 435 2015-11-29 07:36 ./usr/share/doc/snp-sites/changelog.Debian.gz
-rw-r--r-- root/root 2178 2015-11-29 07:36 ./usr/share/doc/snp-sites/copyright
drwxr-xr-x root/root 0 2015-12-04 11:43 ./usr/share/man/
drwxr-xr-x root/root 0 2015-12-04 11:43 ./usr/share/man/man1/
-rw-r--r-- root/root 1177 2015-12-04 11:43 ./usr/share/man/man1/snp-sites.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
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Purging /«BUILDDIR»
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
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Build Architecture: armhf
Build-Space: 5816
Build-Time: 138
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 379
Job: snp-sites_2.0.2-2
Machine Architecture: armhf
Package: snp-sites
Package-Time: 578
Source-Version: 2.0.2-2
Space: 5816
Status: successful
Version: 2.0.2-2
────────────────────────────────────────────────────────────────────────────────
Finished at 20151204-1143
Build needed 00:09:38, 5816k disc space