proteinortho →
5.12+dfsg-1 →
armhf → 2016-03-24 00:43:25
sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on testwandboard
+==============================================================================+
| proteinortho 5.12+dfsg-1 (armhf) 24 Mar 2016 00:34 |
+==============================================================================+
Package: proteinortho
Version: 5.12+dfsg-1
Source Version: 5.12+dfsg-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/proteinortho-YxV6ha/proteinortho-5.12+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/proteinortho-YxV6ha' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-79dbece0-d3d1-445c-bf12-b10ea780afe7' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
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Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [8824 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [10.9 MB]
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| Fetch source files |
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Check APT
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Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'proteinortho' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/proteinortho.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/proteinortho.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 187 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main proteinortho 5.12+dfsg-1 (dsc) [2041 B]
Get:2 http://172.17.0.1/private stretch-staging/main proteinortho 5.12+dfsg-1 (tar) [180 kB]
Get:3 http://172.17.0.1/private stretch-staging/main proteinortho 5.12+dfsg-1 (diff) [4632 B]
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Check architectures
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Check dependencies
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-88iB8y/apt_archive/sbuild-build-depends-core-dummy.deb'.
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Get:3 file:/<<BUILDDIR>>/resolver-88iB8y/apt_archive ./ Release.gpg [299 B]
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| Install core build dependencies (apt-based resolver) |
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Installing build dependencies
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The following NEW packages will be installed:
sbuild-build-depends-core-dummy
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Filtered Build-Depends: debhelper (>= 9), ncbi-blast+
dpkg-deb: building package 'sbuild-build-depends-proteinortho-dummy' in '/<<BUILDDIR>>/resolver-UD9IOL/apt_archive/sbuild-build-depends-proteinortho-dummy.deb'.
OK
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+------------------------------------------------------------------------------+
| Install proteinortho build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autotools-dev bsdmainutils debhelper dh-strip-nondeterminism file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
libcroco3 libexpat1 libffi6 libfile-stripnondeterminism-perl libglib2.0-0
libicu55 libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib libsqlite3-0 libssl1.0.2 libtimedate-perl libunistring0
libxml2 man-db mime-support ncbi-blast+ ncbi-data po-debconf python
python-minimal python2.7 python2.7-minimal
Suggested packages:
wamerican | wordlist whois vacation dh-make gettext-doc autopoint
libasprintf-dev libgettextpo-dev groff less www-browser libmail-box-perl
python-doc python-tk python2.7-doc binfmt-support
Recommended packages:
curl | wget | lynx-cur 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 dh-strip-nondeterminism file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
libcroco3 libexpat1 libffi6 libfile-stripnondeterminism-perl libglib2.0-0
libicu55 libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib libsqlite3-0 libssl1.0.2 libtimedate-perl libunistring0
libxml2 man-db mime-support ncbi-blast+ ncbi-data po-debconf python
python-minimal python2.7 python2.7-minimal
sbuild-build-depends-proteinortho-dummy
0 upgraded, 37 newly installed, 0 to remove and 3 not upgraded.
Need to get 21.0 MB/32.6 MB of archives.
After this operation, 134 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-UD9IOL/apt_archive ./ sbuild-build-depends-proteinortho-dummy 0.invalid.0 [776 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-7 [1083 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.2-1 [88.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.8 [177 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-minimal armhf 2.7.11-4 [381 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf python2.7-minimal armhf 2.7.11-4 [1092 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf python-minimal armhf 2.7.11-1 [40.0 kB]
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Get:13 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-stdlib armhf 2.7.11-4 [1818 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf python2.7 armhf 2.7.11-4 [267 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libpython-stdlib armhf 2.7.11-1 [19.5 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf python armhf 2.7.11-1 [150 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.25-2 [250 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.25-2 [61.2 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.7-2 [111 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20150820.1 [71.7 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.7-2 [1400 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.56-2 [94.9 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.016-1 [6998 B]
Get:30 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160313 [808 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf ncbi-data all 6.1.20120620-10 [3291 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf ncbi-blast+ armhf 2.2.31-4 [7548 kB]
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Setting up dh-strip-nondeterminism (0.016-1) ...
Processing triggers for libc-bin (2.22-3) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26-5 dpkg-dev_1.18.4 g++-5_5.3.1-11 gcc-5_5.3.1-11 libc6-dev_2.22-3 libstdc++-5-dev_5.3.1-11 libstdc++6_5.3.1-11 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.114 apt_1.2.6 autotools-dev_20150820.1 base-files_9.5+rpi1 base-passwd_3.5.39 bash_4.3-14 binutils_2.26-5 bsdmainutils_9.0.8 bsdutils_1:2.27.1-6 build-essential_11.7 bzip2_1.0.6-8 console-setup_1.139 console-setup-linux_1.139 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:5.3.1-1+rpi1 cpp-5_5.3.1-11 dash_0.5.8-2.1 debconf_1.5.59 debfoster_2.7-2 debhelper_9.20160313 debianutils_4.7 dh-strip-nondeterminism_0.016-1 diffutils_1:3.3-3 dmsetup_2:1.02.116-1 dpkg_1.18.4 dpkg-dev_1.18.4 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.6.0+git+20160126-2 g++_4:5.3.1-1+rpi1 g++-5_5.3.1-11 gcc_4:5.3.1-1+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-12 gcc-5_5.3.1-11 gcc-5-base_5.3.1-11 gettext_0.19.7-2 gettext-base_0.19.7-2 gnupg_1.4.20-4 gpgv_1.4.20-4 grep_2.22-1 groff-base_1.22.3-7 gzip_1.6-4 hostname_3.17 ifupdown_0.8.10 init_1.29 init-system-helpers_1.29 initscripts_2.88dsf-59.3 insserv_1.14.0-5.3 intltool-debian_0.35.0+20060710.4 iproute2_4.3.0-1 isc-dhcp-client_4.3.3-8 isc-dhcp-common_4.3.3-8 kbd_2.0.3-2 keyboard-configuration_1.139 klibc-utils_2.0.4-8+rpi1 kmod_22-1 libacl1_2.2.52-3 libapparmor1_2.10-3 libapt-pkg5.0_1.2.6 libarchive-zip-perl_1.56-2 libasan2_5.3.1-11 libatm1_1:2.5.1-1.5 libatomic1_5.3.1-11 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1 libaudit1_1:2.4.5-1 libblkid1_2.27.1-6 libbsd0_0.8.2-1 libbz2-1.0_1.0.6-8 libc-bin_2.22-3 libc-dev-bin_2.22-3 libc6_2.22-3 libc6-dev_2.22-3 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-11 libcomerr2_1.42.13-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libdb5.3_5.3.28-11 libdbus-1-3_1.10.8-1 libdebconfclient0_0.207 libdevmapper1.02.1_2:1.02.116-1 libdns-export100_1:9.9.5.dfsg-12.1 libdpkg-perl_1.18.4 libdrm2_2.4.67-1 libexpat1_2.1.0-7 libfakeroot_1.20.2-1 libfdisk1_2.27.1-6 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.016-1 libgc1c2_1:7.4.2-7.3 libgcc-5-dev_5.3.1-11 libgcc1_1:5.3.1-11 libgcrypt20_1.6.5-2 libgdbm3_1.8.3-13.1 libglib2.0-0_2.46.2-3 libgmp10_2:6.1.0+dfsg-2 libgomp1_5.3.1-11 libgpg-error0_1.21-2 libicu55_55.1-7 libisc-export95_1:9.9.5.dfsg-12.1 libisl15_0.16.1-1 libklibc_2.0.4-8+rpi1 libkmod2_22-1 liblocale-gettext-perl_1.07-1+b1 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.27.1-6 libmpc3_1.0.3-1 libmpfr4_3.1.4-1 libncurses5_6.0+20160213-1 libncursesw5_6.0+20160213-1 libpam-modules_1.1.8-3.2 libpam-modules-bin_1.1.8-3.2 libpam-runtime_1.1.8-3.2 libpam0g_1.1.8-3.2 libpcre3_2:8.38-3 libperl5.22_5.22.1-9 libpipeline1_1.4.1-2 libplymouth4_0.9.2-3 libpng12-0_1.2.54-4 libprocps5_2:3.3.11-3 libpython-stdlib_2.7.11-1 libpython2.7-minimal_2.7.11-4 libpython2.7-stdlib_2.7.11-4 libreadline6_6.3-8+b3 libseccomp2_2.2.3-3 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libsmartcols1_2.27.1-6 libsqlite3-0_3.11.1-1 libss2_1.42.13-1 libssl1.0.2_1.0.2g-1 libstdc++-5-dev_5.3.1-11 libstdc++6_5.3.1-11 libsystemd0_229-2 libtext-charwidth-perl_0.04-7+b6 libtext-iconv-perl_1.7-5+b7 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160213-1 libubsan0_5.3.1-11 libudev1_229-2 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-28 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-6 libxml2_2.9.3+dfsg1-1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160110+rpi1 make_4.1-6 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.04-2 mawk_1.3.3-17 mime-support_3.59 mount_2.27.1-6 multiarch-support_2.22-3 ncbi-blast+_2.2.31-4 ncbi-data_6.1.20120620-10 ncurses-base_6.0+20160213-1 ncurses-bin_6.0+20160213-1 netbase_5.3 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.1-9 perl-base_5.22.1-9 perl-modules-5.22_5.22.1-9 po-debconf_1.0.19 procps_2:3.3.11-3 psmisc_22.21-2.1 python_2.7.11-1 python-minimal_2.7.11-1 python2.7_2.7.11-4 python2.7-minimal_2.7.11-4 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-proteinortho-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_229-2 systemd-sysv_229-2 sysv-rc_2.88dsf-59.3 sysvinit-utils_2.88dsf-59.3 tar_1.28-2.1 tzdata_2016a-1 udev_229-2 util-linux_2.27.1-6 xkb-data_2.17-1 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Thu Mar 17 19:55:09 2016 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./proteinortho_5.12+dfsg-1.dsc
dpkg-source: info: extracting proteinortho in proteinortho-5.12+dfsg
dpkg-source: info: unpacking proteinortho_5.12+dfsg.orig.tar.xz
dpkg-source: info: unpacking proteinortho_5.12+dfsg-1.debian.tar.xz
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying fix_syntax.patch
dpkg-source: info: applying fix_makefile.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-79dbece0-d3d1-445c-bf12-b10ea780afe7
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: source package proteinortho
dpkg-buildpackage: source version 5.12+dfsg-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build proteinortho-5.12+dfsg
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
dh_clean
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_update_autotools_config -a
dh_auto_configure -a
dh_auto_build -a
make -j1
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-5.12+dfsg'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -Wno-unused-result -fPIE -pie -Wl,-z,relro -Wl,-z,now -o proteinortho5_clustering proteinortho5_clustering.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -Wno-unused-result -fPIE -pie -Wl,-z,relro -Wl,-z,now -o proteinortho5_tree po_tree.c
po_tree.c: In function 'void builder(BOOL**, Uint, Uint, char***)':
po_tree.c:110:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i<viecher; i++) {
^
po_tree.c:127:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i<viecher; i++) {
^
po_tree.c: In function 'void merge(Uint*, Uint, Uint, BOOL*, BOOL**, int**, char***)':
po_tree.c:153:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i < ccs; i++) {
^
po_tree.c:168:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i < viecher; i++) {
^
make[1]: Leaving directory '/<<BUILDDIR>>/proteinortho-5.12+dfsg'
dh_auto_test -a
make -j1 test
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-5.12+dfsg'
./proteinortho5.pl -project=test -synteny -singles test/*.faa
Proteinortho with PoFF version 5.12 - An orthology detection tool
******************************************************************
Detected 4 available CPU threads, Detected NCBI BLAST version 2.2.31+
Checking input files
test/C.faa 308 genes
test/E.faa 310 genes
test/L.faa 41 genes
test/M.faa 40 genes
**Step 1**
Generating indices
Building database for 'test/E.faa' (310 sequences)
Building database for 'test/C.faa' (308 sequences)
Building database for 'test/L.faa' (41 sequences)
Building database for 'test/M.faa' (40 sequences)
**Step 2**
Running blast analysis: 0% (0/6)
Running blast analysis: 16.66% (1/6)
Running blast analysis: 33.33% (2/6)
Running blast analysis: 100% (6/6)
Running blast analysis: 83.33% (5/6)
Running blast analysis: 50% (3/6)
Running blast analysis: 66.66% (4/6)
Running blast analysis: 100% (6/6)
-> Output written to test.blast-graph
**Step 3**
Clustering by similarity (Proteinortho mode)
Reading test.blast-graph
4 species
150 paired proteins
218 bidirectional edges
Clustering: 1.33%
Clustering: 2.67%
Clustering: 4.00%
Clustering: 5.33%
Clustering: 6.67%
Clustering: 8.00%
Clustering: 9.33%
Clustering: 10.67%
Clustering: 14.00%
Clustering: 15.33%
Clustering: 16.67%
Clustering: 18.67%
Clustering: 20.67%
Clustering: 22.00%
Clustering: 23.33%
Clustering: 26.00%
Clustering: 27.33%
Clustering: 28.00%
Clustering: 28.67%
Clustering: 30.00%
Clustering: 32.00%
Clustering: 32.67%
Clustering: 47.33%
Clustering: 51.33%
Clustering: 52.00%
Clustering: 53.33%
Clustering: 54.67%
Clustering: 56.00%
Clustering: 57.33%
Clustering: 58.67%
Clustering: 64.00%
Clustering: 65.33%
Clustering: 68.00%
Clustering: 100.00%
Done
Adding singles...
-> Output written to test.proteinortho
Writing graph...
Cleaning edge list...
Removed 33 / 218 edges
Done.
-> Output written to test.proteinortho-graph
Clustering by gene-order (POFF mode)
Reading test.ffadj-graph
4 species
130 paired proteins
155 bidirectional edges
Clustering: 1.54%
Clustering: 3.08%
Clustering: 4.62%
Clustering: 6.15%
Clustering: 7.69%
Clustering: 9.23%
Clustering: 10.77%
Clustering: 12.31%
Clustering: 13.85%
Clustering: 15.38%
Clustering: 16.92%
Clustering: 18.46%
Clustering: 20.00%
Clustering: 21.54%
Clustering: 23.08%
Clustering: 24.62%
Clustering: 26.15%
Clustering: 27.69%
Clustering: 28.46%
Clustering: 29.23%
Clustering: 47.69%
Clustering: 49.23%
Clustering: 50.77%
Clustering: 52.31%
Clustering: 53.85%
Clustering: 55.38%
Clustering: 56.92%
Clustering: 58.46%
Clustering: 60.00%
Clustering: 63.08%
Clustering: 64.62%
Clustering: 66.15%
Clustering: 67.69%
Clustering: 69.23%
Clustering: 70.77%
Clustering: 72.31%
Clustering: 84.62%
Clustering: 87.69%
Clustering: 100.00%
Done
Adding singles...
-> Output written to test.poff
Writing graph...
Cleaning edge list...
Removed 5 / 155 edges
Done.
-> Output written to test.poff-graph
All finished.
Test okay
make[1]: Leaving directory '/<<BUILDDIR>>/proteinortho-5.12+dfsg'
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_installdirs -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-5.12+dfsg'
dh_auto_install --buildsystem=makefile -- install INSTALLDIR=/<<BUILDDIR>>/proteinortho-5.12+dfsg/debian/proteinortho/usr/lib/proteinortho
make -j1 install DESTDIR=/<<BUILDDIR>>/proteinortho-5.12\+dfsg/debian/proteinortho AM_UPDATE_INFO_DIR=no install INSTALLDIR=/<<BUILDDIR>>/proteinortho-5.12\+dfsg/debian/proteinortho/usr/lib/proteinortho
make[2]: Entering directory '/<<BUILDDIR>>/proteinortho-5.12+dfsg'
install -v proteinortho5.pl proteinortho5_clustering proteinortho5_singletons.pl proteinortho5_clean_edges2.pl ffadj_mcs.py po2tree.pl /<<BUILDDIR>>/proteinortho-5.12+dfsg/debian/proteinortho/usr/lib/proteinortho
'proteinortho5.pl' -> '/<<BUILDDIR>>/proteinortho-5.12+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho5.pl'
'proteinortho5_clustering' -> '/<<BUILDDIR>>/proteinortho-5.12+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho5_clustering'
'proteinortho5_singletons.pl' -> '/<<BUILDDIR>>/proteinortho-5.12+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho5_singletons.pl'
'proteinortho5_clean_edges2.pl' -> '/<<BUILDDIR>>/proteinortho-5.12+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho5_clean_edges2.pl'
'ffadj_mcs.py' -> '/<<BUILDDIR>>/proteinortho-5.12+dfsg/debian/proteinortho/usr/lib/proteinortho/ffadj_mcs.py'
'po2tree.pl' -> '/<<BUILDDIR>>/proteinortho-5.12+dfsg/debian/proteinortho/usr/lib/proteinortho/po2tree.pl'
make[2]: 'install' is up to date.
make[2]: Leaving directory '/<<BUILDDIR>>/proteinortho-5.12+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/proteinortho-5.12+dfsg'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
dh_installman -a
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
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package proteinortho: unused substitution variable ${perl:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package proteinortho: unused substitution variable ${perl:Depends}
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'proteinortho-dbgsym' in '../proteinortho-dbgsym_5.12+dfsg-1_armhf.deb'.
dpkg-deb: building package 'proteinortho' in '../proteinortho_5.12+dfsg-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../proteinortho_5.12+dfsg-1_armhf.changes
dpkg-genchanges: warning: package proteinortho-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build proteinortho-5.12+dfsg
dpkg-buildpackage: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160324-0043
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
proteinortho_5.12+dfsg-1_armhf.changes:
---------------------------------------
Format: 1.8
Date: Thu, 17 Mar 2016 20:40:53 +0100
Source: proteinortho
Binary: proteinortho
Architecture: armhf
Version: 5.12+dfsg-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
proteinortho - Detection of (Co-)orthologs in large-scale protein analysis
Changes:
proteinortho (5.12+dfsg-1) unstable; urgency=medium
.
* new upstream version
* make better use of uscan options
* cme fix dpkg-control
* Fix C-Syntax
* Apply fix from upstream to enable building the package
* Better hardening
Checksums-Sha1:
21523ad1c068b47e1a309441678b9466e9fbcf3e 5266 proteinortho-dbgsym_5.12+dfsg-1_armhf.deb
0294e0fdebb70ab65ac360f401e0423b59926270 241490 proteinortho_5.12+dfsg-1_armhf.deb
Checksums-Sha256:
acccacc310875464c0815728ab434b2d859aae5abcc9f76530eb0db4079274ec 5266 proteinortho-dbgsym_5.12+dfsg-1_armhf.deb
72e9376899501e0d9c301db476441226b8e13d35f591480478c0bb68ded52772 241490 proteinortho_5.12+dfsg-1_armhf.deb
Files:
0fff45a244adb79c762dc0fe30eca259 5266 debug extra proteinortho-dbgsym_5.12+dfsg-1_armhf.deb
a5a31153ba268273c7f1e1836165e766 241490 science optional proteinortho_5.12+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
proteinortho-dbgsym_5.12+dfsg-1_armhf.deb
-----------------------------------------
new debian package, version 2.0.
size 5266 bytes: control archive=510 bytes.
461 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: proteinortho-dbgsym
Source: proteinortho
Version: 5.12+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 26
Depends: proteinortho (= 5.12+dfsg-1)
Section: debug
Priority: extra
Homepage: https://www.bioinf.uni-leipzig.de/Software/proteinortho/
Description: Debug symbols for proteinortho
Auto-Built-Package: debug-symbols
Build-Ids: e8020fd989054ec1b50bf7b0ebc13cc51aa19552
drwxr-xr-x root/root 0 2016-03-24 00:43 ./
drwxr-xr-x root/root 0 2016-03-24 00:43 ./usr/
drwxr-xr-x root/root 0 2016-03-24 00:43 ./usr/lib/
drwxr-xr-x root/root 0 2016-03-24 00:43 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-03-24 00:43 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-03-24 00:43 ./usr/lib/debug/.build-id/e8/
-rw-r--r-- root/root 16000 2016-03-24 00:43 ./usr/lib/debug/.build-id/e8/020fd989054ec1b50bf7b0ebc13cc51aa19552.debug
drwxr-xr-x root/root 0 2016-03-24 00:43 ./usr/share/
drwxr-xr-x root/root 0 2016-03-24 00:43 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-03-24 00:43 ./usr/share/doc/proteinortho-dbgsym -> proteinortho
proteinortho_5.12+dfsg-1_armhf.deb
----------------------------------
new debian package, version 2.0.
size 241490 bytes: control archive=1453 bytes.
912 bytes, 17 lines control
1753 bytes, 23 lines md5sums
Package: proteinortho
Version: 5.12+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 355
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2), ncbi-blast+, python
Section: science
Priority: optional
Homepage: https://www.bioinf.uni-leipzig.de/Software/proteinortho/
Description: Detection of (Co-)orthologs in large-scale protein analysis
Proteinortho is a stand-alone tool that is geared towards large datasets
and makes use of distributed computing techniques when run on multi-core
hardware. It implements an extended version of the reciprocal best
alignment heuristic. Proteinortho was applied to compute orthologous
proteins in the complete set of all 717 eubacterial genomes available at
NCBI at the beginning of 2009. Authors succeeded identifying thirty
proteins present in 99% of all bacterial proteomes.
drwxr-xr-x root/root 0 2016-03-24 00:43 ./
drwxr-xr-x root/root 0 2016-03-24 00:42 ./usr/
drwxr-xr-x root/root 0 2016-03-17 19:53 ./usr/bin/
-rwxr-xr-x root/root 52 2016-03-17 19:53 ./usr/bin/proteinortho5
drwxr-xr-x root/root 0 2016-03-24 00:42 ./usr/lib/
drwxr-xr-x root/root 0 2016-03-24 00:43 ./usr/lib/proteinortho/
-rwxr-xr-x root/root 35339 2016-03-24 00:42 ./usr/lib/proteinortho/ffadj_mcs.py
-rwxr-xr-x root/root 4877 2016-03-24 00:42 ./usr/lib/proteinortho/po2tree.pl
-rwxr-xr-x root/root 36447 2016-03-24 00:42 ./usr/lib/proteinortho/proteinortho5.pl
-rwxr-xr-x root/root 1077 2016-03-24 00:42 ./usr/lib/proteinortho/proteinortho5_clean_edges2.pl
-rwxr-xr-x root/root 50744 2016-03-24 00:43 ./usr/lib/proteinortho/proteinortho5_clustering
-rwxr-xr-x root/root 1616 2016-03-24 00:42 ./usr/lib/proteinortho/proteinortho5_singletons.pl
drwxr-xr-x root/root 0 2016-03-24 00:42 ./usr/share/
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| Post Build |
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 2248
Build-Time: 263
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 222
Job: proteinortho_5.12+dfsg-1
Machine Architecture: armhf
Package: proteinortho
Package-Time: 534
Source-Version: 5.12+dfsg-1
Space: 2248
Status: successful
Version: 5.12+dfsg-1
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Finished at 20160324-0043
Build needed 00:08:54, 2248k disc space