snp-sites →
1.3-1 →
armhf → 2014-01-26 08:04:37
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on bm-wb-04
╔══════════════════════════════════════════════════════════════════════════════╗
║ snp-sites 1.3-1 (armhf) 26 Jan 2014 08:00 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: snp-sites
Version: 1.3-1
Source Version: 1.3-1
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/snp-sites-esJoQ6/snp-sites-1.3' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/snp-sites-esJoQ6' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-8d889ad3-bdf9-479d-a3f6-522e1cc12142' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 jessie-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 jessie-staging/main Sources [7217 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8332 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
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Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
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Checking available source versions...
Download source files with APT
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Reading package lists...
Building dependency tree...
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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 46.7 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main snp-sites 1.3-1 (dsc) [1517 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main snp-sites 1.3-1 (tar) [41.8 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main snp-sites 1.3-1 (diff) [3370 B]
Fetched 46.7 kB in 0s (1215 kB/s)
Download complete and in download only mode
Check arch
──────────
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-GRCIc5/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
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Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 2 not upgraded.
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Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9.0.0), autotools-dev, zlib1g-dev, check, dh-autoreconf, d-shlibs, libxml2-utils, docbook, docbook-xsl, xsltproc, asciidoc
Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9.0.0), autotools-dev, zlib1g-dev, check, dh-autoreconf, d-shlibs, libxml2-utils, docbook, docbook-xsl, xsltproc, asciidoc
dpkg-deb: building package `sbuild-build-depends-snp-sites-dummy' in `/«BUILDDIR»/resolver-G9cSGC/apt_archive/sbuild-build-depends-snp-sites-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install snp-sites build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
asciidoc autoconf automake autopoint autotools-dev bsdmainutils check
d-shlibs debhelper dh-autoreconf docbook docbook-xsl file gettext
gettext-base groff-base intltool-debian libasprintf0c2 libcroco3 libexpat1
libffi6 libgcrypt11 libglib2.0-0 libgpg-error0 libmagic1 libpipeline1
libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2
libsqlite3-0 libssl1.0.0 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 autoconf2.13 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 groff rng-tools 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 libasprintf-dev
libgettextpo-dev libglib2.0-data shared-mime-info 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 docbook docbook-xsl file gettext
gettext-base groff-base intltool-debian libasprintf0c2 libcroco3 libexpat1
libffi6 libgcrypt11 libglib2.0-0 libgpg-error0 libmagic1 libpipeline1
libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2
libsqlite3-0 libssl1.0.0 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, 51 newly installed, 0 to remove and 2 not upgraded.
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Get:46 http://172.17.0.1/private/ jessie-staging/main docbook all 4.5-5.1 [453 kB]
Get:47 http://172.17.0.1/private/ jessie-staging/main docbook-xsl all 1.78.1+dfsg-1 [2339 kB]
Get:48 http://172.17.0.1/private/ jessie-staging/main libxml2-utils armhf 2.9.1+dfsg1-3 [96.4 kB]
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Get:50 http://172.17.0.1/private/ jessie-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-1 [212 kB]
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Setting up libmagic1:armhf (1:5.14-2) ...
Setting up libsqlite3-0:armhf (3.8.2-1) ...
Setting up libxml2:armhf (2.9.1+dfsg1-3) ...
Setting up libpython2.7-minimal:armhf (2.7.6-5) ...
Setting up python2.7-minimal (2.7.6-5) ...
Setting up libffi6:armhf (3.0.13-11) ...
Setting up libglib2.0-0:armhf (2.36.4-1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.8-2) ...
Setting up libexpat1:armhf (2.1.0-4) ...
Setting up libsigsegv2:armhf (2.10-2) ...
Setting up libunistring0:armhf (0.9.3-5) ...
Setting up libxslt1.1:armhf (1.1.28-2) ...
Setting up sgml-base (1.26+nmu4) ...
Setting up file (1:5.14-2) ...
Setting up gettext-base (0.18.3.2-1) ...
Setting up mime-support (3.54) ...
update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode
Setting up libpython2.7-stdlib:armhf (2.7.6-5) ...
Setting up m4 (1.4.16-5) ...
Setting up python2.7 (2.7.6-5) ...
Setting up python-minimal (2.7.5-5) ...
Setting up libpython-stdlib:armhf (2.7.5-5) ...
Setting up python (2.7.5-5) ...
Setting up asciidoc (8.6.9-1) ...
Setting up autoconf (2.69-2) ...
Setting up autotools-dev (20130810.1) ...
Setting up automake (1:1.14.1-2) ...
update-alternatives: using /usr/bin/automake-1.14 to provide /usr/bin/automake (automake) in auto mode
Setting up autopoint (0.18.3.2-1) ...
Setting up check:armhf (0.9.10-6) ...
Setting up d-shlibs (0.54) ...
Setting up gettext (0.18.3.2-1) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
Setting up debhelper (9.20131227) ...
Setting up libtool (2.4.2-1.6) ...
Setting up dh-autoreconf (9) ...
Setting up xml-core (0.13+nmu2) ...
Setting up libxml2-utils (2.9.1+dfsg1-3) ...
Setting up xsltproc (1.1.28-2) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-1) ...
Processing triggers for sgml-base (1.26+nmu4) ...
Setting up docbook-xsl (1.78.1+dfsg-1) ...
Setting up sgml-data (2.0.9-1) ...
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 sbuild-build-depends-snp-sites-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.17-97) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.13-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.24-2 dpkg-dev_1.17.5+rpi1 g++-4.8_4.8.2-14 gcc-4.8_4.8.2-14 libc6-dev_2.17-97 libstdc++-4.8-dev_4.8.2-14 libstdc++6_4.8.2-14 linux-libc-dev_3.12.6-2+rpi1
Package versions: apt_0.9.14.2 asciidoc_8.6.9-1 autoconf_2.69-2 automake_1:1.14.1-2 autopoint_0.18.3.2-1 autotools-dev_20130810.1 base-files_7.2+rpi1 base-passwd_3.5.28 bash_4.2+dfsg-1 binutils_2.24-2 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.5 build-essential_11.6 bzip2_1.0.6-5 check_0.9.10-6 coreutils_8.21-1 cpio_2.11+dfsg-1 cpp_4:4.8.2-1 cpp-4.8_4.8.2-14 d-shlibs_0.54 dash_0.5.7-4 debconf_1.5.52 debconf-i18n_1.5.52 debfoster_2.7-1.2 debhelper_9.20131227 debianutils_4.4 dh-autoreconf_9 diffutils_1:3.3-1 docbook_4.5-5.1 docbook-xsl_1.78.1+dfsg-1 dpkg_1.17.5+rpi1 dpkg-dev_1.17.5+rpi1 e2fslibs_1.42.9-2 e2fsprogs_1.42.9-2 fakeroot_1.18.4-2 file_1:5.14-2 findutils_4.4.2-7 g++_4:4.8.2-1 g++-4.8_4.8.2-14 gcc_4:4.8.2-1 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-9+rpi1 gcc-4.8_4.8.2-14 gcc-4.8-base_4.8.2-14 gettext_0.18.3.2-1 gettext-base_0.18.3.2-1 gnupg_1.4.16-1 gpgv_1.4.16-1 grep_2.15-2 groff-base_1.22.2-4 gzip_1.6-3 hostname_3.15 initramfs-tools_0.115 initscripts_2.88dsf-45 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.2-1+rpi1 kmod_16-2 libacl1_2.2.52-1 libapt-pkg4.12_0.9.14.2 libasan0_4.8.2-14 libasprintf0c2_0.18.3.2-1 libatomic1_4.8.2-14 libattr1_1:2.4.47-1 libaudit-common_1:2.3.2-3 libaudit1_1:2.3.2-3 libblkid1_2.20.1-5.5 libbz2-1.0_1.0.6-5 libc-bin_2.17-97 libc-dev-bin_2.17-97 libc6_2.17-97 libc6-dev_2.17-97 libcap2_1:2.22-1.2 libcloog-isl4_0.18.1-3 libcomerr2_1.42.9-2 libcroco3_0.6.8-2 libdb5.1_5.1.29-6 libdbus-1-3_1.7.10-2 libdpkg-perl_1.17.5+rpi1 libexpat1_2.1.0-4 libffi6_3.0.13-11 libgc1c2_1:7.2d-6 libgcc-4.8-dev_4.8.2-14 libgcc1_1:4.8.2-14 libgcrypt11_1.5.3-3 libgdbm3_1.8.3-12 libglib2.0-0_2.36.4-1 libgmp10_2:5.1.3+dfsg-1 libgomp1_4.8.2-14 libgpg-error0_1.12-0.2 libisl10_0.12.1-2 libklibc_2.0.2-1+rpi1 libkmod2_16-2 liblocale-gettext-perl_1.05-7+b3 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.14-2 libmount1_2.20.1-5.5 libmpc3_1.0.1-1 libmpfr4_3.1.2-1 libncurses5_5.9+20130608-1 libncursesw5_5.9+20130608-1 libnih-dbus1_1.0.3-4.2 libnih1_1.0.3-4.2 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libpcre3_1:8.31-2 libpipeline1_1.2.6-1 libprocps0_1:3.3.4-2 libpython-stdlib_2.7.5-5 libpython2.7-minimal_2.7.6-5 libpython2.7-stdlib_2.7.6-5 libreadline6_6.2+dfsg-0.1 libselinux1_2.2.2-1 libsemanage-common_2.2-1 libsemanage1_2.2-1 libsepol1_2.2-1 libsigsegv2_2.10-2 libslang2_2.2.4-16 libsqlite3-0_3.8.2-1 libss2_1.42.9-2 libssl1.0.0_1.0.1f-1 libstdc++-4.8-dev_4.8.2-14 libstdc++6_4.8.2-14 libtext-charwidth-perl_0.04-7+b3 libtext-iconv-perl_1.7-5+b3 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_2.3000-1 libtinfo5_5.9+20130608-1 libtool_2.4.2-1.6 libudev1_204-6 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.3 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.5 libxml2_2.9.1+dfsg1-3 libxml2-utils_2.9.1+dfsg1-3 libxslt1.1_1.1.28-2 linux-libc-dev_3.12.6-2+rpi1 login_1:4.1.5.1-1 lsb-base_4.1+Debian12+rpi1 m4_1.4.16-5 make_3.81-8.3 makedev_2.3.1-93 man-db_2.6.5-3 mawk_1.3.3-17 mime-support_3.54 mount_2.20.1-5.5 mountall_2.52 multiarch-support_2.17-97 ncurses-base_5.9+20130608-1 ncurses-bin_5.9+20130608-1 passwd_1:4.1.5.1-1 patch_2.7.1-4 perl_5.18.2-2 perl-base_5.18.2-2 perl-modules_5.18.2-2 plymouth_0.8.8-6+deb8u3 po-debconf_1.0.16+nmu2 procps_1:3.3.4-2 python_2.7.5-5 python-minimal_2.7.5-5 python2.7_2.7.6-5 python2.7-minimal_2.7.6-5 raspbian-archive-keyring_20120528.2 readline-common_6.2+dfsg-0.1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-snp-sites-dummy_0.invalid.0 sed_4.2.2-3 sensible-utils_0.0.9 sgml-base_1.26+nmu4 sgml-data_2.0.9-1 sysv-rc_2.88dsf-45 sysvinit_2.88dsf-45 sysvinit-core_2.88dsf-45 sysvinit-utils_2.88dsf-45 tar_1.26+dfsg-8 tzdata_2013i-1 udev_204-6 util-linux_2.20.1-5.5 xml-core_0.13+nmu2 xsltproc_1.1.28-2 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1 zlib1g-dev_1:1.2.8.dfsg-1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Wed Jan 15 15:23:40 2014 UTC using DSA key ID C09FD35A
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./snp-sites_1.3-1.dsc
dpkg-source: info: extracting snp-sites in snp-sites-1.3
dpkg-source: info: unpacking snp-sites_1.3.orig.tar.gz
dpkg-source: info: unpacking snp-sites_1.3-1.debian.tar.gz
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
APT_CONFIG=/var/lib/sbuild/apt.conf
COLUMNS=80
CONSOLE=/dev/console
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INIT_VERSION=sysvinit-2.88
LC_ALL=POSIX
LINES=24
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PREVLEVEL=N
PWD=/
RUNLEVEL=2
SCHROOT_ALIAS_NAME=jessie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=jessie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=jessie-staging-armhf-sbuild-8d889ad3-bdf9-479d-a3f6-522e1cc12142
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
init=/sbin/init
previous=N
rootmnt=/root
runlevel=2
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package snp-sites
dpkg-buildpackage: source version 1.3-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build snp-sites-1.3
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
aclocal: warning: couldn't open directory 'm4': No such file or directory
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/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: 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... 805306365
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[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 --param=ssp-buffer-size=4 -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 --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c alignment-file.c -fPIC -DPIC -o .libs/alignment-file.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -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 --param=ssp-buffer-size=4 -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 --param=ssp-buffer-size=4 -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 --param=ssp-buffer-size=4 -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 --param=ssp-buffer-size=4 -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 --param=ssp-buffer-size=4 -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 --param=ssp-buffer-size=4 -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 --param=ssp-buffer-size=4 -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 --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c snp-sites.c -fPIC -DPIC -o .libs/snp-sites.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -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 --param=ssp-buffer-size=4 -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 --param=ssp-buffer-size=4 -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 --param=ssp-buffer-size=4 -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 --param=ssp-buffer-size=4 -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 --param=ssp-buffer-size=4 -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 --param=ssp-buffer-size=4 -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 --param=ssp-buffer-size=4 -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 --param=ssp-buffer-size=4 -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 --param=ssp-buffer-size=4 -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 --param=ssp-buffer-size=4 -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
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 --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o main.o main.c
/bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -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 --param=ssp-buffer-size=4 -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[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 --param=ssp-buffer-size=4 -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 --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o run_all_tests-helper-methods.o `test -f '../tests/helper-methods.c' || echo './'`../tests/helper-methods.c
../tests/helper-methods.c: In function 'compare_files':
../tests/helper-methods.c:46:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(expected_buffer, sizeof(char), numbytes, expected_output_fh);
^
../tests/helper-methods.c:53:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(actual_buffer, sizeof(char), numbytes, actual_output_fh);
^
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -I../tests -g -O2 -fstack-protector --param=ssp-buffer-size=4 -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 --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -o run-all-tests run_all_tests-check-snp-sites.o run_all_tests-helper-methods.o run_all_tests-run-all-tests.o -lm -lcheck libsnp-sites.la -lz -lpthread -lrt
libtool: link: gcc -I../tests -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z -Wl,relro -o .libs/run-all-tests run_all_tests-check-snp-sites.o run_all_tests-helper-methods.o run_all_tests-run-all-tests.o -lm -lcheck ./.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'
FAIL: run-all-tests
make[5]: Entering directory `/«PKGBUILDDIR»/src'
make[5]: Nothing to be done for `all'.
make[5]: Leaving directory `/«PKGBUILDDIR»/src'
============================================================================
Testsuite summary for snp-sites 1
============================================================================
# TOTAL: 1
# PASS: 0
# SKIP: 0
# XFAIL: 0
# FAIL: 1
# XPASS: 0
# ERROR: 0
============================================================================
See src/test-suite.log
============================================================================
make[4]: *** [test-suite.log] Error 1
make[4]: Leaving directory `/«PKGBUILDDIR»/src'
make[3]: *** [check-TESTS] Error 2
make[2]: *** [check-am] Error 2
make[3]: Leaving directory `/«PKGBUILDDIR»/src'
make[2]: Leaving directory `/«PKGBUILDDIR»/src'
make[1]: *** [check-recursive] Error 1
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_auto_test: make -j1 check returned exit code 2
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
Build finished at 20140126-0808
Finished
────────
E: Build failure (dpkg-buildpackage died)
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 5456
Build-Time: 97
Distribution: jessie-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 328
Job: snp-sites_1.3-1
Machine Architecture: armhf
Package: snp-sites
Package-Time: 482
Source-Version: 1.3-1
Space: 5456
Status: attempted
Version: 1.3-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20140126-0808
Build needed 00:08:02, 5456k disc space