kmc →
2.0+dfsg-2 →
armhf → 2015-08-02 08:10:13
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bm-wb-04
╔══════════════════════════════════════════════════════════════════════════════╗
║ kmc 2.0+dfsg-2 (armhf) 02 Aug 2015 07:50 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: kmc
Version: 2.0+dfsg-2
Source Version: 2.0+dfsg-2
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/kmc-8IayN8/kmc-2.0+dfsg' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/kmc-8IayN8' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-44950bb9-b73e-4a18-b640-b446341ea323' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 stretch-staging/main Sources [8184 kB]
Get:3 http://172.17.0.1 stretch-staging/main armhf Packages [10.1 MB]
Ign http://172.17.0.1 stretch-staging/main Translation-en
Fetched 18.3 MB in 38s (475 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
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Checking available source versions...
Download source files with APT
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Reading package lists...
Building dependency tree...
Reading state information...
Need to get 82.9 kB of source archives.
Get:1 http://172.17.0.1/private/ stretch-staging/main kmc 2.0+dfsg-2 (dsc) [1917 B]
Get:2 http://172.17.0.1/private/ stretch-staging/main kmc 2.0+dfsg-2 (tar) [73.7 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main kmc 2.0+dfsg-2 (diff) [7348 B]
Fetched 82.9 kB in 0s (991 kB/s)
Download complete and in download only mode
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-Hd5RMk/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Ign file: ./ InRelease
Get:1 file: ./ Release.gpg [299 B]
Get:2 file: ./ Release [2119 B]
Ign file: ./ Translation-en
Reading package lists...
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 9 not upgraded.
Need to get 0 B/760 B of archives.
After this operation, 0 B of additional disk space will be used.
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(Reading database ... 11966 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, libbz2-dev, libboost-all-dev (>= 1.51), help2man, d-shlibs
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, libbz2-dev, libboost-all-dev (>= 1.51), help2man, d-shlibs
dpkg-deb: building package 'sbuild-build-depends-kmc-dummy' in '/«BUILDDIR»/resolver-LzDSfr/apt_archive/sbuild-build-depends-kmc-dummy.deb'.
OK
Ign file: ./ InRelease
Get:1 file: ./ Release.gpg [299 B]
Get:2 file: ./ Release [2119 B]
Ign file: ./ Translation-en
Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install kmc build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils d-shlibs debhelper file gettext gettext-base groff-base
help2man icu-devtools intltool-debian libasprintf0c2 libboost-all-dev
libboost-atomic-dev libboost-atomic1.55-dev libboost-atomic1.55.0
libboost-chrono-dev libboost-chrono1.55-dev libboost-chrono1.55.0
libboost-context-dev libboost-context1.55-dev libboost-context1.55.0
libboost-coroutine-dev libboost-coroutine1.55-dev libboost-date-time-dev
libboost-date-time1.55-dev libboost-date-time1.55.0 libboost-dev
libboost-exception-dev libboost-exception1.55-dev libboost-filesystem-dev
libboost-filesystem1.55-dev libboost-filesystem1.55.0 libboost-graph-dev
libboost-graph-parallel-dev libboost-graph-parallel1.55-dev
libboost-graph-parallel1.55.0 libboost-graph1.55-dev libboost-graph1.55.0
libboost-iostreams-dev libboost-iostreams1.55-dev libboost-iostreams1.55.0
libboost-locale-dev libboost-locale1.55-dev libboost-locale1.55.0
libboost-log-dev libboost-log1.55-dev libboost-log1.55.0 libboost-math-dev
libboost-math1.55-dev libboost-math1.55.0 libboost-mpi-dev
libboost-mpi-python-dev libboost-mpi-python1.55-dev
libboost-mpi-python1.55.0 libboost-mpi1.55-dev libboost-mpi1.55.0
libboost-program-options-dev libboost-program-options1.55-dev
libboost-program-options1.55.0 libboost-python-dev libboost-python1.55-dev
libboost-python1.55.0 libboost-random-dev libboost-random1.55-dev
libboost-random1.55.0 libboost-regex-dev libboost-regex1.55-dev
libboost-regex1.55.0 libboost-serialization-dev
libboost-serialization1.55-dev libboost-serialization1.55.0
libboost-signals-dev libboost-signals1.55-dev libboost-signals1.55.0
libboost-system-dev libboost-system1.55-dev libboost-system1.55.0
libboost-test-dev libboost-test1.55-dev libboost-test1.55.0
libboost-thread-dev libboost-thread1.55-dev libboost-thread1.55.0
libboost-timer-dev libboost-timer1.55-dev libboost-timer1.55.0
libboost-tools-dev libboost-wave-dev libboost-wave1.55-dev
libboost-wave1.55.0 libboost1.55-dev libboost1.55-tools-dev libbz2-dev
libcr0 libcroco3 libexpat1 libexpat1-dev libffi6 libgfortran3 libglib2.0-0
libhwloc-dev libhwloc5 libibverbs-dev libibverbs1 libicu-dev libicu52
libltdl-dev libltdl7 libmagic1 libopenmpi-dev libopenmpi1.6 libpipeline1
libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev
libpython2.7-minimal libpython2.7-stdlib libsqlite3-0 libssl1.0.0
libunistring0 libxml2 man-db mime-support mpi-default-bin mpi-default-dev
openmpi-bin openmpi-common po-debconf python python-dev python-minimal
python2.7 python2.7-dev python2.7-minimal zlib1g-dev
Suggested packages:
wamerican wordlist whois vacation dh-make gettext-doc groff libboost-doc
graphviz python3 libboost1.55-doc gccxml libmpfrc++-dev libntl-dev xsltproc
doxygen docbook-xml docbook-xsl default-jdk fop blcr-dkms
libhwloc-contrib-plugins icu-doc libtool-doc less www-browser gfortran
openmpi-checkpoint libmail-box-perl python-doc python-tk python2.7-doc
binfmt-support
Recommended packages:
curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev bzip2-doc
libglib2.0-data shared-mime-info xdg-user-dirs libhwloc-plugins libtool
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils d-shlibs debhelper file gettext gettext-base groff-base
help2man icu-devtools intltool-debian libasprintf0c2 libboost-all-dev
libboost-atomic-dev libboost-atomic1.55-dev libboost-atomic1.55.0
libboost-chrono-dev libboost-chrono1.55-dev libboost-chrono1.55.0
libboost-context-dev libboost-context1.55-dev libboost-context1.55.0
libboost-coroutine-dev libboost-coroutine1.55-dev libboost-date-time-dev
libboost-date-time1.55-dev libboost-date-time1.55.0 libboost-dev
libboost-exception-dev libboost-exception1.55-dev libboost-filesystem-dev
libboost-filesystem1.55-dev libboost-filesystem1.55.0 libboost-graph-dev
libboost-graph-parallel-dev libboost-graph-parallel1.55-dev
libboost-graph-parallel1.55.0 libboost-graph1.55-dev libboost-graph1.55.0
libboost-iostreams-dev libboost-iostreams1.55-dev libboost-iostreams1.55.0
libboost-locale-dev libboost-locale1.55-dev libboost-locale1.55.0
libboost-log-dev libboost-log1.55-dev libboost-log1.55.0 libboost-math-dev
libboost-math1.55-dev libboost-math1.55.0 libboost-mpi-dev
libboost-mpi-python-dev libboost-mpi-python1.55-dev
libboost-mpi-python1.55.0 libboost-mpi1.55-dev libboost-mpi1.55.0
libboost-program-options-dev libboost-program-options1.55-dev
libboost-program-options1.55.0 libboost-python-dev libboost-python1.55-dev
libboost-python1.55.0 libboost-random-dev libboost-random1.55-dev
libboost-random1.55.0 libboost-regex-dev libboost-regex1.55-dev
libboost-regex1.55.0 libboost-serialization-dev
libboost-serialization1.55-dev libboost-serialization1.55.0
libboost-signals-dev libboost-signals1.55-dev libboost-signals1.55.0
libboost-system-dev libboost-system1.55-dev libboost-system1.55.0
libboost-test-dev libboost-test1.55-dev libboost-test1.55.0
libboost-thread-dev libboost-thread1.55-dev libboost-thread1.55.0
libboost-timer-dev libboost-timer1.55-dev libboost-timer1.55.0
libboost-tools-dev libboost-wave-dev libboost-wave1.55-dev
libboost-wave1.55.0 libboost1.55-dev libboost1.55-tools-dev libbz2-dev
libcr0 libcroco3 libexpat1 libexpat1-dev libffi6 libgfortran3 libglib2.0-0
libhwloc-dev libhwloc5 libibverbs-dev libibverbs1 libicu-dev libicu52
libltdl-dev libltdl7 libmagic1 libopenmpi-dev libopenmpi1.6 libpipeline1
libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev
libpython2.7-minimal libpython2.7-stdlib libsqlite3-0 libssl1.0.0
libunistring0 libxml2 man-db mime-support mpi-default-bin mpi-default-dev
openmpi-bin openmpi-common po-debconf python python-dev python-minimal
python2.7 python2.7-dev python2.7-minimal sbuild-build-depends-kmc-dummy
zlib1g-dev
0 upgraded, 137 newly installed, 0 to remove and 9 not upgraded.
Need to get 63.2 MB/63.2 MB of archives.
After this operation, 293 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ stretch-staging/main libpipeline1 armhf 1.4.0-1 [24.0 kB]
Get:2 http://172.17.0.1/private/ stretch-staging/main groff-base armhf 1.22.3-1 [1085 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main bsdmainutils armhf 9.0.6 [177 kB]
Get:4 http://172.17.0.1/private/ stretch-staging/main man-db armhf 2.7.0.2-5 [972 kB]
Get:5 http://172.17.0.1/private/ stretch-staging/main libasprintf0c2 armhf 0.19.4-1 [31.5 kB]
Get:6 http://172.17.0.1/private/ stretch-staging/main libmagic1 armhf 1:5.22+15-2 [244 kB]
Get:7 http://172.17.0.1/private/ stretch-staging/main libpython2.7-minimal armhf 2.7.10-3 [380 kB]
Get:8 http://172.17.0.1/private/ stretch-staging/main mime-support all 3.58 [36.0 kB]
Get:9 http://172.17.0.1/private/ stretch-staging/main libexpat1 armhf 2.1.0-7 [59.8 kB]
Get:10 http://172.17.0.1/private/ stretch-staging/main libffi6 armhf 3.2.1-3 [18.5 kB]
Get:11 http://172.17.0.1/private/ stretch-staging/main libsqlite3-0 armhf 3.8.10.2-1 [389 kB]
Get:12 http://172.17.0.1/private/ stretch-staging/main libssl1.0.0 armhf 1.0.2d-1 [882 kB]
Get:13 http://172.17.0.1/private/ stretch-staging/main libpython2.7-stdlib armhf 2.7.10-3 [1815 kB]
Get:14 http://172.17.0.1/private/ stretch-staging/main libpython2.7 armhf 2.7.10-3 [932 kB]
Get:15 http://172.17.0.1/private/ stretch-staging/main libxml2 armhf 2.9.1+dfsg1-5 [703 kB]
Get:16 http://172.17.0.1/private/ stretch-staging/main python2.7-minimal armhf 2.7.10-3 [1163 kB]
Get:17 http://172.17.0.1/private/ stretch-staging/main python-minimal armhf 2.7.9-1 [40.1 kB]
Get:18 http://172.17.0.1/private/ stretch-staging/main python2.7 armhf 2.7.10-3 [259 kB]
Get:19 http://172.17.0.1/private/ stretch-staging/main libpython-stdlib armhf 2.7.9-1 [19.6 kB]
Get:20 http://172.17.0.1/private/ stretch-staging/main python armhf 2.7.9-1 [151 kB]
Get:21 http://172.17.0.1/private/ stretch-staging/main libglib2.0-0 armhf 2.44.1-1.1 [2312 kB]
Get:22 http://172.17.0.1/private/ stretch-staging/main libcroco3 armhf 0.6.8-3 [121 kB]
Get:23 http://172.17.0.1/private/ stretch-staging/main libgfortran3 armhf 5.1.1-14+rpi1 [154 kB]
Get:24 http://172.17.0.1/private/ stretch-staging/main libltdl7 armhf 2.4.2-1.11 [42.5 kB]
Get:25 http://172.17.0.1/private/ stretch-staging/main libexpat1-dev armhf 2.1.0-7 [114 kB]
Get:26 http://172.17.0.1/private/ stretch-staging/main libpython2.7-dev armhf 2.7.10-3 [18.0 MB]
Get:27 http://172.17.0.1/private/ stretch-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:28 http://172.17.0.1/private/ stretch-staging/main libhwloc5 armhf 1.11.0-1 [73.5 kB]
Get:29 http://172.17.0.1/private/ stretch-staging/main libboost-iostreams1.55.0 armhf 1.55.0+dfsg-4 [47.0 kB]
Get:30 http://172.17.0.1/private/ stretch-staging/main file armhf 1:5.22+15-2 [59.9 kB]
Get:31 http://172.17.0.1/private/ stretch-staging/main gettext-base armhf 0.19.4-1 [117 kB]
Get:32 http://172.17.0.1/private/ stretch-staging/main d-shlibs all 0.59 [16.7 kB]
Get:33 http://172.17.0.1/private/ stretch-staging/main gettext armhf 0.19.4-1 [1168 kB]
Get:34 http://172.17.0.1/private/ stretch-staging/main intltool-debian all 0.35.0+20060710.2 [25.9 kB]
Get:35 http://172.17.0.1/private/ stretch-staging/main po-debconf all 1.0.18 [248 kB]
Get:36 http://172.17.0.1/private/ stretch-staging/main debhelper all 9.20150628 [817 kB]
Get:37 http://172.17.0.1/private/ stretch-staging/main help2man armhf 1.47.1 [150 kB]
Get:38 http://172.17.0.1/private/ stretch-staging/main libicu52 armhf 52.1-10 [6553 kB]
Get:39 http://172.17.0.1/private/ stretch-staging/main icu-devtools armhf 52.1-10 [159 kB]
Get:40 http://172.17.0.1/private/ stretch-staging/main libboost1.55-dev armhf 1.55.0+dfsg-4 [5806 kB]
Get:41 http://172.17.0.1/private/ stretch-staging/main libboost-dev armhf 1.55.0.2 [3378 B]
Get:42 http://172.17.0.1/private/ stretch-staging/main libboost1.55-tools-dev armhf 1.55.0+dfsg-4 [975 kB]
Get:43 http://172.17.0.1/private/ stretch-staging/main libboost-tools-dev armhf 1.55.0.2 [3192 B]
Get:44 http://172.17.0.1/private/ stretch-staging/main libboost-atomic1.55.0 armhf 1.55.0+dfsg-4 [28.6 kB]
Get:45 http://172.17.0.1/private/ stretch-staging/main libboost-atomic1.55-dev armhf 1.55.0+dfsg-4 [27.5 kB]
Get:46 http://172.17.0.1/private/ stretch-staging/main libboost-atomic-dev armhf 1.55.0.2 [3330 B]
Get:47 http://172.17.0.1/private/ stretch-staging/main libboost-system1.55.0 armhf 1.55.0+dfsg-4 [30.0 kB]
Get:48 http://172.17.0.1/private/ stretch-staging/main libboost-chrono1.55.0 armhf 1.55.0+dfsg-4 [34.8 kB]
Get:49 http://172.17.0.1/private/ stretch-staging/main libboost-chrono1.55-dev armhf 1.55.0+dfsg-4 [38.6 kB]
Get:50 http://172.17.0.1/private/ stretch-staging/main libboost-chrono-dev armhf 1.55.0.2 [3668 B]
Get:51 http://172.17.0.1/private/ stretch-staging/main libboost-context1.55.0 armhf 1.55.0+dfsg-4 [28.4 kB]
Get:52 http://172.17.0.1/private/ stretch-staging/main libboost-context1.55-dev armhf 1.55.0+dfsg-4 [27.1 kB]
Get:53 http://172.17.0.1/private/ stretch-staging/main libboost-context-dev armhf 1.55.0.2 [3226 B]
Get:54 http://172.17.0.1/private/ stretch-staging/main libboost-coroutine1.55-dev armhf 1.55.0+dfsg-4 [30.5 kB]
Get:55 http://172.17.0.1/private/ stretch-staging/main libboost-coroutine-dev armhf 1.55.0.2 [3290 B]
Get:56 http://172.17.0.1/private/ stretch-staging/main libboost-date-time1.55.0 armhf 1.55.0+dfsg-4 [39.7 kB]
Get:57 http://172.17.0.1/private/ stretch-staging/main libboost-serialization1.55.0 armhf 1.55.0+dfsg-4 [132 kB]
Get:58 http://172.17.0.1/private/ stretch-staging/main libboost-serialization1.55-dev armhf 1.55.0+dfsg-4 [189 kB]
Get:59 http://172.17.0.1/private/ stretch-staging/main libboost-date-time1.55-dev armhf 1.55.0+dfsg-4 [49.2 kB]
Get:60 http://172.17.0.1/private/ stretch-staging/main libboost-date-time-dev armhf 1.55.0.2 [3022 B]
Get:61 http://172.17.0.1/private/ stretch-staging/main libboost-exception1.55-dev armhf 1.55.0+dfsg-4 [26.8 kB]
Get:62 http://172.17.0.1/private/ stretch-staging/main libboost-exception-dev armhf 1.55.0.2 [3016 B]
Get:63 http://172.17.0.1/private/ stretch-staging/main libboost-filesystem1.55.0 armhf 1.55.0+dfsg-4 [54.4 kB]
Get:64 http://172.17.0.1/private/ stretch-staging/main libboost-system1.55-dev armhf 1.55.0+dfsg-4 [30.6 kB]
Get:65 http://172.17.0.1/private/ stretch-staging/main libboost-filesystem1.55-dev armhf 1.55.0+dfsg-4 [62.3 kB]
Get:66 http://172.17.0.1/private/ stretch-staging/main libboost-filesystem-dev armhf 1.55.0.2 [3048 B]
Get:67 http://172.17.0.1/private/ stretch-staging/main libboost-regex1.55.0 armhf 1.55.0+dfsg-4 [237 kB]
Get:68 http://172.17.0.1/private/ stretch-staging/main libboost-graph1.55.0 armhf 1.55.0+dfsg-4 [107 kB]
Get:69 http://172.17.0.1/private/ stretch-staging/main libboost-test1.55.0 armhf 1.55.0+dfsg-4 [177 kB]
Get:70 http://172.17.0.1/private/ stretch-staging/main libboost-test1.55-dev armhf 1.55.0+dfsg-4 [238 kB]
Get:71 http://172.17.0.1/private/ stretch-staging/main libboost-graph1.55-dev armhf 1.55.0+dfsg-4 [130 kB]
Get:72 http://172.17.0.1/private/ stretch-staging/main libboost-graph-dev armhf 1.55.0.2 [3126 B]
Get:73 http://172.17.0.1/private/ stretch-staging/main libcr0 armhf 0.8.5-2.2 [30.0 kB]
Get:74 http://172.17.0.1/private/ stretch-staging/main libibverbs1 armhf 1.1.8-1.1 [28.5 kB]
Get:75 http://172.17.0.1/private/ stretch-staging/main libopenmpi1.6 armhf 1.6.5-10+rpi1 [1240 kB]
Get:76 http://172.17.0.1/private/ stretch-staging/main libboost-mpi1.55.0 armhf 1.55.0+dfsg-4 [52.3 kB]
Get:77 http://172.17.0.1/private/ stretch-staging/main libboost-graph-parallel1.55.0 armhf 1.55.0+dfsg-4 [71.9 kB]
Get:78 http://172.17.0.1/private/ stretch-staging/main libboost-graph-parallel1.55-dev armhf 1.55.0+dfsg-4 [82.6 kB]
Get:79 http://172.17.0.1/private/ stretch-staging/main libboost-graph-parallel-dev armhf 1.55.0.2 [3158 B]
Get:80 http://172.17.0.1/private/ stretch-staging/main libicu-dev armhf 52.1-10 [7452 kB]
Get:81 http://172.17.0.1/private/ stretch-staging/main libboost-regex1.55-dev armhf 1.55.0+dfsg-4 [328 kB]
Get:82 http://172.17.0.1/private/ stretch-staging/main libboost-iostreams1.55-dev armhf 1.55.0+dfsg-4 [56.7 kB]
Get:83 http://172.17.0.1/private/ stretch-staging/main libboost-iostreams-dev armhf 1.55.0.2 [3020 B]
Get:84 http://172.17.0.1/private/ stretch-staging/main libboost-thread1.55.0 armhf 1.55.0+dfsg-4 [48.8 kB]
Get:85 http://172.17.0.1/private/ stretch-staging/main libboost-locale1.55.0 armhf 1.55.0+dfsg-4 [216 kB]
Get:86 http://172.17.0.1/private/ stretch-staging/main libboost-locale1.55-dev armhf 1.55.0+dfsg-4 [327 kB]
Get:87 http://172.17.0.1/private/ stretch-staging/main libboost-locale-dev armhf 1.55.0.2 [3368 B]
Get:88 http://172.17.0.1/private/ stretch-staging/main libboost-log1.55.0 armhf 1.55.0+dfsg-4 [464 kB]
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Get:124 http://172.17.0.1/private/ stretch-staging/main libboost-signals-dev armhf 1.55.0.2 [3086 B]
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Get:128 http://172.17.0.1/private/ stretch-staging/main libboost-timer1.55.0 armhf 1.55.0+dfsg-4 [32.3 kB]
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Get:131 http://172.17.0.1/private/ stretch-staging/main libboost-wave1.55.0 armhf 1.55.0+dfsg-4 [168 kB]
Get:132 http://172.17.0.1/private/ stretch-staging/main libboost-wave1.55-dev armhf 1.55.0+dfsg-4 [252 kB]
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Get:134 http://172.17.0.1/private/ stretch-staging/main libboost-all-dev armhf 1.55.0.2 [3352 B]
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Get:136 http://172.17.0.1/private/ stretch-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-2 [199 kB]
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Setting up libboost-wave1.55.0:armhf (1.55.0+dfsg-4) ...
Setting up libboost-wave1.55-dev:armhf (1.55.0+dfsg-4) ...
Setting up libboost-wave-dev:armhf (1.55.0.2) ...
Setting up libboost-all-dev (1.55.0.2) ...
Setting up libbz2-dev:armhf (1.0.6-8) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2) ...
Setting up sbuild-build-depends-kmc-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.19-19) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25-10 dpkg-dev_1.18.1 g++-4.9_4.9.3-2 gcc-4.9_4.9.3-2 libc6-dev_2.19-19 libstdc++-4.9-dev_4.9.3-2 libstdc++6_5.1.1-14+rpi1 linux-libc-dev_3.16.7-ckt4-1+rpi1+b2
Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.9.10 base-files_9.2+rpi1 base-passwd_3.5.38 bash_4.3-12 binutils_2.25-10 bsdmainutils_9.0.6 bsdutils_1:2.26.2-6 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:4.9.2-4+rpi1 cpp-4.9_4.9.3-2 d-shlibs_0.59 dash_0.5.7-4 debconf_1.5.57 debfoster_2.7-2 debhelper_9.20150628 debianutils_4.5.1 diffutils_1:3.3-1 dmsetup_2:1.02.90-2.2 dpkg_1.18.1 dpkg-dev_1.18.1 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.22+15-2 findutils_4.4.2-9 g++_4:4.9.2-4+rpi1 g++-4.9_4.9.3-2 gcc_4:4.9.2-4+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.4-4 gcc-4.9_4.9.3-2 gcc-4.9-base_4.9.3-2 gcc-5-base_5.1.1-14+rpi1 gettext_0.19.4-1 gettext-base_0.19.4-1 gnupg_1.4.19-3 gpgv_1.4.19-3 grep_2.21-2 groff-base_1.22.3-1 gzip_1.6-4 help2man_1.47.1 hostname_3.15 icu-devtools_52.1-10 init_1.23 init-system-helpers_1.23 initramfs-tools_0.120 initscripts_2.88dsf-59.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.2 klibc-utils_2.0.4-2+rpi1 kmod_21-1 libacl1_2.2.52-2 libapparmor1_2.9.2-3 libapt-pkg4.12_1.0.9.10 libasan1_4.9.3-2 libasprintf0c2_0.19.4-1 libatomic1_5.1.1-14+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.2-1 libaudit1_1:2.4.2-1 libblkid1_2.26.2-6 libboost-all-dev_1.55.0.2 libboost-atomic-dev_1.55.0.2 libboost-atomic1.55-dev_1.55.0+dfsg-4 libboost-atomic1.55.0_1.55.0+dfsg-4 libboost-chrono-dev_1.55.0.2 libboost-chrono1.55-dev_1.55.0+dfsg-4 libboost-chrono1.55.0_1.55.0+dfsg-4 libboost-context-dev_1.55.0.2 libboost-context1.55-dev_1.55.0+dfsg-4 libboost-context1.55.0_1.55.0+dfsg-4 libboost-coroutine-dev_1.55.0.2 libboost-coroutine1.55-dev_1.55.0+dfsg-4 libboost-date-time-dev_1.55.0.2 libboost-date-time1.55-dev_1.55.0+dfsg-4 libboost-date-time1.55.0_1.55.0+dfsg-4 libboost-dev_1.55.0.2 libboost-exception-dev_1.55.0.2 libboost-exception1.55-dev_1.55.0+dfsg-4 libboost-filesystem-dev_1.55.0.2 libboost-filesystem1.55-dev_1.55.0+dfsg-4 libboost-filesystem1.55.0_1.55.0+dfsg-4 libboost-graph-dev_1.55.0.2 libboost-graph-parallel-dev_1.55.0.2 libboost-graph-parallel1.55-dev_1.55.0+dfsg-4 libboost-graph-parallel1.55.0_1.55.0+dfsg-4 libboost-graph1.55-dev_1.55.0+dfsg-4 libboost-graph1.55.0_1.55.0+dfsg-4 libboost-iostreams-dev_1.55.0.2 libboost-iostreams1.55-dev_1.55.0+dfsg-4 libboost-iostreams1.55.0_1.55.0+dfsg-4 libboost-locale-dev_1.55.0.2 libboost-locale1.55-dev_1.55.0+dfsg-4 libboost-locale1.55.0_1.55.0+dfsg-4 libboost-log-dev_1.55.0.2 libboost-log1.55-dev_1.55.0+dfsg-4 libboost-log1.55.0_1.55.0+dfsg-4 libboost-math-dev_1.55.0.2 libboost-math1.55-dev_1.55.0+dfsg-4 libboost-math1.55.0_1.55.0+dfsg-4 libboost-mpi-dev_1.55.0.2 libboost-mpi-python-dev_1.55.0.2 libboost-mpi-python1.55-dev_1.55.0+dfsg-4 libboost-mpi-python1.55.0_1.55.0+dfsg-4 libboost-mpi1.55-dev_1.55.0+dfsg-4 libboost-mpi1.55.0_1.55.0+dfsg-4 libboost-program-options-dev_1.55.0.2 libboost-program-options1.55-dev_1.55.0+dfsg-4 libboost-program-options1.55.0_1.55.0+dfsg-4 libboost-python-dev_1.55.0.2 libboost-python1.55-dev_1.55.0+dfsg-4 libboost-python1.55.0_1.55.0+dfsg-4 libboost-random-dev_1.55.0.2 libboost-random1.55-dev_1.55.0+dfsg-4 libboost-random1.55.0_1.55.0+dfsg-4 libboost-regex-dev_1.55.0.2 libboost-regex1.55-dev_1.55.0+dfsg-4 libboost-regex1.55.0_1.55.0+dfsg-4 libboost-serialization-dev_1.55.0.2 libboost-serialization1.55-dev_1.55.0+dfsg-4 libboost-serialization1.55.0_1.55.0+dfsg-4 libboost-signals-dev_1.55.0.2 libboost-signals1.55-dev_1.55.0+dfsg-4 libboost-signals1.55.0_1.55.0+dfsg-4 libboost-system-dev_1.55.0.2 libboost-system1.55-dev_1.55.0+dfsg-4 libboost-system1.55.0_1.55.0+dfsg-4 libboost-test-dev_1.55.0.2 libboost-test1.55-dev_1.55.0+dfsg-4 libboost-test1.55.0_1.55.0+dfsg-4 libboost-thread-dev_1.55.0.2 libboost-thread1.55-dev_1.55.0+dfsg-4 libboost-thread1.55.0_1.55.0+dfsg-4 libboost-timer-dev_1.55.0.2 libboost-timer1.55-dev_1.55.0+dfsg-4 libboost-timer1.55.0_1.55.0+dfsg-4 libboost-tools-dev_1.55.0.2 libboost-wave-dev_1.55.0.2 libboost-wave1.55-dev_1.55.0+dfsg-4 libboost-wave1.55.0_1.55.0+dfsg-4 libboost1.55-dev_1.55.0+dfsg-4 libboost1.55-tools-dev_1.55.0+dfsg-4 libbz2-1.0_1.0.6-8 libbz2-dev_1.0.6-8 libc-bin_2.19-19 libc-dev-bin_2.19-19 libc6_2.19-19 libc6-dev_2.19-19 libcap2_1:2.24-9 libcap2-bin_1:2.24-9 libcloog-isl4_0.18.3-1 libcomerr2_1.42.13-1 libcr0_0.8.5-2.2 libcroco3_0.6.8-3 libcryptsetup4_2:1.6.6-5 libdb5.3_5.3.28-9 libdbus-1-3_1.8.20-1 libdebconfclient0_0.194 libdevmapper1.02.1_2:1.02.90-2.2 libdpkg-perl_1.18.1 libdrm2_2.4.62-1 libexpat1_2.1.0-7 libexpat1-dev_2.1.0-7 libfakeroot_1.20.2-1 libfdisk1_2.26.2-6 libffi6_3.2.1-3 libgc1c2_1:7.2d-6.4 libgcc-4.9-dev_4.9.3-2 libgcc1_1:5.1.1-14+rpi1 libgcrypt20_1.6.3-2 libgdbm3_1.8.3-13.1 libgfortran3_5.1.1-14+rpi1 libglib2.0-0_2.44.1-1.1 libgmp10_2:6.0.0+dfsg-7+rpi1 libgomp1_5.1.1-14+rpi1 libgpg-error0_1.19-2 libhwloc-dev_1.11.0-1 libhwloc5_1.11.0-1 libibverbs-dev_1.1.8-1.1 libibverbs1_1.1.8-1.1 libicu-dev_52.1-10 libicu52_52.1-10 libisl13_0.14-2 libklibc_2.0.4-2+rpi1 libkmod2_21-1 liblocale-gettext-perl_1.05-9 libltdl-dev_2.4.2-1.11 libltdl7_2.4.2-1.11 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.22+15-2 libmount1_2.26.2-6 libmpc3_1.0.3-1 libmpfr4_3.1.3-1 libncurses5_5.9+20150516-2 libncursesw5_5.9+20150516-2 libnih-dbus1_1.0.3-4.3 libnih1_1.0.3-4.3 libopenmpi-dev_1.6.5-10+rpi1 libopenmpi1.6_1.6.5-10+rpi1 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpcre3_2:8.35-7 libpipeline1_1.4.0-1 libpng12-0_1.2.50-2 libprocps3_2:3.3.9-9 libprocps4_2:3.3.10-2 libpython-dev_2.7.9-1 libpython-stdlib_2.7.9-1 libpython2.7_2.7.10-3 libpython2.7-dev_2.7.10-3 libpython2.7-minimal_2.7.10-3 libpython2.7-stdlib_2.7.10-3 libreadline6_6.3-8 libseccomp2_2.2.1-2 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-2 libslang2_2.3.0-2 libsmartcols1_2.26.2-6 libsqlite3-0_3.8.10.2-1 libss2_1.42.13-1 libssl1.0.0_1.0.2d-1 libstdc++-4.9-dev_4.9.3-2 libstdc++6_5.1.1-14+rpi1 libsystemd0_222-2 libtext-charwidth-perl_0.04-7+b4 libtext-iconv-perl_1.7-5+b5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_2.3000-2 libtinfo5_5.9+20150516-2 libubsan0_5.1.1-14+rpi1 libudev1_222-2 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-25 libustr-1.0-1_1.0.4-5 libuuid1_2.26.2-6 libxml2_2.9.1+dfsg1-5 linux-libc-dev_3.16.7-ckt4-1+rpi1+b2 login_1:4.2-3 lsb-base_4.1+Debian13+rpi1+nmu1 make_4.0-8.1 makedev_2.3.1-93 man-db_2.7.0.2-5 mawk_1.3.3-17 mime-support_3.58 mount_2.26.2-6 mountall_2.54 mpi-default-bin_1.0.2+nmu2 mpi-default-dev_1.0.2+nmu2 multiarch-support_2.19-19 ncurses-base_5.9+20150516-2 ncurses-bin_5.9+20150516-2 openmpi-bin_1.6.5-10+rpi1 openmpi-common_1.6.5-10+rpi1 passwd_1:4.2-3 patch_2.7.5-1 perl_5.20.2-6 perl-base_5.20.2-6 perl-modules_5.20.2-6 plymouth_0.9.0-9 po-debconf_1.0.18 procps_2:3.3.10-2 python_2.7.9-1 python-dev_2.7.9-1 python-minimal_2.7.9-1 python2.7_2.7.10-3 python2.7-dev_2.7.10-3 python2.7-minimal_2.7.10-3 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-kmc-dummy_0.invalid.0 sed_4.2.2-6.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_222-2 systemd-sysv_222-2 sysv-rc_2.88dsf-59.2 sysvinit-utils_2.88dsf-59.2 tar_1.27.1-2 tzdata_2015e-1 udev_222-2 util-linux_2.26.2-6 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2 zlib1g-dev_1:1.2.8.dfsg-2
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Tue Jul 28 06:07:30 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./kmc_2.0+dfsg-2.dsc
dpkg-source: info: extracting kmc in kmc-2.0+dfsg
dpkg-source: info: unpacking kmc_2.0+dfsg.orig.tar.gz
dpkg-source: info: unpacking kmc_2.0+dfsg-2.debian.tar.xz
dpkg-source: info: applying debian-dependent-makefile.patch
dpkg-source: info: applying remove-references-to-asmlib
dpkg-source: info: applying remove-use-of-asmlib-subroutines.patch
dpkg-source: info: applying change-kmc-zlib-and-libz2-to-deb-zlib-and-libbz2
dpkg-source: info: applying remove-call-to-asmlib-sub-in-kbsorter
dpkg-source: info: applying remove-embedded-libraries-from-makefile
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-44950bb9-b73e-4a18-b640-b446341ea323
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package kmc
dpkg-buildpackage: source version 2.0+dfsg-2
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build kmc-2.0+dfsg
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
make -j1 clean
make[1]: Entering directory '/«BUILDDIR»/kmc-2.0+dfsg'
rm kmer_counter/*.o
rm: cannot remove 'kmer_counter/*.o': No such file or directory
makefile:27: recipe for target 'clean' failed
make[1]: [clean] Error 1 (ignored)
rm kmc_api/*.o
rm: cannot remove 'kmc_api/*.o': No such file or directory
make[1]: [clean] Error 1 (ignored)
makefile:27: recipe for target 'clean' failed
rm kmc_dump/*.o
rm: cannot remove 'kmc_dump/*.o': No such file or directory
make[1]: [clean] Error 1 (ignored)
makefile:27: recipe for target 'clean' failed
rm -rf bin
make[1]: Leaving directory '/«BUILDDIR»/kmc-2.0+dfsg'
dh_clean
rm -f debian/kmc.substvars
rm -f debian/kmc.*.debhelper
rm -rf debian/kmc/
rm -rf debian/.debhelper/
rm -f debian/*.debhelper.log
rm -f debian/files
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} + \) -o \
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
rm -f *-stamp
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_auto_configure -a
dh_auto_build -a
make -j1
make[1]: Entering directory '/«BUILDDIR»/kmc-2.0+dfsg'
g++ -Wall -O3 -fopenmp -std=c++11 -I /usr/include/boost -D_FORTIFY_SOURCE=2 -c kmer_counter/kmer_counter.cpp -o kmer_counter/kmer_counter.o
In file included from kmer_counter/kmc.h:16:0,
from kmer_counter/kmer_counter.cpp:18:
kmer_counter/kmer.h: In static member function 'static void CKmerBinSorter_Impl<CKmer<X_SIZE>, SIZE>::CompactKxmers(CKmerBinSorter<CKmer<X_SIZE>, SIZE>&) [with unsigned int SIZE = 1u]':
kmer_counter/kmer.h:541:17: warning: 'kmer.CKmer<1u>::data' may be used uninitialized in this function [-Wmaybe-uninitialized]
return data >> n;
^
In file included from kmer_counter/kmc.h:28:0,
from kmer_counter/kmer_counter.cpp:18:
kmer_counter/kb_sorter.h:1007:15: note: 'kmer.CKmer<1u>::data' was declared here
CKmer<SIZE> kmer, next_kmer;
^
kmer_counter/kb_sorter.h:1013:29: warning: 'counter_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
count = ptr.kxmer_counters[counter_pos];
^
kmer_counter/kb_sorter.h: In static member function 'static void CKmerBinSorter_Impl<CKmer<X_SIZE>, SIZE>::CompactKxmers(CKmerBinSorter<CKmer<X_SIZE>, SIZE>&) [with unsigned int SIZE = 2u]':
kmer_counter/kb_sorter.h:1013:29: warning: 'counter_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
kmer_counter/kb_sorter.h: In static member function 'static void CKmerBinSorter_Impl<CKmer<X_SIZE>, SIZE>::CompactKxmers(CKmerBinSorter<CKmer<X_SIZE>, SIZE>&) [with unsigned int SIZE = 3u]':
kmer_counter/kb_sorter.h:1013:29: warning: 'counter_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
kmer_counter/kb_sorter.h: In static member function 'static void CKmerBinSorter_Impl<CKmer<X_SIZE>, SIZE>::CompactKxmers(CKmerBinSorter<CKmer<X_SIZE>, SIZE>&) [with unsigned int SIZE = 4u]':
kmer_counter/kb_sorter.h:1013:29: warning: 'counter_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
kmer_counter/kb_sorter.h: In static member function 'static void CKmerBinSorter_Impl<CKmer<X_SIZE>, SIZE>::CompactKxmers(CKmerBinSorter<CKmer<X_SIZE>, SIZE>&) [with unsigned int SIZE = 5u]':
kmer_counter/kb_sorter.h:1013:29: warning: 'counter_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
kmer_counter/kb_sorter.h: In static member function 'static void CKmerBinSorter_Impl<CKmer<X_SIZE>, SIZE>::CompactKxmers(CKmerBinSorter<CKmer<X_SIZE>, SIZE>&) [with unsigned int SIZE = 6u]':
kmer_counter/kb_sorter.h:1013:29: warning: 'counter_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
kmer_counter/kb_sorter.h: In static member function 'static void CKmerBinSorter_Impl<CKmer<X_SIZE>, SIZE>::CompactKxmers(CKmerBinSorter<CKmer<X_SIZE>, SIZE>&) [with unsigned int SIZE = 7u]':
kmer_counter/kb_sorter.h:1013:29: warning: 'counter_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
kmer_counter/kb_sorter.h: In static member function 'static void CKmerBinSorter_Impl<CKmer<X_SIZE>, SIZE>::CompactKxmers(CKmerBinSorter<CKmer<X_SIZE>, SIZE>&) [with unsigned int SIZE = 8u]':
kmer_counter/kb_sorter.h:1013:29: warning: 'counter_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -Wall -O3 -fopenmp -std=c++11 -I /usr/include/boost -D_FORTIFY_SOURCE=2 -c kmer_counter/mmer.cpp -o kmer_counter/mmer.o
g++ -Wall -O3 -fopenmp -std=c++11 -I /usr/include/boost -D_FORTIFY_SOURCE=2 -c kmer_counter/mem_disk_file.cpp -o kmer_counter/mem_disk_file.o
g++ -Wall -O3 -fopenmp -std=c++11 -I /usr/include/boost -D_FORTIFY_SOURCE=2 -c kmer_counter/rev_byte.cpp -o kmer_counter/rev_byte.o
g++ -Wall -O3 -fopenmp -std=c++11 -I /usr/include/boost -D_FORTIFY_SOURCE=2 -c kmer_counter/fastq_reader.cpp -o kmer_counter/fastq_reader.o
g++ -Wall -O3 -fopenmp -std=c++11 -I /usr/include/boost -D_FORTIFY_SOURCE=2 -c kmer_counter/timer.cpp -o kmer_counter/timer.o
g++ -Wall -O3 -fopenmp -std=c++11 -I /usr/include/boost -D_FORTIFY_SOURCE=2 -c kmer_counter/radix.cpp -o kmer_counter/radix.o
g++ -Wall -O3 -fopenmp -std=c++11 -I /usr/include/boost -D_FORTIFY_SOURCE=2 -c kmer_counter/kb_completer.cpp -o kmer_counter/kb_completer.o
kmer_counter/kb_completer.cpp: In member function 'void CKmerBinCompleter::ProcessBins()':
kmer_counter/kb_completer.cpp:148:4: warning: 'bin_id' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (s_mapper->get_bin_id(i) == bin_id)
^
g++ -Wall -O3 -fopenmp -std=c++11 -I /usr/include/boost -D_FORTIFY_SOURCE=2 -c kmer_counter/kb_storer.cpp -o kmer_counter/kb_storer.o
g++ -Wall -O3 -fopenmp -std=c++11 -I /usr/include/boost -D_FORTIFY_SOURCE=2 -c kmer_counter/kmer.cpp -o kmer_counter/kmer.o
mkdir -p bin
g++ -D_FORTIFY_SOURCE=2 -lm -fopenmp -O3 -std=c++11 -o bin/kmc kmer_counter/kmer_counter.o kmer_counter/mem_disk_file.o kmer_counter/rev_byte.o kmer_counter/mmer.o kmer_counter/fastq_reader.o kmer_counter/timer.o kmer_counter/radix.o kmer_counter/kb_completer.o kmer_counter/kb_storer.o kmer_counter/kmer.o /usr/lib/arm-linux-gnueabihf/libboost_thread.a /usr/lib/arm-linux-gnueabihf/libboost_filesystem.a /usr/lib/arm-linux-gnueabihf/libboost_system.a -Wl,-z,relro -lz -lbz2
g++ -Wall -O3 -fopenmp -std=c++11 -I /usr/include/boost -D_FORTIFY_SOURCE=2 -c kmc_dump/nc_utils.cpp -o kmc_dump/nc_utils.o
g++ -Wall -O3 -fopenmp -std=c++11 -I /usr/include/boost -D_FORTIFY_SOURCE=2 -c kmc_api/mmer.cpp -o kmc_api/mmer.o
g++ -Wall -O3 -fopenmp -std=c++11 -I /usr/include/boost -D_FORTIFY_SOURCE=2 -c kmc_dump/kmc_dump.cpp -o kmc_dump/kmc_dump.o
g++ -Wall -O3 -fopenmp -std=c++11 -I /usr/include/boost -D_FORTIFY_SOURCE=2 -c kmc_api/kmc_file.cpp -o kmc_api/kmc_file.o
kmc_api/kmc_file.cpp: In member function 'void CKMCFile::Reload_sufix_file_buf()':
kmc_api/kmc_file.cpp:437:58: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread (sufix_file_buf, 1, (size_t) part_size, file_suf);
^
kmc_api/kmc_file.cpp: In member function 'bool CKMCFile::RestartListing()':
kmc_api/kmc_file.cpp:483:58: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread (sufix_file_buf, 1, (size_t) part_size, file_suf);
^
kmc_api/kmc_file.cpp: In member function 'uint64 CKMCFile::KmerCount()':
kmc_api/kmc_file.cpp:623:14: warning: 'kmer.CKmerAPI::byte_alignment' may be used uninitialized in this function [-Wmaybe-uninitialized]
CKmerAPI kmer(kmer_length);
^
g++ -Wall -O3 -fopenmp -std=c++11 -I /usr/include/boost -D_FORTIFY_SOURCE=2 -c kmc_api/kmer_api.cpp -o kmc_api/kmer_api.o
mkdir -p bin
g++ -D_FORTIFY_SOURCE=2 -lm -fopenmp -O3 -std=c++11 -o bin/kmc_dump kmc_dump/nc_utils.o kmc_api/mmer.o kmc_dump/kmc_dump.o kmc_api/kmc_file.o kmc_api/kmer_api.o -Wl,-z,relro
make[1]: Leaving directory '/«BUILDDIR»/kmc-2.0+dfsg'
dh_auto_test -a
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
rm -f debian/kmc.substvars
rm -f debian/kmc.*.debhelper
rm -rf debian/kmc/
dh_auto_install -a
install -d debian/kmc
debian/rules override_dh_install
make[1]: Entering directory '/«BUILDDIR»/kmc-2.0+dfsg'
dh_install
install -d debian/kmc//bin
cp --reflink=auto -a ./bin/kmc debian/kmc//bin/
cp --reflink=auto -a ./bin/kmc_dump debian/kmc//bin/
make[1]: Leaving directory '/«BUILDDIR»/kmc-2.0+dfsg'
dh_installdocs -a
install -d debian/kmc/usr/share/doc/kmc
install -p -m0644 debian/copyright debian/kmc/usr/share/doc/kmc/copyright
dh_installchangelogs -a
install -p -m0644 debian/changelog debian/kmc/usr/share/doc/kmc/changelog.Debian
debian/rules override_dh_installman
make[1]: Entering directory '/«BUILDDIR»/kmc-2.0+dfsg'
mkdir -p /«BUILDDIR»/kmc-2.0+dfsg/debian/man
/«BUILDDIR»/kmc-2.0+dfsg/debian/usage_to_man
Can't exec "1": No such file or directory at /«BUILDDIR»/kmc-2.0+dfsg/debian/usage_to_man line 19.
Creating manpages
Manpage creation complete
Manpage creation complete
dh_installman --
install -d debian/kmc/usr/share/man/man1/
install -p -m0644 man/kmc.1 debian/kmc/usr/share/man/man1/kmc.1
install -p -m0644 man/kmc_dump.1 debian/kmc/usr/share/man/man1/kmc_dump.1
man --recode UTF-8 ./kmc\.1 > kmc\.1\.new
chmod 644 kmc.1.new
mv -f kmc.1.new kmc.1
man --recode UTF-8 ./kmc_dump\.1 > kmc_dump\.1\.new
chmod 644 kmc_dump.1.new
mv -f kmc_dump.1.new kmc_dump.1
make[1]: Leaving directory '/«BUILDDIR»/kmc-2.0+dfsg'
dh_perl -a
dh_link -a
dh_compress -a
cd debian/kmc
chmod a-x usr/share/man/man1/kmc.1 usr/share/man/man1/kmc_dump.1 usr/share/doc/kmc/changelog.Debian
gzip -9nf usr/share/man/man1/kmc.1 usr/share/man/man1/kmc_dump.1 usr/share/doc/kmc/changelog.Debian
cd '/«BUILDDIR»/kmc-2.0+dfsg'
dh_fixperms -a
find debian/kmc -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
find debian/kmc ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/kmc/usr/share/doc -type f ! -regex 'debian/kmc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/kmc/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 0755
find debian/kmc/usr/share/man debian/kmc/usr/man/ debian/kmc/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 0644
find debian/kmc -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 0644
find debian/kmc/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 0644
find debian/kmc/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 0644
find debian/kmc -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
find debian/kmc/usr/lib/arm-linux-gnueabihf/perl5/5.20 debian/kmc/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
find debian/kmc/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
find debian/kmc/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
dh_strip -a
strip --remove-section=.comment --remove-section=.note debian/kmc/bin/kmc
strip --remove-section=.comment --remove-section=.note debian/kmc/bin/kmc_dump
dh_makeshlibs -a
rm -f debian/kmc/DEBIAN/shlibs
dh_shlibdeps -a
install -d debian/kmc/DEBIAN
dpkg-shlibdeps -Tdebian/kmc.substvars debian/kmc/bin/kmc debian/kmc/bin/kmc_dump
dpkg-shlibdeps: warning: debian/kmc/bin/kmc contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/kmc/bin/kmc_dump contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dh_installdeb -a
dh_gencontrol -a
echo misc:Depends= >> debian/kmc.substvars
echo misc:Pre-Depends= >> debian/kmc.substvars
dpkg-gencontrol -pkmc -ldebian/changelog -Tdebian/kmc.substvars -Pdebian/kmc
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
chmod 0644 debian/kmc/DEBIAN/control
chown 0:0 debian/kmc/DEBIAN/control
dh_md5sums -a
(cd debian/kmc >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
chmod 0644 debian/kmc/DEBIAN/md5sums
chown 0:0 debian/kmc/DEBIAN/md5sums
dh_builddeb -a
dpkg-deb --build debian/kmc ..
dpkg-deb: building package 'kmc' in '../kmc_2.0+dfsg-2_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../kmc_2.0+dfsg-2_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build kmc-2.0+dfsg
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20150802-0809
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
kmc_2.0+dfsg-2_armhf.changes:
─────────────────────────────
Format: 1.8
Date: Tue, 28 Jul 2015 08:05:11 +0200
Source: kmc
Binary: kmc
Architecture: armhf
Version: 2.0+dfsg-2
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
kmc - count kmers in genomic sequences
Closes: 793835 793843
Changes:
kmc (2.0+dfsg-2) unstable; urgency=medium
.
* Set BOOST_LIB path fit for any arch
Closes: #793843
* Drop -m64 option
Closes: #793835
Checksums-Sha1:
974e1ff41a764622f7f1c816ba0f34c608076169 191330 kmc_2.0+dfsg-2_armhf.deb
Checksums-Sha256:
02d9b43cf91c4ec1888dbae3466847c3b8d1b85849039d59d0df98372ad0f6f7 191330 kmc_2.0+dfsg-2_armhf.deb
Files:
eade077bfc26cf5ad952dd29e98bc15a 191330 science optional kmc_2.0+dfsg-2_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
kmc_2.0+dfsg-2_armhf.deb
────────────────────────
new debian package, version 2.0.
size 191330 bytes: control archive=1289 bytes.
1608 bytes, 30 lines control
352 bytes, 6 lines md5sums
Package: kmc
Version: 2.0+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 752
Depends: libbz2-1.0, libc6 (>= 2.17), libgcc1 (>= 1:4.4.0), libgomp1 (>= 4.9), libstdc++6 (>= 4.9), zlib1g (>= 1:1.2.6)
Section: science
Priority: optional
Homepage: https://github.com/js21/kmc
Description: count kmers in genomic sequences
The kmc software is designed for counting k-mers (sequences of
consecutive k symbols) in a set of reads K-mer counting is
important for many bioinformatics applications, e.g.,
developing de Bruijn graph assemblers.
Building de Bruijn graphs is a commonly used approach for genome
assembly with data from second-generation sequencer.
Unfortunately, sequencing errors (frequent in practice)
results in huge memory requirements for de Bruijn graphs, as well
as long build time. One of the popular approaches to handle this
problem is filtering the input reads in such a way that unique k-mers
(very likely obtained as a result of an error) are discarded.
.
Thus, KMC scans the raw reads and produces a compact representation
of all non-unique reads accompanied with number of their occurrences.
The algorithm implemented in KMC makes use mostly of disk space rather
than RAM, which allows one to use KMC even on rather typical personal
computers. When run at high-end server (what is necessary for KMC
competitors) it outperforms them in both memory requirements and
speed of computation. The disk space necessary for computation is in
order of the size of input data (usually it is smaller).
drwxr-xr-x root/root 0 2015-08-02 08:09 ./
drwxr-xr-x root/root 0 2015-08-02 08:08 ./bin/
-rwxr-xr-x root/root 731200 2015-08-02 08:08 ./bin/kmc
-rwxr-xr-x root/root 22080 2015-08-02 08:08 ./bin/kmc_dump
drwxr-xr-x root/root 0 2015-08-02 08:08 ./usr/
drwxr-xr-x root/root 0 2015-08-02 08:08 ./usr/share/
drwxr-xr-x root/root 0 2015-08-02 08:08 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-08-02 08:08 ./usr/share/doc/kmc/
-rw-r--r-- root/root 270 2015-07-28 06:05 ./usr/share/doc/kmc/changelog.Debian.gz
-rw-r--r-- root/root 1027 2015-07-28 06:05 ./usr/share/doc/kmc/copyright
drwxr-xr-x root/root 0 2015-08-02 08:08 ./usr/share/man/
drwxr-xr-x root/root 0 2015-08-02 08:08 ./usr/share/man/man1/
-rw-r--r-- root/root 1081 2015-08-02 08:08 ./usr/share/man/man1/kmc.1.gz
-rw-r--r-- root/root 611 2015-08-02 08:08 ./usr/share/man/man1/kmc_dump.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 5636
Build-Time: 516
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 568
Job: kmc_2.0+dfsg-2
Machine Architecture: armhf
Package: kmc
Package-Time: 1154
Source-Version: 2.0+dfsg-2
Space: 5636
Status: successful
Version: 2.0+dfsg-2
────────────────────────────────────────────────────────────────────────────────
Finished at 20150802-0809
Build needed 00:19:14, 5636k disc space