augustus →
3.2.2+dfsg-1 →
armhf → 2016-04-25 07:42:49
sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on bm-wb-04
+==============================================================================+
| augustus 3.2.2+dfsg-1 (armhf) 25 Apr 2016 07:14 |
+==============================================================================+
Package: augustus
Version: 3.2.2+dfsg-1
Source Version: 3.2.2+dfsg-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/augustus-QwzX_w/augustus-3.2.2+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/augustus-QwzX_w' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-54f17822-5085-46a5-a2da-cb3eea74e05f' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [8925 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.0 MB]
Fetched 19.9 MB in 21s (909 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'augustus' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/augustus.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/augustus.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 44.9 MB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main augustus 3.2.2+dfsg-1 (dsc) [2264 B]
Get:2 http://172.17.0.1/private stretch-staging/main augustus 3.2.2+dfsg-1 (tar) [44.9 MB]
Get:3 http://172.17.0.1/private stretch-staging/main augustus 3.2.2+dfsg-1 (diff) [17.3 kB]
Fetched 44.9 MB in 5s (7703 kB/s)
Download complete and in download only mode
Check architectures
-------------------
Check dependencies
------------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-KwyG6e/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-KwyG6e/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-KwyG6e/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-KwyG6e/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-KwyG6e/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-KwyG6e/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-KwyG6e/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-KwyG6e/apt_archive ./ Sources [214 B]
Get:5 file:/<<BUILDDIR>>/resolver-KwyG6e/apt_archive ./ Packages [526 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-KwyG6e/apt_archive/./Release.gpg: Signature by key 3493EC2B8E6DC280C121C60435506D9A48F77B2E uses weak digest algorithm (SHA1)
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
0 upgraded, 1 newly installed, 0 to remove and 25 not upgraded.
Need to get 0 B/762 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-KwyG6e/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [762 B]
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sbuild-build-depends-core-dummy.
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(Reading database ... 13579 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) ...
W: No sandbox user '_apt' on the system, can not drop privileges
Merged Build-Depends: debhelper (>= 9), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbam-dev, libhts-dev, libncurses5-dev, asciidoctor
Filtered Build-Depends: debhelper (>= 9), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbam-dev, libhts-dev, libncurses5-dev, asciidoctor
dpkg-deb: building package 'sbuild-build-depends-augustus-dummy' in '/<<BUILDDIR>>/resolver-bteJND/apt_archive/sbuild-build-depends-augustus-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-bteJND/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-bteJND/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-bteJND/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-bteJND/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-bteJND/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-bteJND/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-bteJND/apt_archive ./ Sources [277 B]
Get:5 file:/<<BUILDDIR>>/resolver-bteJND/apt_archive ./ Packages [595 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-bteJND/apt_archive/./Release.gpg: Signature by key 3493EC2B8E6DC280C121C60435506D9A48F77B2E uses weak digest algorithm (SHA1)
Reading package lists...
+------------------------------------------------------------------------------+
| Install augustus build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
asciidoctor autoconf automake autopoint autotools-dev bsdmainutils
ca-certificates debhelper dh-autoreconf dh-strip-nondeterminism file gettext
gettext-base gfortran gfortran-5 groff-base icu-devtools intltool-debian
libamd2.4.1 libarchive-zip-perl libbam-dev libbamtools-dev libbamtools2.4.0
libblas-common libblas-dev libblas3 libboost-iostreams-dev
libboost-iostreams1.58-dev libboost-iostreams1.58.0 libboost-regex1.58-dev
libboost-regex1.58.0 libboost1.58-dev libbsd0 libbtf1.2.1 libcamd2.4.1
libccolamd2.9.1 libcholmod3.0.6 libcolamd2.9.1 libcroco3 libcsparse3.1.4
libcxsparse3.1.4 libffi6 libfile-stripnondeterminism-perl libgfortran-5-dev
libgfortran3 libglib2.0-0 libgsl-dev libgsl2 libhts-dev libhts1 libicu-dev
libicu55 libklu1.3.3 liblapack-dev liblapack3 libldl2.2.1 liblpsolve55-dev
libmagic1 libncurses5-dev libpipeline1 libruby2.3 libsigsegv2 libspqr2.0.2
libsqlite3-0 libsqlite3-dev libssl1.0.2 libsuitesparse-dev
libsuitesparseconfig4.4.6 libtinfo-dev libtool libumfpack5.7.1 libunistring0
libxml2 libyaml-0-2 m4 man-db openssl po-debconf rake ruby ruby-did-you-mean
ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby2.3
rubygems-integration zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-doc
gfortran-5-doc libgfortran3-dbg groff libbamtools-doc liblapack-doc-man
liblapack-doc libboost1.58-doc libboost-atomic1.58-dev
libboost-chrono1.58-dev libboost-context1.58-dev libboost-coroutine1.58-dev
libboost-date-time1.58-dev libboost-exception1.58-dev
libboost-filesystem1.58-dev libboost-graph1.58-dev
libboost-graph-parallel1.58-dev libboost-locale1.58-dev libboost-log1.58-dev
libboost-math1.58-dev libboost-mpi1.58-dev libboost-mpi-python1.58-dev
libboost-program-options1.58-dev libboost-python1.58-dev
libboost-random1.58-dev libboost-serialization1.58-dev
libboost-signals1.58-dev libboost-system1.58-dev libboost-test1.58-dev
libboost-thread1.58-dev libboost-timer1.58-dev libboost-wave1.58-dev
libboost1.58-tools-dev libmpfrc++-dev libntl-dev gsl-ref-psdoc | gsl-doc-pdf
| gsl-doc-info | gsl-ref-html icu-doc ncurses-doc sqlite3-doc libtool-doc
gcj-jdk less www-browser libmail-box-perl ri ruby-dev bundler
Recommended packages:
curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
libltdl-dev xml-core libmail-sendmail-perl zip fonts-lato libjs-jquery
The following NEW packages will be installed:
asciidoctor autoconf automake autopoint autotools-dev bsdmainutils
ca-certificates debhelper dh-autoreconf dh-strip-nondeterminism file gettext
gettext-base gfortran gfortran-5 groff-base icu-devtools intltool-debian
libamd2.4.1 libarchive-zip-perl libbam-dev libbamtools-dev libbamtools2.4.0
libblas-common libblas-dev libblas3 libboost-iostreams-dev
libboost-iostreams1.58-dev libboost-iostreams1.58.0 libboost-regex1.58-dev
libboost-regex1.58.0 libboost1.58-dev libbsd0 libbtf1.2.1 libcamd2.4.1
libccolamd2.9.1 libcholmod3.0.6 libcolamd2.9.1 libcroco3 libcsparse3.1.4
libcxsparse3.1.4 libffi6 libfile-stripnondeterminism-perl libgfortran-5-dev
libgfortran3 libglib2.0-0 libgsl-dev libgsl2 libhts-dev libhts1 libicu-dev
libicu55 libklu1.3.3 liblapack-dev liblapack3 libldl2.2.1 liblpsolve55-dev
libmagic1 libncurses5-dev libpipeline1 libruby2.3 libsigsegv2 libspqr2.0.2
libsqlite3-0 libsqlite3-dev libssl1.0.2 libsuitesparse-dev
libsuitesparseconfig4.4.6 libtinfo-dev libtool libumfpack5.7.1 libunistring0
libxml2 libyaml-0-2 m4 man-db openssl po-debconf rake ruby ruby-did-you-mean
ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby2.3
rubygems-integration sbuild-build-depends-augustus-dummy zlib1g-dev
0 upgraded, 89 newly installed, 0 to remove and 25 not upgraded.
Need to get 71.6 MB/71.6 MB of archives.
After this operation, 367 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-bteJND/apt_archive ./ sbuild-build-depends-augustus-dummy 0.invalid.0 [836 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 9.0.10 [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 libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libyaml-0-2 armhf 0.1.6-3 [41.5 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf libboost-iostreams1.58.0 armhf 1.58.0+dfsg-5+b1 [48.7 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf libssl1.0.2 armhf 1.0.2g-1 [886 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.25-2 [250 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.25-2 [61.2 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.7-2 [111 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libsqlite3-0 armhf 3.12.1-1 [463 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libicu55 armhf 55.1-7 [7380 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.3+dfsg1-1 [800 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf openssl armhf 1.0.2g-1 [666 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf ca-certificates all 20160104 [200 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf rubygems-integration all 1.10 [4882 B]
Get:22 http://172.17.0.1/private stretch-staging/main armhf rake all 10.5.0-2 [49.4 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf ruby-did-you-mean all 1.0.0-2 [11.2 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf ruby-minitest all 5.8.4-2 [50.3 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf ruby-net-telnet all 0.1.1-2 [12.5 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf ruby-power-assert all 0.2.7-1 [7578 B]
Get:27 http://172.17.0.1/private stretch-staging/main armhf ruby-test-unit all 3.1.7-2 [69.6 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libffi6 armhf 3.2.1-4 [18.5 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf libruby2.3 armhf 2.3.0-5 [2834 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf ruby2.3 armhf 2.3.0-5 [167 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf ruby armhf 1:2.3.0+4 [10.6 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf asciidoctor all 1.5.4-1 [163 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20150820.1 [71.7 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.7-2 [424 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.48.0-1 [2540 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.7-2 [1400 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.57-1 [95.1 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.016-1 [6998 B]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-0.1 [200 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160403 [800 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 5.3.1-14 [153 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf libgfortran-5-dev armhf 5.3.1-14 [182 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf gfortran-5 armhf 5.3.1-14 [23.7 MB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf gfortran armhf 4:5.3.1-1+rpi1 [1362 B]
Get:52 http://172.17.0.1/private stretch-staging/main armhf icu-devtools armhf 55.1-7 [163 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libsuitesparseconfig4.4.6 armhf 1:4.4.6-1 [16.6 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libamd2.4.1 armhf 1:4.4.6-1 [25.8 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf libbam-dev armhf 0.1.19-2 [109 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf libblas-common armhf 3.6.0-2 [13.5 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf libblas3 armhf 3.6.0-2 [110 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libblas-dev armhf 3.6.0-2 [116 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf libboost1.58-dev armhf 1.58.0+dfsg-5+b1 [6232 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf libboost-regex1.58.0 armhf 1.58.0+dfsg-5+b1 [226 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libicu-dev armhf 55.1-7 [8339 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf libboost-regex1.58-dev armhf 1.58.0+dfsg-5+b1 [312 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf libboost-iostreams1.58-dev armhf 1.58.0+dfsg-5+b1 [58.4 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf libboost-iostreams-dev armhf 1.58.0.1+b1 [3388 B]
Get:65 http://172.17.0.1/private stretch-staging/main armhf libbtf1.2.1 armhf 1:4.4.6-1 [17.1 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf libcamd2.4.1 armhf 1:4.4.6-1 [23.5 kB]
Get:67 http://172.17.0.1/private stretch-staging/main armhf libccolamd2.9.1 armhf 1:4.4.6-1 [24.4 kB]
Get:68 http://172.17.0.1/private stretch-staging/main armhf libcolamd2.9.1 armhf 1:4.4.6-1 [21.5 kB]
Get:69 http://172.17.0.1/private stretch-staging/main armhf liblapack3 armhf 3.6.0-2 [1382 kB]
Get:70 http://172.17.0.1/private stretch-staging/main armhf libcholmod3.0.6 armhf 1:4.4.6-1 [192 kB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf libcsparse3.1.4 armhf 1:4.4.6-1 [31.2 kB]
Get:72 http://172.17.0.1/private stretch-staging/main armhf libcxsparse3.1.4 armhf 1:4.4.6-1 [43.7 kB]
Get:73 http://172.17.0.1/private stretch-staging/main armhf libgsl2 armhf 2.1+dfsg-2 [697 kB]
Get:74 http://172.17.0.1/private stretch-staging/main armhf libgsl-dev armhf 2.1+dfsg-2 [812 kB]
Get:75 http://172.17.0.1/private stretch-staging/main armhf libhts1 armhf 1.3-2+rpi1 [207 kB]
Get:76 http://172.17.0.1/private stretch-staging/main armhf libhts-dev armhf 1.3-2+rpi1 [260 kB]
Get:77 http://172.17.0.1/private stretch-staging/main armhf libklu1.3.3 armhf 1:4.4.6-1 [45.6 kB]
Get:78 http://172.17.0.1/private stretch-staging/main armhf liblapack-dev armhf 3.6.0-2 [1355 kB]
Get:79 http://172.17.0.1/private stretch-staging/main armhf libldl2.2.1 armhf 1:4.4.6-1 [16.9 kB]
Get:80 http://172.17.0.1/private stretch-staging/main armhf libumfpack5.7.1 armhf 1:4.4.6-1 [123 kB]
Get:81 http://172.17.0.1/private stretch-staging/main armhf libspqr2.0.2 armhf 1:4.4.6-1 [61.0 kB]
Get:82 http://172.17.0.1/private stretch-staging/main armhf libsuitesparse-dev armhf 1:4.4.6-1 [574 kB]
Get:83 http://172.17.0.1/private stretch-staging/main armhf liblpsolve55-dev armhf 5.5.0.13-7+b2 [352 kB]
Get:84 http://172.17.0.1/private stretch-staging/main armhf libtinfo-dev armhf 6.0+20160319-1 [65.7 kB]
Get:85 http://172.17.0.1/private stretch-staging/main armhf libncurses5-dev armhf 6.0+20160319-1 [153 kB]
Get:86 http://172.17.0.1/private stretch-staging/main armhf libsqlite3-dev armhf 3.12.1-1 [592 kB]
Get:87 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:88 http://172.17.0.1/private stretch-staging/main armhf libbamtools2.4.0 armhf 2.4.0+dfsg-6 [159 kB]
Get:89 http://172.17.0.1/private stretch-staging/main armhf libbamtools-dev armhf 2.4.0+dfsg-6 [212 kB]
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update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode
Setting up libldl2.2.1:armhf (1:4.4.6-1) ...
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Setting up libtinfo-dev:armhf (6.0+20160319-1) ...
Setting up libncurses5-dev:armhf (6.0+20160319-1) ...
Setting up libsqlite3-dev:armhf (3.12.1-1) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up libbamtools2.4.0 (2.4.0+dfsg-6) ...
Setting up libbamtools-dev (2.4.0+dfsg-6) ...
Setting up rake (10.5.0-2) ...
Setting up libruby2.3:armhf (2.3.0-5) ...
Setting up dh-autoreconf (12) ...
Setting up ruby2.3 (2.3.0-5) ...
Setting up ruby (1:2.3.0+4) ...
Setting up asciidoctor (1.5.4-1) ...
Setting up debhelper (9.20160403) ...
Setting up sbuild-build-depends-augustus-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.016-1) ...
Processing triggers for libc-bin (2.22-5) ...
Processing triggers for ca-certificates (20160104) ...
Updating certificates in /etc/ssl/certs...
173 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26-8 dpkg-dev_1.18.4 g++-5_5.3.1-14 gcc-5_5.3.1-14 libc6-dev_2.22-5 libstdc++-4.9-dev_4.9.3-12 libstdc++-5-dev_5.3.1-14 libstdc++6_5.3.1-14 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-3 adduser_3.114 apt_1.2.10 asciidoctor_1.5.4-1 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.7-2 autotools-dev_20150820.1 base-files_9.6+rpi1 base-passwd_3.5.39 bash_4.3-14 binutils_2.26-8 bsdmainutils_9.0.10 bsdutils_1:2.27.1-6 build-essential_11.7 bzip2_1.0.6-8 ca-certificates_20160104 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:5.3.1-1+rpi1 cpp-5_5.3.1-14 dash_0.5.8-2.2 debconf_1.5.59 debfoster_2.7-2 debhelper_9.20160403 debianutils_4.7 dh-autoreconf_12 dh-strip-nondeterminism_0.016-1 diffutils_1:3.3-3 dmsetup_2:1.02.120-1 dpkg_1.18.4 dpkg-dev_1.18.4 e2fslibs_1.43~WIP.2016.03.15-2 e2fsprogs_1.43~WIP.2016.03.15-2 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_5.3.1-14 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_5.3.1-14 gcc-5-base_5.3.1-14 gettext_0.19.7-2 gettext-base_0.19.7-2 gfortran_4:5.3.1-1+rpi1 gfortran-5_5.3.1-14 gnupg_1.4.20-5 gpgv_1.4.20-5 grep_2.22-1 groff-base_1.22.3-7 gzip_1.6-5 hostname_3.17 icu-devtools_55.1-7 init_1.29 init-system-helpers_1.29 initscripts_2.88dsf-59.3 insserv_1.14.0-5.3 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-8+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libamd2.4.1_1:4.4.6-1 libapparmor1_2.10-4 libapt-pkg4.12_1.0.9.10 libapt-pkg5.0_1.2.10 libarchive-zip-perl_1.57-1 libasan1_4.9.3-12 libasan2_5.3.1-14 libatomic1_5.3.1-14 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1 libaudit1_1:2.4.5-1 libbam-dev_0.1.19-2 libbamtools-dev_2.4.0+dfsg-6 libbamtools2.4.0_2.4.0+dfsg-6 libblas-common_3.6.0-2 libblas-dev_3.6.0-2 libblas3_3.6.0-2 libblkid1_2.27.1-6 libboost-iostreams-dev_1.58.0.1+b1 libboost-iostreams1.58-dev_1.58.0+dfsg-5+b1 libboost-iostreams1.58.0_1.58.0+dfsg-5+b1 libboost-regex1.58-dev_1.58.0+dfsg-5+b1 libboost-regex1.58.0_1.58.0+dfsg-5+b1 libboost1.58-dev_1.58.0+dfsg-5+b1 libbsd0_0.8.2-1 libbtf1.2.1_1:4.4.6-1 libbz2-1.0_1.0.6-8 libc-bin_2.22-5 libc-dev-bin_2.22-5 libc6_2.22-5 libc6-dev_2.22-5 libcamd2.4.1_1:4.4.6-1 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-14 libccolamd2.9.1_1:4.4.6-1 libcholmod3.0.6_1:4.4.6-1 libcolamd2.9.1_1:4.4.6-1 libcomerr2_1.43~WIP.2016.03.15-2 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libcsparse3.1.4_1:4.4.6-1 libcxsparse3.1.4_1:4.4.6-1 libdb5.3_5.3.28-11 libdbus-1-3_1.10.8-1 libdebconfclient0_0.208 libdevmapper1.02.1_2:1.02.120-1 libdpkg-perl_1.18.4 libdrm2_2.4.67-1 libfakeroot_1.20.2-1 libfdisk1_2.27.1-6 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.016-1 libgc1c2_1:7.4.2-7.4 libgcc-4.9-dev_4.9.3-12 libgcc-5-dev_5.3.1-14 libgcc1_1:5.3.1-14 libgcrypt20_1.6.5-2 libgdbm3_1.8.3-13.1 libgfortran-5-dev_5.3.1-14 libgfortran3_5.3.1-14 libglib2.0-0_2.48.0-1 libgmp10_2:6.1.0+dfsg-2 libgomp1_5.3.1-14 libgpg-error0_1.21-2 libgsl-dev_2.1+dfsg-2 libgsl2_2.1+dfsg-2 libhts-dev_1.3-2+rpi1 libhts1_1.3-2+rpi1 libicu-dev_55.1-7 libicu55_55.1-7 libisl15_0.16.1-1 libklibc_2.0.4-8+rpi1 libklu1.3.3_1:4.4.6-1 libkmod2_22-1.1 liblapack-dev_3.6.0-2 liblapack3_3.6.0-2 libldl2.2.1_1:4.4.6-1 liblpsolve55-dev_5.5.0.13-7+b2 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+20160319-1 libncurses5-dev_6.0+20160319-1 libncursesw5_6.0+20160319-1 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_2:8.38-3.1 libperl5.22_5.22.1-9 libpipeline1_1.4.1-2 libpng12-0_1.2.54-6 libprocps3_2:3.3.9-9 libprocps5_2:3.3.11-3 libreadline6_6.3-8+b3 libruby2.3_2.3.0-5 libseccomp2_2.3.0-1 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libsigsegv2_2.10-5 libslang2_2.3.0-2.3 libsmartcols1_2.27.1-6 libspqr2.0.2_1:4.4.6-1 libsqlite3-0_3.12.1-1 libsqlite3-dev_3.12.1-1 libss2_1.43~WIP.2016.03.15-2 libssl1.0.2_1.0.2g-1 libstdc++-4.9-dev_4.9.3-12 libstdc++-5-dev_5.3.1-14 libstdc++6_5.3.1-14 libsuitesparse-dev_1:4.4.6-1 libsuitesparseconfig4.4.6_1:4.4.6-1 libsystemd0_229-4 libtimedate-perl_2.3000-2 libtinfo-dev_6.0+20160319-1 libtinfo5_6.0+20160319-1 libtool_2.4.6-0.1 libubsan0_5.3.1-14 libudev1_229-4 libumfpack5.7.1_1:4.4.6-1 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-28 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-6 libxml2_2.9.3+dfsg1-1 libyaml-0-2_0.1.6-3 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160110+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.05-1 mawk_1.3.3-17 mount_2.27.1-6 multiarch-support_2.22-5 nano_2.5.3-2 ncurses-base_6.0+20160319-1 ncurses-bin_6.0+20160319-1 openssl_1.0.2g-1 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.1-9 perl-base_5.22.1-9 perl-modules-5.22_5.22.1-9 po-debconf_1.0.19 procps_2:3.3.11-3 rake_10.5.0-2 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 ruby_1:2.3.0+4 ruby-did-you-mean_1.0.0-2 ruby-minitest_5.8.4-2 ruby-net-telnet_0.1.1-2 ruby-power-assert_0.2.7-1 ruby-test-unit_3.1.7-2 ruby2.3_2.3.0-5 rubygems-integration_1.10 sbuild-build-depends-augustus-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_229-4 systemd-sysv_229-4 sysv-rc_2.88dsf-59.3 sysvinit-utils_2.88dsf-59.3 tar_1.28-2.1 tzdata_2016c-0+deb8u1 udev_229-4 util-linux_2.27.1-6 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sun Apr 3 06:03:27 2016 UTC using RSA key ID AFE826FB
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./augustus_3.2.2+dfsg-1.dsc
dpkg-source: info: extracting augustus in augustus-3.2.2+dfsg
dpkg-source: info: unpacking augustus_3.2.2+dfsg.orig.tar.xz
dpkg-source: info: unpacking augustus_3.2.2+dfsg-1.debian.tar.xz
dpkg-source: info: applying search_config_path
dpkg-source: info: applying set_installdir
dpkg-source: info: applying keep_cflags
dpkg-source: info: applying buildflags.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-54f17822-5085-46a5-a2da-cb3eea74e05f
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: source package augustus
dpkg-buildpackage: source version 3.2.2+dfsg-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build augustus-3.2.2+dfsg
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg'
/usr/bin/make -C auxprogs/bam2hints clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/bam2hints'
rm -f bam2hints.o bam2hints ../../bin/bam2hints
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/bam2hints'
/usr/bin/make -C auxprogs/homGeneMapping/src clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/homGeneMapping/src'
rm -f homGeneMapping gene.o genome.o
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/homGeneMapping/src'
/usr/bin/make -C auxprogs/joingenes clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/joingenes'
rm -rf *o joingenes; rm -rf ../../bin/joingenes
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/joingenes'
rm -rf bin
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg'
dh_clean -O--parallel
debian/rules build-arch
dh build-arch --parallel
dh_testdir -a -O--parallel
dh_update_autotools_config -a -O--parallel
dh_auto_configure -a -O--parallel
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg'
mkdir -p bin
/usr/bin/make -C auxprogs/bam2hints
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/bam2hints'
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -pie -Wl,-z,relro -Wl,-z,now -c bam2hints.cc -o bam2hints.o -I/usr/include/bamtools
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -fPIE -pie -Wl,-z,relro -Wl,-z,now -o bam2hints bam2hints.o -lbamtools -lz
cp bam2hints ../../bin
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/bam2hints'
/usr/bin/make -C auxprogs/homGeneMapping/src
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/homGeneMapping/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -o gene.o gene.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -o genome.o genome.cc -I../include
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -o homGeneMapping main.cc gene.o genome.o -I../include -fPIE -pie -Wl,-z,relro -Wl,-z,now
cp homGeneMapping ../../../bin/homGeneMapping
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/homGeneMapping/src'
/usr/bin/make -C auxprogs/checkTargetSortedness
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/checkTargetSortedness'
gcc -g -Wall -O2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -pie -Wl,-z,relro -Wl,-z,now -c checkTargetSortedness.c -o checkTargetSortedness.o -I/usr/include/samtools -I.
gcc -g -Wall -O2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -pie -Wl,-z,relro -Wl,-z,now checkTargetSortedness.o -o checkTargetSortedness -lbam -lcurses -lm -lz -lpthread
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/checkTargetSortedness'
/usr/bin/make -C auxprogs/joingenes
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/joingenes'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x joingenes.cpp
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x jg_transcript.cpp
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x jg_ios.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x joingenes.o jg_transcript.o jg_ios.o -o joingenes -fPIE -pie -Wl,-z,relro -Wl,-z,now
cp joingenes ../../bin/
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/joingenes'
dh_auto_build
make -j4
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg'
mkdir -p bin
cd src && make
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o genbank.o genbank.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o properties.o properties.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o pp_profile.o pp_profile.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o pp_hitseq.o pp_hitseq.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o pp_scoring.o pp_scoring.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o statemodel.o statemodel.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o namgene.o namgene.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o types.o types.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o gene.o gene.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o evaluation.o evaluation.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o motif.o motif.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o geneticcode.o geneticcode.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o hints.o hints.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o extrinsicinfo.o extrinsicinfo.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o projectio.o projectio.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o intronmodel.o intronmodel.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o exonmodel.o exonmodel.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o igenicmodel.o igenicmodel.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o utrmodel.o utrmodel.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o merkmal.o merkmal.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o vitmatrix.o vitmatrix.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o lldouble.o lldouble.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o mea.o mea.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o graph.o graph.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o meaPath.o meaPath.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o exoncand.o exoncand.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o randseqaccess.o randseqaccess.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o fasta.o fasta.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o ncmodel.o ncmodel.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o commontrain.o commontrain.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o igenictrain.o igenictrain.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o introntrain.o introntrain.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o exontrain.o exontrain.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o utrtrain.o utrtrain.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o dummy.o dummy.cc -I../include
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -fPIE -pie -Wl,-z,relro -Wl,-z,now -o prepareAlign pp_prepare_align.cc
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o pp_fastBlockSearcher.o pp_fastBlockSearcher.cc -I../include
cp prepareAlign ../bin/
echo "-Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT" > cxxflags
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -fPIE -pie -Wl,-z,relro -Wl,-z,now -o augustus augustus.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o dummy.o -I../include -lboost_iostreams
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -fPIE -pie -Wl,-z,relro -Wl,-z,now -o fastBlockSearch fastBlockSearch.cc pp_fastBlockSearcher.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -I../include -lboost_iostreams
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -fPIE -pie -Wl,-z,relro -Wl,-z,now -o etraining etraining.cc commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o -I../include -lboost_iostreams
cp fastBlockSearch ../bin/
cp augustus ../bin/
cp etraining ../bin/
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/src'
cd auxprogs && make
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs'
cd bam2hints; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/bam2hints'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: 'bam2hints' is up to date.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/bam2hints'
cd compileSpliceCands; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/compileSpliceCands'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
gcc -Wall -pedantic -ansi -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c compileSpliceCands.c
compileSpliceCands.c: In function 'getChromosome':
compileSpliceCands.c:226:2: warning: this decimal constant is unsigned only in ISO C90
s = malloc(3500000000);
^
compileSpliceCands.c: In function 'parseList':
compileSpliceCands.c:350:32: warning: 'left' may be used uninitialized in this function [-Wmaybe-uninitialized]
findPossibleSpliceSites(left->name,actualChromosome,left->startPos,left->endPos,right->startPos,right->endPos,left->strand,right->strand);
^
compileSpliceCands.c: In function 'main':
compileSpliceCands.c:563:3: warning: 'chromosomeLength' may be used uninitialized in this function [-Wmaybe-uninitialized]
parseList(&L,actualChromosome,chromosomeLength,oldname,maxSpliceSiteDiff,threshold,maxIntronLength);
^
cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o list.o list.c
gcc -o compileSpliceCands compileSpliceCands.o list.o -fPIE -pie -Wl,-z,relro -Wl,-z,now;
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/compileSpliceCands'
cd filterBam; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/filterBam'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
(cd src;make)
make[5]: Entering directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/filterBam/src'
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -pie -Wl,-z,relro -Wl,-z,now -std=c++0x -Wdate-time -D_FORTIFY_SOURCE=2 -c filterBam.cc -o filterBam.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -pie -Wl,-z,relro -Wl,-z,now -std=c++0x -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/MatePairs.cc -o MatePairs.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -pie -Wl,-z,relro -Wl,-z,now -std=c++0x -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/getReferenceName.cc -o getReferenceName.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -pie -Wl,-z,relro -Wl,-z,now -std=c++0x -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/initOptions.cc -o initOptions.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -pie -Wl,-z,relro -Wl,-z,now -std=c++0x -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/SingleAlignment.cc -o SingleAlignment.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -pie -Wl,-z,relro -Wl,-z,now -std=c++0x -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/printElapsedTime.cc -o printElapsedTime.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -pie -Wl,-z,relro -Wl,-z,now -std=c++0x -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/sumMandIOperations.cc -o sumMandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -pie -Wl,-z,relro -Wl,-z,now -std=c++0x -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/sumDandIOperations.cc -o sumDandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -pie -Wl,-z,relro -Wl,-z,now -std=c++0x -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/PairednessCoverage.cc -o PairednessCoverage.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -pie -Wl,-z,relro -Wl,-z,now -std=c++0x -fPIE -pie -Wl,-z,relro -Wl,-z,now filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -lbamtools -lz
filterBam compiled with BAMTOOLS=/usr/include/bamtools
cp filterBam ../../../bin/filterBam
make[5]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/filterBam/src'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/filterBam'
cd homGeneMapping; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/homGeneMapping'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
(cd src; make)
make[5]: Entering directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/homGeneMapping/src'
make[5]: Nothing to be done for 'all'.
make[5]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/homGeneMapping/src'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/homGeneMapping'
cd joingenes; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/joingenes'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs/joingenes'
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg/auxprogs'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg'
asciidoctor -a docdate='' -b manpage debian/mansrc/*adoc
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg'
dh_auto_test -a -O--parallel
fakeroot debian/rules binary-arch
dh binary-arch --parallel
dh_testroot -a -O--parallel
dh_prep -a -O--parallel
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg'
mkdir -p debian/augustus/usr/bin
install bin/* debian/augustus/usr/bin
install auxprogs/checkTargetSortedness/checkTargetSortedness \
debian/augustus/usr/bin
install auxprogs/homGeneMapping/src/homGeneMapping \
debian/augustus/usr/bin
install auxprogs/joingenes/joingenes \
debian/augustus/usr/bin
mkdir -p debian/augustus/usr/share/augustus
cp -r scripts debian/augustus/usr/share/augustus
chmod -R -x debian/augustus/usr/share/augustus/scripts/*
chmod +x debian/augustus/usr/share/augustus/scripts/checkUTR \
debian/augustus/usr/share/augustus/scripts/*.pl
mkdir -p debian/augustus-doc/usr/share/doc/augustus
cp README* debian/augustus-doc/usr/share/doc/augustus
cp docs/*.txt debian/augustus-doc/usr/share/doc/augustus
cp -r docs/tutorial \
debian/augustus-doc/usr/share/doc/augustus
mkdir -p debian/augustus-data/usr/share/augustus
cp -r config debian/augustus-data/usr/share/augustus
find debian/augustus-data/usr/share/augustus \
-type f -exec chmod -x {} \;
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg'
dh_installdocs -a -O--parallel
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg'
dh_installchangelogs -k HISTORY.TXT
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg'
dh_installman -a -O--parallel
dh_perl -a -O--parallel
dh_link -a -O--parallel
dh_strip_nondeterminism -a -O--parallel
debian/rules override_dh_compress
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg'
dh_compress -Xtutorial
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.2+dfsg'
dh_fixperms -a -O--parallel
dh_strip -a -O--parallel
dh_makeshlibs -a -O--parallel
dh_shlibdeps -a -O--parallel
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/augustus/usr/bin/checkTargetSortedness was not linked against libncurses.so.5 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/augustus/usr/bin/checkTargetSortedness was not linked against libtinfo.so.5 (it uses none of the library's symbols)
dh_installdeb -a -O--parallel
dh_gencontrol -a -O--parallel
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package augustus: unused substitution variable ${perl:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package augustus: unused substitution variable ${perl:Depends}
dh_md5sums -a -O--parallel
dh_builddeb -a -O--parallel
dpkg-deb: building package 'augustus-dbgsym' in '../augustus-dbgsym_3.2.2+dfsg-1_armhf.deb'.
dpkg-deb: building package 'augustus' in '../augustus_3.2.2+dfsg-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../augustus_3.2.2+dfsg-1_armhf.changes
dpkg-genchanges: warning: package augustus-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 augustus-3.2.2+dfsg
dpkg-buildpackage: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160425-0736
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
augustus_3.2.2+dfsg-1_armhf.changes:
------------------------------------
Format: 1.8
Date: Sat, 02 Apr 2016 20:13:40 +0000
Source: augustus
Binary: augustus augustus-data augustus-doc
Architecture: armhf
Version: 3.2.2+dfsg-1
Distribution: stretch-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Sascha Steinbiss <sascha@steinbiss.name>
Description:
augustus - gene prediction in eukaryotic genomes
augustus-data - data files for AUGUSTUS
augustus-doc - documentation files for AUGUSTUS
Closes: 819355
Changes:
augustus (3.2.2+dfsg-1) unstable; urgency=low
.
* Initial release (Closes: #819355)
Checksums-Sha1:
aef04118c50a873f120acfaaa6088b82d94c26fe 14114304 augustus-dbgsym_3.2.2+dfsg-1_armhf.deb
b2037c94a2f01ffe896d5f085fc0687ba232de6e 950106 augustus_3.2.2+dfsg-1_armhf.deb
Checksums-Sha256:
0ffb9605c75d110ab8deae9e1f0f99b3166410fd7254f87bb48a4755a5e81473 14114304 augustus-dbgsym_3.2.2+dfsg-1_armhf.deb
923bf9e0bf660ca4f004f0799f4c10979cfa2d9a7ce5a054dec9e86a92ae8fbd 950106 augustus_3.2.2+dfsg-1_armhf.deb
Files:
0534f782545803cf6907e76dcc32119d 14114304 debug extra augustus-dbgsym_3.2.2+dfsg-1_armhf.deb
f782bb4cf540c40280a03f69851914ef 950106 science optional augustus_3.2.2+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
augustus-dbgsym_3.2.2+dfsg-1_armhf.deb
--------------------------------------
new debian package, version 2.0.
size 14114304 bytes: control archive=939 bytes.
763 bytes, 13 lines control
954 bytes, 9 lines md5sums
Package: augustus-dbgsym
Source: augustus
Version: 3.2.2+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 14413
Depends: augustus (= 3.2.2+dfsg-1)
Section: debug
Priority: extra
Homepage: http://bioinf.uni-greifswald.de/augustus/
Description: Debug symbols for augustus
Auto-Built-Package: debug-symbols
Build-Ids: 01d4456fb487b510aca54eb48e0d4efbeec57cd6 07d6993d6088bc95f473a743b668d1b27f91e1e7 39b8681ccbe51f2908d8f09cf807affc3e7f4689 71fb9533eee5d4217ba5f8a6606b9f6cfa1744f6 84120c9b16eb3a0146d6af7c25056d337f2a0268 94476864c1c8b7b3702b5d43e569855ff06b3e6c d36b7ce3777056a3b8005f696faee0d1a89bbd36 d63dccefa151e9b29e7a2e38bcf9483cddf6c760 df1517691575ba1937d575bef069345bee82a3b8
drwxr-xr-x root/root 0 2016-04-25 07:35 ./
drwxr-xr-x root/root 0 2016-04-25 07:35 ./usr/
drwxr-xr-x root/root 0 2016-04-25 07:34 ./usr/lib/
drwxr-xr-x root/root 0 2016-04-25 07:34 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-04-25 07:35 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-04-25 07:35 ./usr/lib/debug/.build-id/01/
-rw-r--r-- root/root 923208 2016-04-25 07:35 ./usr/lib/debug/.build-id/01/d4456fb487b510aca54eb48e0d4efbeec57cd6.debug
drwxr-xr-x root/root 0 2016-04-25 07:35 ./usr/lib/debug/.build-id/07/
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augustus_3.2.2+dfsg-1_armhf.deb
-------------------------------
new debian package, version 2.0.
size 950106 bytes: control archive=4354 bytes.
1273 bytes, 21 lines control
8396 bytes, 111 lines md5sums
Package: augustus
Version: 3.2.2+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4048
Depends: libbamtools2.4.0, libboost-iostreams1.58.0, libc6 (>= 2.15), libgcc1 (>= 1:4.0), libncurses5 (>= 6), libstdc++6 (>= 5.2), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3), libgsl2, augustus-data, libhts1
Section: science
Priority: optional
Homepage: http://bioinf.uni-greifswald.de/augustus/
Description: gene prediction in eukaryotic genomes
AUGUSTUS is a software for gene prediction in eukaryotic genomic sequences
that is based on a generalized hidden Markov model (HMM), a probabilistic
model of a sequence and its gene structure. After learning gene structures
from a reference annotation, AUGUSTUS uses the HMM to recognize genes in a new
sequence and annotates it with the regions of identified genes. External hints,
e.g. from RNA sequencing, EST or protein alignments etc. can be used to guide
and improve the gene finding process. The result is the set of most likely gene
structures that comply with all given user constraints, if such gene
structures exist.
AUGUSTUS already includes prebuilt HMMs for many species, as well as scripts
to train custom models using annotated genomes.
drwxr-xr-x root/root 0 2016-04-25 07:35 ./
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drwxr-xr-x root/root 0 2016-04-25 07:35 ./usr/bin/
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-rwxr-xr-x root/root 120372 2016-04-25 07:35 ./usr/bin/joingenes
-rwxr-xr-x root/root 30228 2016-04-25 07:35 ./usr/bin/prepareAlign
drwxr-xr-x root/root 0 2016-04-25 07:34 ./usr/share/
drwxr-xr-x root/root 0 2016-04-25 07:34 ./usr/share/augustus/
drwxr-xr-x root/root 0 2016-04-25 07:34 ./usr/share/augustus/scripts/
-rw-r--r-- root/root 12539 2016-04-25 07:34 ./usr/share/augustus/scripts/README.autoAug
-rw-r--r-- root/root 12247 2016-04-25 07:34 ./usr/share/augustus/scripts/SplicedAlignment.pm
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drwxr-xr-x root/root 0 2016-04-25 07:34 ./usr/share/doc/
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-rw-r--r-- root/root 3365 2016-04-02 21:12 ./usr/share/doc/augustus/copyright
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drwxr-xr-x root/root 0 2016-04-25 07:34 ./usr/share/man/man1/
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+------------------------------------------------------------------------------+
| Post Build |
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+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 679004
Build-Time: 789
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 464
Job: augustus_3.2.2+dfsg-1
Machine Architecture: armhf
Package: augustus
Package-Time: 1331
Source-Version: 3.2.2+dfsg-1
Space: 679004
Status: successful
Version: 3.2.2+dfsg-1
--------------------------------------------------------------------------------
Finished at 20160425-0736
Build needed 00:22:11, 679004k disc space