smalt →
0.7.6-4 →
armhf → 2014-10-25 09:46:23
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on bm-wb-03
╔══════════════════════════════════════════════════════════════════════════════╗
║ smalt 0.7.6-4 (armhf) 25 Oct 2014 09:06 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: smalt
Version: 0.7.6-4
Source Version: 0.7.6-4
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/smalt-Y1bqGB/smalt-0.7.6' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/smalt-Y1bqGB' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-46166857-fd83-434d-a66e-3f85678d7707' 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 [7675 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8863 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
Fetched 16.5 MB in 30s (541 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
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Checking available source versions...
Download source files with APT
──────────────────────────────
Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'smalt' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/smalt/trunk/
Need to get 72.3 MB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main smalt 0.7.6-4 (dsc) [2080 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main smalt 0.7.6-4 (tar) [72.3 MB]
Get:3 http://172.17.0.1/private/ jessie-staging/main smalt 0.7.6-4 (diff) [4512 B]
Fetched 72.3 MB in 15s (4524 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-ZZe1dL/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
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 34 not upgraded.
Need to get 0 B/810 B of archives.
After this operation, 0 B of additional disk space will be used.
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 11075 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
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), zlib1g-dev, python, samtools, libbambamc-dev, autotools-dev
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), zlib1g-dev, python, samtools, libbambamc-dev, autotools-dev
dpkg-deb: building package `sbuild-build-depends-smalt-dummy' in `/«BUILDDIR»/resolver-k6KkGv/apt_archive/sbuild-build-depends-smalt-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install smalt build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
autotools-dev bsdmainutils debhelper file gettext gettext-base groff-base
intltool-debian libasprintf0c2 libbambamc-dev libbambamc0 libcroco3
libexpat1 libffi6 libglib2.0-0 libmagic1 libpipeline1 libpython-stdlib
libpython2.7-minimal libpython2.7-stdlib libsqlite3-0 libssl1.0.0
libunistring0 libxml2 man-db mime-support pkg-config po-debconf python
python-minimal python2.7 python2.7-minimal samtools zlib1g-dev
Suggested packages:
wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser
libmail-box-perl python-doc python-tk python2.7-doc binfmt-support
Recommended packages:
curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
libglib2.0-data shared-mime-info xdg-user-dirs xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
autotools-dev bsdmainutils debhelper file gettext gettext-base groff-base
intltool-debian libasprintf0c2 libbambamc-dev libbambamc0 libcroco3
libexpat1 libffi6 libglib2.0-0 libmagic1 libpipeline1 libpython-stdlib
libpython2.7-minimal libpython2.7-stdlib libsqlite3-0 libssl1.0.0
libunistring0 libxml2 man-db mime-support pkg-config po-debconf python
python-minimal python2.7 python2.7-minimal samtools
sbuild-build-depends-smalt-dummy zlib1g-dev
0 upgraded, 35 newly installed, 0 to remove and 34 not upgraded.
Need to get 14.3 MB/14.3 MB of archives.
After this operation, 44.3 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.3.1-1 [21.8 kB]
Get:2 http://172.17.0.1/private/ jessie-staging/main libssl1.0.0 armhf 1.0.1j-1 [843 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main groff-base armhf 1.22.2-8 [1045 kB]
Get:4 http://172.17.0.1/private/ jessie-staging/main bsdmainutils armhf 9.0.5 [206 kB]
Get:5 http://172.17.0.1/private/ jessie-staging/main man-db armhf 2.7.0.2-2 [972 kB]
Get:6 http://172.17.0.1/private/ jessie-staging/main libasprintf0c2 armhf 0.19.2-3 [30.7 kB]
Get:7 http://172.17.0.1/private/ jessie-staging/main libmagic1 armhf 1:5.19-2 [232 kB]
Get:8 http://172.17.0.1/private/ jessie-staging/main libsqlite3-0 armhf 3.8.6-1 [363 kB]
Get:9 http://172.17.0.1/private/ jessie-staging/main libxml2 armhf 2.9.1+dfsg1-4 [698 kB]
Get:10 http://172.17.0.1/private/ jessie-staging/main libpython2.7-minimal armhf 2.7.8-7 [372 kB]
Get:11 http://172.17.0.1/private/ jessie-staging/main python2.7-minimal armhf 2.7.8-7 [1145 kB]
Get:12 http://172.17.0.1/private/ jessie-staging/main libffi6 armhf 3.1-2 [18.1 kB]
Get:13 http://172.17.0.1/private/ jessie-staging/main libglib2.0-0 armhf 2.42.0-2 [2333 kB]
Get:14 http://172.17.0.1/private/ jessie-staging/main libcroco3 armhf 0.6.8-3 [121 kB]
Get:15 http://172.17.0.1/private/ jessie-staging/main libexpat1 armhf 2.1.0-6 [60.2 kB]
Get:16 http://172.17.0.1/private/ jessie-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:17 http://172.17.0.1/private/ jessie-staging/main file armhf 1:5.19-2 [57.8 kB]
Get:18 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.19.2-3 [116 kB]
Get:19 http://172.17.0.1/private/ jessie-staging/main mime-support all 3.57 [35.8 kB]
Get:20 http://172.17.0.1/private/ jessie-staging/main libpython2.7-stdlib armhf 2.7.8-7 [1804 kB]
Get:21 http://172.17.0.1/private/ jessie-staging/main python2.7 armhf 2.7.8-7 [247 kB]
Get:22 http://172.17.0.1/private/ jessie-staging/main python-minimal armhf 2.7.8-1 [39.8 kB]
Get:23 http://172.17.0.1/private/ jessie-staging/main libpython-stdlib armhf 2.7.8-1 [19.2 kB]
Get:24 http://172.17.0.1/private/ jessie-staging/main python armhf 2.7.8-1 [150 kB]
Get:25 http://172.17.0.1/private/ jessie-staging/main autotools-dev all 20140911.1 [70.5 kB]
Get:26 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.19.2-3 [1164 kB]
Get:27 http://172.17.0.1/private/ jessie-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:28 http://172.17.0.1/private/ jessie-staging/main po-debconf all 1.0.16+nmu3 [220 kB]
Get:29 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20141003 [811 kB]
Get:30 http://172.17.0.1/private/ jessie-staging/main libbambamc0 armhf 0.0.50-1 [30.3 kB]
Get:31 http://172.17.0.1/private/ jessie-staging/main pkg-config armhf 0.28-1 [55.1 kB]
Get:32 http://172.17.0.1/private/ jessie-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-1+rpi1 [192 kB]
Get:33 http://172.17.0.1/private/ jessie-staging/main libbambamc-dev armhf 0.0.50-1 [39.4 kB]
Get:34 http://172.17.0.1/private/ jessie-staging/main samtools armhf 0.1.19-1 [523 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 14.3 MB in 3s (3750 kB/s)
Selecting previously unselected package libpipeline1:armhf.
(Reading database ... 11075 files and directories currently installed.)
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Unpacking libpipeline1:armhf (1.3.1-1) ...
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Preparing to unpack .../groff-base_1.22.2-8_armhf.deb ...
Unpacking groff-base (1.22.2-8) ...
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Selecting previously unselected package libbambamc-dev.
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Unpacking sbuild-build-depends-smalt-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.3.1-1) ...
Setting up libssl1.0.0:armhf (1.0.1j-1) ...
Setting up groff-base (1.22.2-8) ...
Setting up bsdmainutils (9.0.5) ...
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 man-db (2.7.0.2-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libasprintf0c2:armhf (0.19.2-3) ...
Setting up libmagic1:armhf (1:5.19-2) ...
Setting up libsqlite3-0:armhf (3.8.6-1) ...
Setting up libxml2:armhf (2.9.1+dfsg1-4) ...
Setting up libpython2.7-minimal:armhf (2.7.8-7) ...
Setting up python2.7-minimal (2.7.8-7) ...
Setting up libffi6:armhf (3.1-2) ...
Setting up libglib2.0-0:armhf (2.42.0-2) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.8-3) ...
Setting up libexpat1:armhf (2.1.0-6) ...
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up file (1:5.19-2) ...
Setting up gettext-base (0.19.2-3) ...
Setting up mime-support (3.57) ...
Setting up libpython2.7-stdlib:armhf (2.7.8-7) ...
Setting up python2.7 (2.7.8-7) ...
Setting up python-minimal (2.7.8-1) ...
Setting up libpython-stdlib:armhf (2.7.8-1) ...
Setting up python (2.7.8-1) ...
Setting up autotools-dev (20140911.1) ...
Setting up gettext (0.19.2-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu3) ...
Setting up debhelper (9.20141003) ...
Setting up libbambamc0 (0.0.50-1) ...
Setting up pkg-config (0.28-1) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-1+rpi1) ...
Setting up libbambamc-dev (0.0.50-1) ...
Setting up samtools (0.1.19-1) ...
Setting up sbuild-build-depends-smalt-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.19-11) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.16-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.24.51.20140918-1 dpkg-dev_1.17.13 g++-4.9_4.9.1-15 gcc-4.8_4.8.3-11 gcc-4.9_4.9.1-15 libc6-dev_2.19-11 libstdc++-4.9-dev_4.9.1-15 libstdc++6_4.9.1-15 linux-libc-dev_3.14.4-1+rpi1+b4
Package versions: apt_1.0.9.1 autotools-dev_20140911.1 base-files_7.5+rpi1 base-passwd_3.5.36 bash_4.3-9.2 binutils_2.24.51.20140918-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.9 build-essential_11.7 bzip2_1.0.6-7 coreutils_8.23-2 cpio_2.11+dfsg-2 cpp_4:4.9.1-1 cpp-4.8_4.8.3-11 cpp-4.9_4.9.1-15 dash_0.5.7-4 debconf_1.5.53 debfoster_2.7-2 debhelper_9.20141003 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.13 dpkg-dev_1.17.13 e2fslibs_1.42.12-1 e2fsprogs_1.42.12-1 fakeroot_1.20.1-1.1 file_1:5.19-2 findutils_4.4.2-9 g++_4:4.9.1-1 g++-4.9_4.9.1-15 gcc_4:4.9.1-1 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8_4.8.3-11 gcc-4.8-base_4.8.3-11 gcc-4.9_4.9.1-15 gcc-4.9-base_4.9.1-15 gettext_0.19.2-3 gettext-base_0.19.2-3 gnupg_1.4.18-4 gpgv_1.4.18-4 grep_2.20-3 groff-base_1.22.2-8 gzip_1.6-3 hostname_3.15 init_1.21 initramfs-tools_0.116 initscripts_2.88dsf-53.4 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.3-1+rpi1 kmod_18-3 libacl1_2.2.52-2 libapt-pkg4.12_1.0.9.1 libasan0_4.8.3-11 libasan1_4.9.1-15 libasprintf0c2_0.19.2-3 libatomic1_4.9.1-15 libattr1_1:2.4.47-2 libaudit-common_1:2.4-1 libaudit1_1:2.4-1 libbambamc-dev_0.0.50-1 libbambamc0_0.0.50-1 libblkid1_2.20.1-5.9 libbz2-1.0_1.0.6-7 libc-bin_2.19-11 libc-dev-bin_2.19-11 libc6_2.19-11 libc6-dev_2.19-11 libcap2_1:2.24-6 libcgi-pm-perl_4.03-1 libcloog-isl4_0.18.2-1 libcomerr2_1.42.12-1 libcroco3_0.6.8-3 libdb5.1_5.1.29-6 libdb5.3_5.3.28-6 libdbus-1-3_1.8.6-2 libdebconfclient0_0.192 libdpkg-perl_1.17.13 libdrm2_2.4.56-1 libexpat1_2.1.0-6 libfakeroot_1.20.1-1.1 libffi6_3.1-2 libgc1c2_1:7.2d-6.3 libgcc-4.8-dev_4.8.3-11 libgcc-4.9-dev_4.9.1-15 libgcc1_1:4.9.1-15 libgdbm3_1.8.3-13 libglib2.0-0_2.42.0-2 libgmp10_2:6.0.0+dfsg-4+rpi1 libgomp1_4.9.1-15 libisl10_0.12.2-2 libklibc_2.0.3-1+rpi1 libkmod2_18-3 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.19-2 libmount1_2.20.1-5.9 libmpc3_1.0.2-1 libmpfr4_3.1.2-1 libncurses5_5.9+20140913-1 libncursesw5_5.9+20140913-1 libpackage-constants-perl_0.04-1 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_1:8.35-3 libpipeline1_1.3.1-1 libpng12-0_1.2.50-2 libprocps0_1:3.3.4-2 libprocps3_1:3.3.9-7 libpython-stdlib_2.7.8-1 libpython2.7-minimal_2.7.8-7 libpython2.7-stdlib_2.7.8-7 libreadline6_6.3-8 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-2 libslang2_2.3.0-1 libsqlite3-0_3.8.6-1 libss2_1.42.12-1 libssl1.0.0_1.0.1j-1 libstdc++-4.9-dev_4.9.1-15 libstdc++6_4.9.1-15 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140913-1 libubsan0_4.9.1-15 libudev1_208-8 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-24 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.9 libxml2_2.9.1+dfsg1-4 linux-libc-dev_3.14.4-1+rpi1+b4 login_1:4.2-2 lsb-base_4.1+Debian13+rpi1 make_4.0-8 makedev_2.3.1-93 man-db_2.7.0.2-2 mawk_1.3.3-17 mime-support_3.57 mount_2.20.1-5.9 multiarch-support_2.19-11 nano_2.2.6-3 ncurses-base_5.9+20140913-1 ncurses-bin_5.9+20140913-1 passwd_1:4.2-2 patch_2.7.1-6 perl_5.20.1-1 perl-base_5.20.1-1 perl-modules_5.20.1-1 pkg-config_0.28-1 plymouth_0.9.0-7 po-debconf_1.0.16+nmu3 procps_1:3.3.9-7 python_2.7.8-1 python-minimal_2.7.8-1 python2.7_2.7.8-7 python2.7-minimal_2.7.8-7 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 samtools_0.1.19-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-smalt-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 startpar_0.59-3 sysv-rc_2.88dsf-53.4 sysvinit_2.88dsf-53.4 sysvinit-core_2.88dsf-53.4 sysvinit-utils_2.88dsf-53.4 tar_1.27.1-2 tzdata_2014g-1 udev_208-8 util-linux_2.20.1-5.9 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1+rpi1 zlib1g-dev_1:1.2.8.dfsg-1+rpi1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Tue Oct 14 15:15:26 2014 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./smalt_0.7.6-4.dsc
dpkg-source: info: extracting smalt in smalt-0.7.6
dpkg-source: info: unpacking smalt_0.7.6.orig.tar.gz
dpkg-source: info: unpacking smalt_0.7.6-4.debian.tar.xz
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-46166857-fd83-434d-a66e-3f85678d7707
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 smalt
dpkg-buildpackage: source version 0.7.6-4
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build smalt-0.7.6
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean --with autotools_dev # this fails because auf broken upstream autoconf stuff: - - with autoreconf
dh_testdir
debian/rules override_dh_auto_clean
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_clean
rm -rf test/*.pyc misc/*.pyc test/tmp
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_autotools-dev_restoreconfig
dh_clean
debian/rules build-arch
dh build-arch --with autotools_dev # this fails because auf broken upstream autoconf stuff: - - with autoreconf
dh_testdir -a
dh_autotools-dev_updateconfig -a
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 for icc... no
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 for style of include used by make... GNU
checking dependency style of gcc... none
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for ranlib... ranlib
checking for a Python interpreter with version >= 2.6... python
checking for python... /usr/bin/python
checking for python version... 2.7
checking for python platform... linux2
checking for python script directory... ${prefix}/lib/python2.7/dist-packages
checking for python extension module directory... ${exec_prefix}/lib/python2.7/dist-packages
checking for samtools... yes
checking for sam_open in -lbam... no
checking for BAMBAMC... yes
checking for gzread in -lz... yes
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 math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking pthread.h usability... yes
checking pthread.h presence... yes
checking for pthread.h... yes
checking semaphore.h usability... yes
checking semaphore.h presence... yes
checking for semaphore.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdint.h... (cached) yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking emmintrin.h usability... no
checking emmintrin.h presence... no
checking for emmintrin.h... no
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating test/Makefile
config.status: creating test/data/Makefile
config.status: creating misc/Makefile
config.status: creating config.h
config.status: executing depfiles commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
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'
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c elib.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c filio.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c sequence.c
rm -f libseq.a
ar cru libseq.a elib.o filio.o sequence.o
ranlib libseq.a
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-score.o `test -f 'score.c' || echo './'`score.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-diffstr.o `test -f 'diffstr.c' || echo './'`diffstr.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-alibuffer.o `test -f 'alibuffer.c' || echo './'`alibuffer.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-alignment.o `test -f 'alignment.c' || echo './'`alignment.c
alignment.c:478:13: warning: 'blankALITRACK' defined but not used [-Wunused-function]
static void blankALITRACK(ALITRACK *trackp, const ALIBAND *bandp)
^
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-sort.o `test -f 'sort.c' || echo './'`sort.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-array.o `test -f 'array.c' || echo './'`array.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-interval.o `test -f 'interval.c' || echo './'`interval.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-hashidx.o `test -f 'hashidx.c' || echo './'`hashidx.c
hashidx.c: In function 'countPerfectKey':
hashidx.c:191:77: warning: unused parameter 'tuplectr' [-Wunused-parameter]
static int countPerfectKey(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr)
^
hashidx.c: In function 'countCollisionKey':
hashidx.c:206:79: warning: unused parameter 'tuplectr' [-Wunused-parameter]
static int countCollisionKey(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr)
^
hashidx.c: In function 'collectWords':
hashidx.c:223:74: warning: unused parameter 'tuplectr' [-Wunused-parameter]
static int collectWords(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr)
^
hashidx.c: In function 'countWords':
hashidx.c:265:72: warning: unused parameter 'tuplectr' [-Wunused-parameter]
static int countWords(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr)
^
hashidx.c: At top level:
hashidx.c:446:18: warning: 'getWordHisto' defined but not used [-Wunused-function]
static WORDNUM_t getWordHisto(WORDNUM_t *counts, HASHNUM_t n, const HashTable *htp)
^
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-hashhit.o `test -f 'hashhit.c' || echo './'`hashhit.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-segment.o `test -f 'segment.c' || echo './'`segment.c
segment.c:1330:13: warning: 'labelSEGCANDWithinInsertRange' defined but not used [-Wunused-function]
static void labelSEGCANDWithinInsertRange (SEGCAND *candAp, SEGNUM_t nsegA,
^
segment.c:1375:12: warning: 'checkCANDARRsequential' defined but not used [-Wunused-function]
static int checkCANDARRsequential(const CANDARR candr, SEGNUM_t *rvc_offs)
^
rm -f libsgm.a
ar cru libsgm.a libsgm_a-score.o libsgm_a-diffstr.o libsgm_a-alibuffer.o libsgm_a-alignment.o libsgm_a-sort.o libsgm_a-array.o libsgm_a-interval.o libsgm_a-hashidx.o libsgm_a-hashhit.o libsgm_a-segment.o libseq.a
ranlib libsgm.a
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-smalt.o `test -f 'smalt.c' || echo './'`smalt.c
smalt.c: In function 'cleanupSmaltOutput':
smalt.c:659:39: warning: unused parameter 'errmsgp' [-Wunused-parameter]
static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op)
^
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-menu.o `test -f 'menu.c' || echo './'`menu.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-threads.o `test -f 'threads.c' || echo './'`threads.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-infmt.o `test -f 'infmt.c' || echo './'`infmt.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-results.o `test -f 'results.c' || echo './'`results.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-resultpairs.o `test -f 'resultpairs.c' || echo './'`resultpairs.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-report.o `test -f 'report.c' || echo './'`report.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-rmap.o `test -f 'rmap.c' || echo './'`rmap.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-insert.o `test -f 'insert.c' || echo './'`insert.c
gcc -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -o smalt smalt-smalt.o smalt-menu.o smalt-threads.o smalt-infmt.o smalt-results.o smalt-resultpairs.o smalt-report.o smalt-rmap.o smalt-insert.o libsgm.a libseq.a -lbambamc -lz -lm -lpthread -lz
make[3]: Leaving directory '/«PKGBUILDDIR»/src'
Making all in test
make[3]: Entering directory '/«PKGBUILDDIR»/test'
make[4]: Entering directory '/«PKGBUILDDIR»/test'
make[4]: Nothing to be done for 'all-am'.
make[4]: Leaving directory '/«PKGBUILDDIR»/test'
make[3]: Leaving directory '/«PKGBUILDDIR»/test'
Making all in misc
make[3]: Entering directory '/«PKGBUILDDIR»/misc'
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c simread.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c rsample.c
gcc -I../src/ -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -o simread simread.o rsample.o ../src/libsgm.a ../src/libseq.a -lm -lz
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c fetchseq.c
gcc -I../src/ -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -o fetchseq fetchseq.o ../src/libseq.a -lz
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c splitreads.c
gcc -I../src/ -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -o splitreads splitreads.o ../src/libseq.a -lz
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c mixreads.c
gcc -I../src/ -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -o mixreads mixreads.o ../src/libseq.a -lz
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c splitmates.c
gcc -I../src/ -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -o splitmates splitmates.o ../src/libseq.a -lz
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c readstats.c
gcc -I../src/ -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -o readstats readstats.o ../src/libseq.a -lz
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c trunkreads.c
gcc -I../src/ -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -o trunkreads trunkreads.o ../src/libseq.a -lz
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c basqcol.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c basqual.c
gcc -I../src/ -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -o basqcol basqcol.o basqual.o ../src/libseq.a -lz
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c simqual.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o diffstr.o `test -f '../src/diffstr.c' || echo './'`../src/diffstr.c
gcc -I../src/ -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -o simqual simqual.o basqual.o diffstr.o ../src/libseq.a -lm -lz
make[3]: Leaving directory '/«PKGBUILDDIR»/misc'
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[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/«PKGBUILDDIR»/src'
Making check in test
make[2]: Entering directory '/«PKGBUILDDIR»/test'
make[3]: Entering directory '/«PKGBUILDDIR»/test'
make sequenceReverseComplement_test smalt_Xali_test
make[4]: Entering directory '/«PKGBUILDDIR»/test'
gcc -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c sequenceReverseComplement_test.c
gcc -I../src/ -I../test -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -o sequenceReverseComplement_test sequenceReverseComplement_test.o ../src/libseq.a -lz
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-smalt.o `test -f '../src/smalt.c' || echo './'`../src/smalt.c
../src/smalt.c: In function 'cleanupSmaltOutput':
../src/smalt.c:659:39: warning: unused parameter 'errmsgp' [-Wunused-parameter]
static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op)
^
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-menu.o `test -f '../src/menu.c' || echo './'`../src/menu.c
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-threads.o `test -f '../src/threads.c' || echo './'`../src/threads.c
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-infmt.o `test -f '../src/infmt.c' || echo './'`../src/infmt.c
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-results.o `test -f '../src/results.c' || echo './'`../src/results.c
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-resultpairs.o `test -f '../src/resultpairs.c' || echo './'`../src/resultpairs.c
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-insert.o `test -f '../src/insert.c' || echo './'`../src/insert.c
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-report.o `test -f '../src/report.c' || echo './'`../src/report.c
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-rmap.o `test -f '../src/rmap.c' || echo './'`../src/rmap.c
gcc -I../src/ -I../test -Wall -Wextra -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -o smalt_Xali_test smalt_Xali_test-smalt.o smalt_Xali_test-menu.o smalt_Xali_test-threads.o smalt_Xali_test-infmt.o smalt_Xali_test-results.o smalt_Xali_test-resultpairs.o smalt_Xali_test-insert.o smalt_Xali_test-report.o smalt_Xali_test-rmap.o ../src/libsgm.a ../src/libseq.a -lbambamc -lz -lm -lpthread -lz
make[4]: Leaving directory '/«PKGBUILDDIR»/test'
make check-TESTS
make[4]: Entering directory '/«PKGBUILDDIR»/test'
PASS: splitReads_test.py
PASS: results_split_test.py
PASS: ouform_cigar_test.py
PASS: sample_test.py
PASS: cigar_test.py
PASS: mthread_test.py
PASS: ioform_test.py
PASS: xali_test.py
PASS: bam_cigar_test.py
==================
All 9 tests passed
==================
make[4]: Leaving directory '/«PKGBUILDDIR»/test'
make[3]: Leaving directory '/«PKGBUILDDIR»/test'
make[2]: Leaving directory '/«PKGBUILDDIR»/test'
Making check in misc
make[2]: Entering directory '/«PKGBUILDDIR»/misc'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/«PKGBUILDDIR»/misc'
make[2]: Entering directory '/«PKGBUILDDIR»'
make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
fakeroot debian/rules binary-arch
dh binary-arch --with autotools_dev # this fails because auf broken upstream autoconf stuff: - - with autoreconf
dh_testroot -a
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/«PKGBUILDDIR»'
# upstream install does install more files than needed
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
dh_compress -a
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package `smalt' in `../smalt_0.7.6-4_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../smalt_0.7.6-4_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build smalt-0.7.6
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20141025-0944
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
smalt_0.7.6-4_armhf.changes:
────────────────────────────
Format: 1.8
Date: Tue, 14 Oct 2014 13:33:15 +0200
Source: smalt
Binary: smalt smalt-examples
Architecture: armhf
Version: 0.7.6-4
Distribution: jessie-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
smalt - Sequence Mapping and Alignment Tool
smalt-examples - Sequence Mapping and Alignment Tool (examples)
Closes: 765256
Changes:
smalt (0.7.6-4) unstable; urgency=medium
.
* cme fix dpkg-control
* Use autotools-dev / since dh-autoreconf does not work this hopefully also
Closes: #765256
Checksums-Sha1:
b870a1abdf7949a22e7f06ba3c30a118c1f82e0c 93524 smalt_0.7.6-4_armhf.deb
Checksums-Sha256:
7d8e447e02c07039dfed429705fa9f5dd23028d9b05a83b8bee0251c31ff84e0 93524 smalt_0.7.6-4_armhf.deb
Files:
7f708f55a66f4abb343af90ae6790d56 93524 science optional smalt_0.7.6-4_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
smalt_0.7.6-4_armhf.deb
───────────────────────
new debian package, version 2.0.
size 93524 bytes: control archive=1199 bytes.
1300 bytes, 30 lines control
334 bytes, 5 lines md5sums
Package: smalt
Version: 0.7.6-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 234
Depends: libbambamc0, libc6 (>= 2.7), zlib1g (>= 1:1.2.0.2)
Section: science
Priority: optional
Homepage: http://www.sanger.ac.uk/resources/software/smalt/
Description: Sequence Mapping and Alignment Tool
SMALT efficiently aligns DNA sequencing reads with a reference genome.
It Reads from a wide range of sequencing platforms, for example Illumina,
Roche-454, Ion Torrent, PacBio or ABI-Sanger, can be processed including
paired reads.
.
The software employs a perfect hash index of short words (< 20
nucleotides long), sampled at equidistant steps along the genomic
reference sequences.
.
For each read, potentially matching segments in the reference are
identified from seed matches in the index and subsequently aligned with
the read using a banded Smith-Waterman algorithm.
.
The best gapped alignments of each read is reported including a score
for the reliability of the best mapping. The user can adjust the
trade-off between sensitivity and speed by tuning the length and spacing
of the hashed words.
.
A mode for the detection of split (chimeric) reads is provided.
Multi-threaded program execution is supported.
drwxr-xr-x root/root 0 2014-10-25 09:44 ./
drwxr-xr-x root/root 0 2014-10-25 09:44 ./usr/
drwxr-xr-x root/root 0 2014-10-25 09:44 ./usr/bin/
-rwxr-xr-x root/root 194256 2014-10-25 09:44 ./usr/bin/smalt
drwxr-xr-x root/root 0 2014-10-25 09:44 ./usr/lib/
drwxr-xr-x root/root 0 2014-10-25 09:44 ./usr/lib/smalt/
drwxr-xr-x root/root 0 2014-10-25 09:44 ./usr/lib/smalt/test/
-rwxr-xr-x root/root 42528 2014-10-25 09:44 ./usr/lib/smalt/test/sequenceReverseComplement_test
drwxr-xr-x root/root 0 2014-10-25 09:44 ./usr/share/
drwxr-xr-x root/root 0 2014-10-25 09:44 ./usr/share/doc/
drwxr-xr-x root/root 0 2014-10-25 09:44 ./usr/share/doc/smalt/
-rw-r--r-- root/root 1182 2014-04-08 13:05 ./usr/share/doc/smalt/copyright
-rw-r--r-- root/root 438 2014-10-14 14:22 ./usr/share/doc/smalt/changelog.Debian.gz
drwxr-xr-x root/root 0 2014-10-25 09:44 ./usr/share/man/
drwxr-xr-x root/root 0 2014-10-25 09:44 ./usr/share/man/man1/
-rw-r--r-- root/root 884 2014-10-25 09:44 ./usr/share/man/man1/smalt.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 79384
Build-Time: 1968
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 227
Job: smalt_0.7.6-4
Machine Architecture: armhf
Package: smalt
Package-Time: 2273
Source-Version: 0.7.6-4
Space: 79384
Status: successful
Version: 0.7.6-4
────────────────────────────────────────────────────────────────────────────────
Finished at 20141025-0944
Build needed 00:37:53, 79384k disc space