kmc →
2.3+dfsg-3 →
armhf → 2016-03-16 05:23:59
sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on bm-wb-04
+==============================================================================+
| kmc 2.3+dfsg-3 (armhf) 16 Mar 2016 04:53 |
+==============================================================================+
Package: kmc
Version: 2.3+dfsg-3
Source Version: 2.3+dfsg-3
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/kmc-GJpAu4/kmc-2.3+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/kmc-GJpAu4' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-2843213c-8f81-4e82-942a-c3a506ff263f' 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 [8806 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [10.9 MB]
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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: 'kmc' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/kmc.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/kmc.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 163 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main kmc 2.3+dfsg-3 (dsc) [2114 B]
Get:2 http://172.17.0.1/private stretch-staging/main kmc 2.3+dfsg-3 (tar) [129 kB]
Get:3 http://172.17.0.1/private stretch-staging/main kmc 2.3+dfsg-3 (diff) [31.2 kB]
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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-yKnNts/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-yKnNts/apt_archive ./ InRelease
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Get:3 file:/<<BUILDDIR>>/resolver-yKnNts/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-yKnNts/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-yKnNts/apt_archive ./ Sources [214 B]
Get:5 file:/<<BUILDDIR>>/resolver-yKnNts/apt_archive ./ Packages [526 B]
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+------------------------------------------------------------------------------+
| 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 75 not upgraded.
Need to get 0 B/766 B of archives.
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Get:1 file:/<<BUILDDIR>>/resolver-yKnNts/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [766 B]
debconf: delaying package configuration, since apt-utils is not installed
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Merged Build-Depends: debhelper (>= 9), dh-exec, zlib1g-dev, libbz2-dev, help2man, asciidoctor, d-shlibs
Filtered Build-Depends: debhelper (>= 9), dh-exec, zlib1g-dev, libbz2-dev, help2man, asciidoctor, d-shlibs
dpkg-deb: building package 'sbuild-build-depends-kmc-dummy' in '/<<BUILDDIR>>/resolver-0oQe2F/apt_archive/sbuild-build-depends-kmc-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-0oQe2F/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-0oQe2F/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-0oQe2F/apt_archive ./ Release [2119 B]
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Get:3 file:/<<BUILDDIR>>/resolver-0oQe2F/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-0oQe2F/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-0oQe2F/apt_archive ./ Sources [248 B]
Get:5 file:/<<BUILDDIR>>/resolver-0oQe2F/apt_archive ./ Packages [565 B]
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+------------------------------------------------------------------------------+
| Install kmc 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 autotools-dev bsdmainutils ca-certificates d-shlibs debhelper
dh-exec dh-strip-nondeterminism file gettext gettext-base groff-base
help2man intltool-debian libarchive-zip-perl libbz2-dev libcroco3 libffi6
libfile-stripnondeterminism-perl libglib2.0-0 libicu55
liblocale-gettext-perl libmagic1 libpipeline1 libruby2.3 libssl1.0.2
libunistring0 libxml2 libyaml-0-2 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:
wamerican | wordlist whois vacation dh-make gettext-doc autopoint
libasprintf-dev libgettextpo-dev groff less www-browser libmail-box-perl ri
ruby-dev bundler
Recommended packages:
curl | wget | lynx-cur bzip2-doc libglib2.0-data shared-mime-info
xdg-user-dirs xml-core libmail-sendmail-perl zip fonts-lato libjs-jquery
The following NEW packages will be installed:
asciidoctor autotools-dev bsdmainutils ca-certificates d-shlibs debhelper
dh-exec dh-strip-nondeterminism file gettext gettext-base groff-base
help2man intltool-debian libarchive-zip-perl libbz2-dev libcroco3 libffi6
libfile-stripnondeterminism-perl libglib2.0-0 libicu55
liblocale-gettext-perl libmagic1 libpipeline1 libruby2.3 libssl1.0.2
libunistring0 libxml2 libyaml-0-2 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-kmc-dummy
zlib1g-dev
0 upgraded, 43 newly installed, 0 to remove and 75 not upgraded.
Need to get 22.0 MB/22.0 MB of archives.
After this operation, 77.7 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-0oQe2F/apt_archive ./ sbuild-build-depends-kmc-dummy 0.invalid.0 [808 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf liblocale-gettext-perl armhf 1.07-1+b1 [18.0 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-7 [1083 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.6 [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 libssl1.0.2 armhf 1.0.2g-1 [886 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.25-2 [250 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.25-2 [61.2 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.7-2 [111 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libicu55 armhf 55.1-7 [7380 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.3+dfsg1-1 [800 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf openssl armhf 1.0.2g-1 [666 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf ca-certificates all 20160104 [200 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf rubygems-integration all 1.10 [4882 B]
Get:18 http://172.17.0.1/private stretch-staging/main armhf rake all 10.5.0-2 [49.4 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf ruby-did-you-mean all 1.0.0-2 [11.2 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf ruby-minitest all 5.8.4-2 [50.3 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf ruby-net-telnet all 0.1.1-2 [12.5 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf ruby-power-assert all 0.2.7-1 [7578 B]
Get:23 http://172.17.0.1/private stretch-staging/main armhf ruby-test-unit all 3.1.7-2 [69.6 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libffi6 armhf 3.2.1-4 [18.5 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libruby2.3 armhf 2.3.0-4 [2833 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf ruby2.3 armhf 2.3.0-4 [167 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf ruby all 1:2.3.0+1 [10.2 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf asciidoctor all 1.5.4-1 [163 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20150820.1 [71.7 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf d-shlibs all 0.66 [16.8 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.46.2-3 [2482 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
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Get:34 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.56-2 [94.9 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.016-1 [6998 B]
Get:39 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160306 [815 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf help2man armhf 1.47.3 [154 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libbz2-dev armhf 1.0.6-8 [27.8 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf dh-exec armhf 0.23 [24.9 kB]
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update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
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Setting up libfile-stripnondeterminism-perl (0.016-1) ...
Setting up help2man (1.47.3) ...
Setting up libbz2-dev:armhf (1.0.6-8) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up rake (10.5.0-2) ...
Setting up libruby2.3:armhf (2.3.0-4) ...
Setting up dh-strip-nondeterminism (0.016-1) ...
Setting up debhelper (9.20160306) ...
Setting up dh-exec (0.23) ...
Setting up ruby2.3 (2.3.0-4) ...
Setting up ruby (1:2.3.0+1) ...
Setting up asciidoctor (1.5.4-1) ...
Setting up sbuild-build-depends-kmc-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.21-7) ...
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_2.26-3 dpkg-dev_1.18.4 g++-5_5.3.1-8+rpi1 gcc-5_5.3.1-8+rpi1 libc6-dev_2.21-7 libstdc++-4.9-dev_4.9.3-10 libstdc++-5-dev_5.3.1-8+rpi1 libstdc++6_5.3.1-8+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-3 adduser_3.113+nmu3 apt_1.2.3 asciidoctor_1.5.4-1 autotools-dev_20150820.1 base-files_9.5+rpi1 base-passwd_3.5.39 bash_4.3-14 binutils_2.26-3 bsdmainutils_9.0.6 bsdutils_1:2.27.1-3 build-essential_11.7 bzip2_1.0.6-8 ca-certificates_20160104 coreutils_8.24-1 cpio_2.11+dfsg-4.1 cpp_4:5.3.1-1+rpi1 cpp-5_5.3.1-8+rpi1 d-shlibs_0.66 dash_0.5.8-2.1 debconf_1.5.58 debfoster_2.7-2 debhelper_9.20160306 debianutils_4.7 dh-exec_0.23 dh-strip-nondeterminism_0.016-1 diffutils_1:3.3-3 dmsetup_2:1.02.115-2 dpkg_1.18.4 dpkg-dev_1.18.4 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.6.0+git+20160126-2 g++_4:5.3.1-1+rpi1 g++-5_5.3.1-8+rpi1 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_4.9.3-10 gcc-5_5.3.1-8+rpi1 gcc-5-base_5.3.1-8+rpi1 gettext_0.19.7-2 gettext-base_0.19.7-2 gnupg_1.4.20-1 gpgv_1.4.20-1 grep_2.22-1 groff-base_1.22.3-7 gzip_1.6-4 help2man_1.47.3 hostname_3.16 init_1.24 init-system-helpers_1.24 initramfs-tools_0.120 initscripts_2.88dsf-59.2 insserv_1.14.0-5.2 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-7+rpi1 kmod_22-1 libacl1_2.2.52-3 libapparmor1_2.10-3 libapt-pkg4.12_1.0.9.10 libapt-pkg5.0_1.2.3 libarchive-zip-perl_1.56-2 libasan1_4.9.3-10 libasan2_5.3.1-8+rpi1 libatomic1_5.3.1-8+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1 libaudit1_1:2.4.5-1 libblkid1_2.27.1-3 libbz2-1.0_1.0.6-8 libbz2-dev_1.0.6-8 libc-bin_2.21-7 libc-dev-bin_2.21-7 libc6_2.21-7 libc6-dev_2.21-7 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-8+rpi1 libcomerr2_1.42.13-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libdb5.3_5.3.28-11 libdbus-1-3_1.10.6-1 libdebconfclient0_0.204 libdevmapper1.02.1_2:1.02.115-2 libdpkg-perl_1.18.4 libdrm2_2.4.66-2 libfakeroot_1.20.2-1 libfdisk1_2.27.1-3 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.016-1 libgc1c2_1:7.4.2-7.3 libgcc-4.9-dev_4.9.3-10 libgcc-5-dev_5.3.1-8+rpi1 libgcc1_1:5.3.1-8+rpi1 libgcrypt20_1.6.4-5 libgdbm3_1.8.3-13.1 libglib2.0-0_2.46.2-3 libgmp10_2:6.1.0+dfsg-2 libgomp1_5.3.1-8+rpi1 libgpg-error0_1.21-1 libicu55_55.1-7 libisl15_0.16.1-1 libklibc_2.0.4-7+rpi1 libkmod2_22-1 liblocale-gettext-perl_1.07-1+b1 liblz4-1_0.0~r131-1 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.27.1-3 libmpc3_1.0.3-1 libmpfr4_3.1.3-2 libncurses5_6.0+20151024-2 libncursesw5_6.0+20151024-2 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_2:8.38-1 libperl5.22_5.22.1-5 libpipeline1_1.4.1-2 libpng12-0_1.2.54-1 libprocps3_2:3.3.9-9 libprocps5_2:3.3.11-3 libreadline6_6.3-8+b3 libruby2.3_2.3.0-4 libseccomp2_2.2.3-2 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libslang2_2.3.0-2+b1 libsmartcols1_2.27.1-3 libss2_1.42.13-1 libssl1.0.2_1.0.2g-1 libstdc++-4.9-dev_4.9.3-10 libstdc++-5-dev_5.3.1-8+rpi1 libstdc++6_5.3.1-8+rpi1 libsystemd0_228-6 libtimedate-perl_2.3000-2 libtinfo5_6.0+20151024-2 libubsan0_5.3.1-8+rpi1 libudev1_228-6 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-28 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-3 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 make_4.1-5 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.04-1 mawk_1.3.3-17 mount_2.27.1-3 multiarch-support_2.21-7 nano_2.5.1-1 ncurses-base_6.0+20151024-2 ncurses-bin_6.0+20151024-2 openssl_1.0.2g-1 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.1-5 perl-base_5.22.1-5 perl-modules-5.22_5.22.1-7 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+1 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_2.3.0-4 rubygems-integration_1.10 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_228-6 systemd-sysv_228-6 sysv-rc_2.88dsf-59.2 sysvinit-utils_2.88dsf-59.2 tar_1.28-2.1 tzdata_2016a-1 udev_228-6 util-linux_2.27.1-3 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 Thu Mar 10 22:22:19 2016 UTC using RSA key ID F09F4872
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./kmc_2.3+dfsg-3.dsc
dpkg-source: info: extracting kmc in kmc-2.3+dfsg
dpkg-source: info: unpacking kmc_2.3+dfsg.orig.tar.gz
dpkg-source: info: unpacking kmc_2.3+dfsg-3.debian.tar.xz
dpkg-source: info: applying disable-asmlib
dpkg-source: info: applying use-shared-libs
dpkg-source: info: applying hardening
dpkg-source: info: applying 0005-Add-static-library-target-to-makefile.patch
dpkg-source: info: applying 0007-Use-standard-compiler-environment-variables.patch
dpkg-source: info: applying spelling
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-2843213c-8f81-4e82-942a-c3a506ff263f
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: source package kmc
dpkg-buildpackage: source version 2.3+dfsg-3
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build kmc-2.3+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>>/kmc-2.3+dfsg'
rm -rf /<<BUILDDIR>>/kmc-2.3+dfsg/debian/man_src/*.html /<<BUILDDIR>>/kmc-2.3+dfsg/debian/man_src/*.?
rm -rf /<<BUILDDIR>>/kmc-2.3+dfsg/debian/man
dh_auto_clean --
make -j4 clean
make[2]: Entering directory '/<<BUILDDIR>>/kmc-2.3+dfsg'
makefile:56: target 'kmc_api/mmer.o' given more than once in the same rule
rm kmer_counter/*.o
rm: cannot remove 'kmer_counter/*.o': No such file or directory
makefile:80: recipe for target 'clean' failed
make[2]: [clean] Error 1 (ignored)
rm kmc_api/*.o
rm: cannot remove 'kmc_api/*.o': No such file or directory
makefile:80: recipe for target 'clean' failed
make[2]: [clean] Error 1 (ignored)
rm kmc_dump/*.o
rm: cannot remove 'kmc_dump/*.o': No such file or directory
makefile:80: recipe for target 'clean' failed
make[2]: [clean] Error 1 (ignored)
rm kmc_tools/*.o
rm: cannot remove 'kmc_tools/*.o': No such file or directory
makefile:80: recipe for target 'clean' failed
make[2]: [clean] Error 1 (ignored)
rm -rf bin
rm -f libkmc.a
make[2]: Leaving directory '/<<BUILDDIR>>/kmc-2.3+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/kmc-2.3+dfsg'
dh_clean -O--parallel
rm -f debian/debhelper-build-stamp
rm -f debian/kmc.substvars
rm -f debian/kmc.*.debhelper
rm -rf debian/kmc/
rm -f debian/libkmc-dev.substvars
rm -f debian/libkmc-dev.*.debhelper
rm -rf debian/libkmc-dev/
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 --parallel
dh_testdir -a -O--parallel
dh_update_autotools_config -a -O--parallel
dh_auto_configure -a -O--parallel
dh_auto_build -a -O--parallel
make -j4
make[1]: Entering directory '/<<BUILDDIR>>/kmc-2.3+dfsg'
makefile:56: target 'kmc_api/mmer.o' given more than once in the same rule
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -c kmer_counter/kmer_counter.cpp -o kmer_counter/kmer_counter.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -c kmer_counter/mmer.cpp -o kmer_counter/mmer.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -c kmer_counter/mem_disk_file.cpp -o kmer_counter/mem_disk_file.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -c kmer_counter/rev_byte.cpp -o kmer_counter/rev_byte.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -c kmer_counter/bkb_writer.cpp -o kmer_counter/bkb_writer.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -c kmer_counter/bkb_reader.cpp -o kmer_counter/bkb_reader.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -c kmer_counter/fastq_reader.cpp -o kmer_counter/fastq_reader.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -c kmer_counter/timer.cpp -o kmer_counter/timer.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -c kmer_counter/radix.cpp -o kmer_counter/radix.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -c kmer_counter/kb_completer.cpp -o kmer_counter/kb_completer.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -c kmer_counter/kb_storer.cpp -o kmer_counter/kb_storer.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -c kmer_counter/kmer.cpp -o kmer_counter/kmer.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -c kmer_counter/prob_qual.cpp -o kmer_counter/prob_qual.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -c kmc_dump/nc_utils.cpp -o kmc_dump/nc_utils.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -c kmc_api/mmer.cpp -o kmc_api/mmer.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -c kmc_dump/kmc_dump.cpp -o kmc_dump/kmc_dump.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -c kmc_api/kmc_file.cpp -o kmc_api/kmc_file.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -c kmc_api/kmer_api.cpp -o kmc_api/kmer_api.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -Wall -O3 -fopenmp -std=c++14 -c kmc_tools/kmc_header.cpp -o kmc_tools/kmc_header.o
kmc_api/kmc_file.cpp: In member function 'bool CKMCFile::BinarySearch(int64, int64, const CKmerAPI&, uint64&, uint32)':
kmc_api/kmc_file.cpp:1360:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (index_start >= total_kmers)
^
kmc_api/kmc_file.cpp: In member function 'void CKMCFile::Reload_sufix_file_buf()':
kmc_api/kmc_file.cpp:607:57: 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:653:58: 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);
^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -Wall -O3 -fopenmp -std=c++14 -c kmc_tools/kmc_tools.cpp -o kmc_tools/kmc_tools.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -Wall -O3 -fopenmp -std=c++14 -c kmc_tools/nc_utils.cpp -o kmc_tools/nc_utils.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -Wall -O3 -fopenmp -std=c++14 -c kmc_tools/parameters_parser.cpp -o kmc_tools/parameters_parser.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -Wall -O3 -fopenmp -std=c++14 -c kmc_tools/parser.cpp -o kmc_tools/parser.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -Wall -O3 -fopenmp -std=c++14 -c kmc_tools/tokenizer.cpp -o kmc_tools/tokenizer.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -Wall -O3 -fopenmp -std=c++14 -c kmc_tools/fastq_filter.cpp -o kmc_tools/fastq_filter.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -Wall -O3 -fopenmp -std=c++14 -c kmc_tools/fastq_reader.cpp -o kmc_tools/fastq_reader.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -Wall -O3 -fopenmp -std=c++14 -c kmc_tools/fastq_writer.cpp -o kmc_tools/fastq_writer.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DDISABLE_ASMLIB -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -fopenmp -std=c++11 -Wall -O3 -fopenmp -std=c++14 -c kmc_tools/percent_progress.cpp -o kmc_tools/percent_progress.o
ar rcs libkmc.a kmc_api/mmer.o kmc_api/kmc_file.o kmc_api/kmer_api.o
ranlib libkmc.a
mkdir -p bin
g++ -Wl,-z,relro -lm -lz -lbz2 -fopenmp -lpthread -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
mkdir -p bin
g++ -Wl,-z,relro -lm -lz -lbz2 -fopenmp -lpthread -o bin/kmc_tools kmc_tools/kmc_header.o kmc_tools/kmc_tools.o kmc_tools/nc_utils.o kmc_tools/parameters_parser.o kmc_tools/parser.o kmc_tools/tokenizer.o kmc_tools/fastq_filter.o kmc_tools/fastq_reader.o kmc_tools/fastq_writer.o kmc_tools/percent_progress.o kmc_api/mmer.o kmc_api/kmc_file.o kmc_api/kmer_api.o
mkdir -p bin
g++ -Wl,-z,relro -lm -lz -lbz2 -fopenmp -lpthread -o bin/kmc kmer_counter/kmer_counter.o kmer_counter/mmer.o kmer_counter/mem_disk_file.o kmer_counter/rev_byte.o kmer_counter/bkb_writer.o kmer_counter/bkb_reader.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 kmer_counter/prob_qual.o
make[1]: Leaving directory '/<<BUILDDIR>>/kmc-2.3+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
rm -f debian/kmc.substvars
rm -f debian/kmc.*.debhelper
rm -rf debian/kmc/
rm -f debian/libkmc-dev.substvars
rm -f debian/libkmc-dev.*.debhelper
rm -rf debian/libkmc-dev/
dh_auto_install -a -O--parallel
install -d debian/kmc
install -d debian/libkmc-dev
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/kmc-2.3+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/
cp --reflink=auto -a ./bin/kmc_tools debian/kmc//bin/
install -d debian/libkmc-dev/usr/include/kmc
cp --reflink=auto -a ./kmc_api/kmc_file.h debian/libkmc-dev/usr/include/kmc/
cp --reflink=auto -a ./kmc_api/kmer_api.h debian/libkmc-dev/usr/include/kmc/
cp --reflink=auto -a ./kmc_api/kmer_defs.h debian/libkmc-dev/usr/include/kmc/
cp --reflink=auto -a ./kmc_api/mmer.h debian/libkmc-dev/usr/include/kmc/
cp --reflink=auto -a ./kmc_api/stdafx.h debian/libkmc-dev/usr/include/kmc/
install -d debian/libkmc-dev/usr/lib/arm-linux-gnueabihf
cp --reflink=auto -a ./libkmc.a debian/libkmc-dev/usr/lib/arm-linux-gnueabihf/
make[1]: Leaving directory '/<<BUILDDIR>>/kmc-2.3+dfsg'
dh_installdocs -a -O--parallel
install -d debian/kmc/usr/share/doc/kmc
install -p -m0644 debian/copyright debian/kmc/usr/share/doc/kmc/copyright
install -d debian/libkmc-dev/usr/share/doc/libkmc-dev
install -p -m0644 debian/copyright debian/libkmc-dev/usr/share/doc/libkmc-dev/copyright
dh_installchangelogs -a -O--parallel
install -p -m0644 debian/changelog debian/kmc/usr/share/doc/kmc/changelog.Debian
install -p -m0644 debian/changelog debian/libkmc-dev/usr/share/doc/libkmc-dev/changelog.Debian
debian/rules override_dh_installman
make[1]: Entering directory '/<<BUILDDIR>>/kmc-2.3+dfsg'
mkdir -p /<<BUILDDIR>>/kmc-2.3+dfsg/debian/man
/<<BUILDDIR>>/kmc-2.3+dfsg/debian/usage_to_man
Can't exec "1": No such file or directory at /<<BUILDDIR>>/kmc-2.3+dfsg/debian/usage_to_man line 19.
Creating manpages
Manpage creation complete
Manpage creation complete
asciidoctor -a docdate='' -b manpage /<<BUILDDIR>>/kmc-2.3+dfsg/debian/man_src/*.adoc
cp /<<BUILDDIR>>/kmc-2.3+dfsg/debian/man_src/*.? /<<BUILDDIR>>/kmc-2.3+dfsg/debian/man
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
install -p -m0644 debian/man/kmc_tools-compact.1 debian/kmc/usr/share/man/man1/kmc_tools-compact.1
install -p -m0644 debian/man/kmc_tools-complex.1 debian/kmc/usr/share/man/man1/kmc_tools-complex.1
install -p -m0644 debian/man/kmc_tools-counters_subtract.1 debian/kmc/usr/share/man/man1/kmc_tools-counters_subtract.1
install -p -m0644 debian/man/kmc_tools-dump.1 debian/kmc/usr/share/man/man1/kmc_tools-dump.1
install -p -m0644 debian/man/kmc_tools-filter.1 debian/kmc/usr/share/man/man1/kmc_tools-filter.1
install -p -m0644 debian/man/kmc_tools-histogram.1 debian/kmc/usr/share/man/man1/kmc_tools-histogram.1
install -p -m0644 debian/man/kmc_tools-intersect.1 debian/kmc/usr/share/man/man1/kmc_tools-intersect.1
install -p -m0644 debian/man/kmc_tools-kmers_subtract.1 debian/kmc/usr/share/man/man1/kmc_tools-kmers_subtract.1
install -p -m0644 debian/man/kmc_tools-sort.1 debian/kmc/usr/share/man/man1/kmc_tools-sort.1
install -p -m0644 debian/man/kmc_tools-union.1 debian/kmc/usr/share/man/man1/kmc_tools-union.1
install -p -m0644 debian/man/kmc_tools.1 debian/kmc/usr/share/man/man1/kmc_tools.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
man --recode UTF-8 ./kmc_tools\-compact\.1 > kmc_tools\-compact\.1\.new
chmod 644 kmc_tools-compact.1.new
mv -f kmc_tools-compact.1.new kmc_tools-compact.1
man --recode UTF-8 ./kmc_tools\-complex\.1 > kmc_tools\-complex\.1\.new
chmod 644 kmc_tools-complex.1.new
mv -f kmc_tools-complex.1.new kmc_tools-complex.1
man --recode UTF-8 ./kmc_tools\-counters_subtract\.1 > kmc_tools\-counters_subtract\.1\.new
chmod 644 kmc_tools-counters_subtract.1.new
mv -f kmc_tools-counters_subtract.1.new kmc_tools-counters_subtract.1
man --recode UTF-8 ./kmc_tools\-dump\.1 > kmc_tools\-dump\.1\.new
chmod 644 kmc_tools-dump.1.new
mv -f kmc_tools-dump.1.new kmc_tools-dump.1
man --recode UTF-8 ./kmc_tools\-filter\.1 > kmc_tools\-filter\.1\.new
chmod 644 kmc_tools-filter.1.new
mv -f kmc_tools-filter.1.new kmc_tools-filter.1
man --recode UTF-8 ./kmc_tools\-histogram\.1 > kmc_tools\-histogram\.1\.new
chmod 644 kmc_tools-histogram.1.new
mv -f kmc_tools-histogram.1.new kmc_tools-histogram.1
man --recode UTF-8 ./kmc_tools\-intersect\.1 > kmc_tools\-intersect\.1\.new
chmod 644 kmc_tools-intersect.1.new
mv -f kmc_tools-intersect.1.new kmc_tools-intersect.1
man --recode UTF-8 ./kmc_tools\-kmers_subtract\.1 > kmc_tools\-kmers_subtract\.1\.new
chmod 644 kmc_tools-kmers_subtract.1.new
mv -f kmc_tools-kmers_subtract.1.new kmc_tools-kmers_subtract.1
man --recode UTF-8 ./kmc_tools\-sort\.1 > kmc_tools\-sort\.1\.new
chmod 644 kmc_tools-sort.1.new
mv -f kmc_tools-sort.1.new kmc_tools-sort.1
man --recode UTF-8 ./kmc_tools\-union\.1 > kmc_tools\-union\.1\.new
chmod 644 kmc_tools-union.1.new
mv -f kmc_tools-union.1.new kmc_tools-union.1
man --recode UTF-8 ./kmc_tools\.1 > kmc_tools\.1\.new
chmod 644 kmc_tools.1.new
mv -f kmc_tools.1.new kmc_tools.1
make[1]: Leaving directory '/<<BUILDDIR>>/kmc-2.3+dfsg'
dh_perl -a -O--parallel
dh_link -a -O--parallel
dh_strip_nondeterminism -a -O--parallel
dh_compress -a -O--parallel
cd debian/kmc
chmod a-x usr/share/doc/kmc/changelog.Debian usr/share/man/man1/kmc.1 usr/share/man/man1/kmc_dump.1 usr/share/man/man1/kmc_tools-compact.1 usr/share/man/man1/kmc_tools-complex.1 usr/share/man/man1/kmc_tools-counters_subtract.1 usr/share/man/man1/kmc_tools-dump.1 usr/share/man/man1/kmc_tools-filter.1 usr/share/man/man1/kmc_tools-histogram.1 usr/share/man/man1/kmc_tools-intersect.1 usr/share/man/man1/kmc_tools-kmers_subtract.1 usr/share/man/man1/kmc_tools-sort.1 usr/share/man/man1/kmc_tools-union.1 usr/share/man/man1/kmc_tools.1
gzip -9nf usr/share/doc/kmc/changelog.Debian usr/share/man/man1/kmc.1 usr/share/man/man1/kmc_dump.1 usr/share/man/man1/kmc_tools-compact.1 usr/share/man/man1/kmc_tools-complex.1 usr/share/man/man1/kmc_tools-counters_subtract.1 usr/share/man/man1/kmc_tools-dump.1 usr/share/man/man1/kmc_tools-filter.1 usr/share/man/man1/kmc_tools-histogram.1 usr/share/man/man1/kmc_tools-intersect.1 usr/share/man/man1/kmc_tools-kmers_subtract.1 usr/share/man/man1/kmc_tools-sort.1 usr/share/man/man1/kmc_tools-union.1 usr/share/man/man1/kmc_tools.1
cd '/<<BUILDDIR>>/kmc-2.3+dfsg'
cd debian/libkmc-dev
chmod a-x usr/share/doc/libkmc-dev/changelog.Debian
gzip -9nf usr/share/doc/libkmc-dev/changelog.Debian
cd '/<<BUILDDIR>>/kmc-2.3+dfsg'
dh_fixperms -a -O--parallel
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/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/usr/lib/arm-linux-gnueabihf/perl5/5.22 debian/kmc/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
find debian/kmc -perm -5 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
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
find debian/libkmc-dev -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
find debian/libkmc-dev ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/libkmc-dev/usr/share/doc -type f ! -regex 'debian/libkmc-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libkmc-dev/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 0755
find debian/libkmc-dev/usr/share/man debian/libkmc-dev/usr/man/ debian/libkmc-dev/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libkmc-dev/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libkmc-dev/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libkmc-dev/usr/lib/arm-linux-gnueabihf/perl5/5.22 debian/libkmc-dev/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
find debian/libkmc-dev -perm -5 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libkmc-dev/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
dh_strip -a -O--parallel
install -d debian/.debhelper/kmc/dbgsym-root/usr/lib/debug/.build-id/f3
objcopy --only-keep-debug --compress-debug-sections debian/kmc/bin/kmc debian/.debhelper/kmc/dbgsym-root/usr/lib/debug/.build-id/f3/26785d383b3e9e1fcb7a34b8aecea8b794c437.debug
chmod 0644 debian/.debhelper/kmc/dbgsym-root/usr/lib/debug/.build-id/f3/26785d383b3e9e1fcb7a34b8aecea8b794c437.debug
strip --remove-section=.comment --remove-section=.note debian/kmc/bin/kmc
objcopy --add-gnu-debuglink debian/.debhelper/kmc/dbgsym-root/usr/lib/debug/.build-id/f3/26785d383b3e9e1fcb7a34b8aecea8b794c437.debug debian/kmc/bin/kmc
install -d debian/.debhelper/kmc/dbgsym-root/usr/lib/debug/.build-id/2d
objcopy --only-keep-debug --compress-debug-sections debian/kmc/bin/kmc_dump debian/.debhelper/kmc/dbgsym-root/usr/lib/debug/.build-id/2d/1a3efd1f0c0d0ec2fc39431665ec6fe66a431c.debug
chmod 0644 debian/.debhelper/kmc/dbgsym-root/usr/lib/debug/.build-id/2d/1a3efd1f0c0d0ec2fc39431665ec6fe66a431c.debug
strip --remove-section=.comment --remove-section=.note debian/kmc/bin/kmc_dump
objcopy --add-gnu-debuglink debian/.debhelper/kmc/dbgsym-root/usr/lib/debug/.build-id/2d/1a3efd1f0c0d0ec2fc39431665ec6fe66a431c.debug debian/kmc/bin/kmc_dump
install -d debian/.debhelper/kmc/dbgsym-root/usr/lib/debug/.build-id/a7
objcopy --only-keep-debug --compress-debug-sections debian/kmc/bin/kmc_tools debian/.debhelper/kmc/dbgsym-root/usr/lib/debug/.build-id/a7/18e71e5bc5fa2fd47d750fcf0a37e00ca88f19.debug
chmod 0644 debian/.debhelper/kmc/dbgsym-root/usr/lib/debug/.build-id/a7/18e71e5bc5fa2fd47d750fcf0a37e00ca88f19.debug
strip --remove-section=.comment --remove-section=.note debian/kmc/bin/kmc_tools
objcopy --add-gnu-debuglink debian/.debhelper/kmc/dbgsym-root/usr/lib/debug/.build-id/a7/18e71e5bc5fa2fd47d750fcf0a37e00ca88f19.debug debian/kmc/bin/kmc_tools
install -d debian/.debhelper/kmc/dbgsym-root/usr/share/doc
ln -s kmc debian/.debhelper/kmc/dbgsym-root/usr/share/doc/kmc-dbgsym
strip --strip-debug --remove-section=.comment --remove-section=.note --enable-deterministic-archives debian/libkmc-dev/usr/lib/arm-linux-gnueabihf/libkmc.a
dh_makeshlibs -a -O--parallel
rm -f debian/kmc/DEBIAN/shlibs
rm -f debian/libkmc-dev/DEBIAN/shlibs
dh_shlibdeps -a -O--parallel
install -d debian/kmc/DEBIAN
dpkg-shlibdeps -Tdebian/kmc.substvars debian/kmc/bin/kmc debian/kmc/bin/kmc_dump debian/kmc/bin/kmc_tools
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
dpkg-shlibdeps: warning: debian/kmc/bin/kmc_tools contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/kmc/bin/kmc debian/kmc/bin/kmc_dump debian/kmc/bin/kmc_tools were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
install -d debian/libkmc-dev/DEBIAN
dh_installdeb -a -O--parallel
dh_gencontrol -a -O--parallel
echo misc:Depends= >> debian/kmc.substvars
echo misc:Pre-Depends= >> debian/kmc.substvars
install -d debian/.debhelper/kmc/dbgsym-root/DEBIAN
dpkg-gencontrol -pkmc -ldebian/changelog -Tdebian/kmc.substvars -Pdebian/.debhelper/kmc/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=extra -DAuto-Built-Package=debug-symbols -DPackage=kmc-dbgsym "-DDepends=kmc (= \${binary:Version})" "-DDescription=Debug symbols for kmc" "-DBuild-Ids=2d1a3efd1f0c0d0ec2fc39431665ec6fe66a431c a718e71e5bc5fa2fd47d750fcf0a37e00ca88f19 f326785d383b3e9e1fcb7a34b8aecea8b794c437" -DSection=debug -UMulti-Arch -UReplaces -UBreaks
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
chmod 0644 debian/.debhelper/kmc/dbgsym-root/DEBIAN/control
chown 0:0 debian/.debhelper/kmc/dbgsym-root/DEBIAN/control
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
echo misc:Depends= >> debian/libkmc-dev.substvars
echo misc:Pre-Depends= >> debian/libkmc-dev.substvars
dpkg-gencontrol -plibkmc-dev -ldebian/changelog -Tdebian/libkmc-dev.substvars -Pdebian/libkmc-dev
dpkg-gencontrol: warning: Depends field of package libkmc-dev: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
chmod 0644 debian/libkmc-dev/DEBIAN/control
chown 0:0 debian/libkmc-dev/DEBIAN/control
dh_md5sums -a -O--parallel
(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
(cd debian/.debhelper/kmc/dbgsym-root >/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/.debhelper/kmc/dbgsym-root/DEBIAN/md5sums
chown 0:0 debian/.debhelper/kmc/dbgsym-root/DEBIAN/md5sums
(cd debian/libkmc-dev >/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/libkmc-dev/DEBIAN/md5sums
chown 0:0 debian/libkmc-dev/DEBIAN/md5sums
dh_builddeb -a -O--parallel
dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/kmc/dbgsym-root ..
dpkg-deb --build debian/libkmc-dev ..
dpkg-deb: building package 'kmc-dbgsym' in '../kmc-dbgsym_2.3+dfsg-3_armhf.deb'.
dpkg-deb: building package 'libkmc-dev' in '../libkmc-dev_2.3+dfsg-3_armhf.deb'.
dpkg-deb --build debian/kmc ..
dpkg-deb: building package 'kmc' in '../kmc_2.3+dfsg-3_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../kmc_2.3+dfsg-3_armhf.changes
dpkg-genchanges: warning: package kmc-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 kmc-2.3+dfsg
dpkg-buildpackage: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160316-0519
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
kmc_2.3+dfsg-3_armhf.changes:
-----------------------------
Format: 1.8
Date: Thu, 10 Mar 2016 22:02:44 +0000
Source: kmc
Binary: kmc libkmc-dev
Architecture: armhf
Version: 2.3+dfsg-3
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Sascha Steinbiss <sascha@steinbiss.name>
Description:
kmc - count kmers in genomic sequences
libkmc-dev - library to access KMC k-mer count files
Changes:
kmc (2.3+dfsg-3) unstable; urgency=medium
.
* Switch to asciidoctor for reproducible man page building.
* Prevent strange FTBFS on some platforms caused by ronn.
Checksums-Sha1:
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244a75181dc9dcd36957fe3743f3df6b7cf9687e 436478 kmc_2.3+dfsg-3_armhf.deb
e9fa4dad10228f1fc70459a9b0c57210fe612bd4 25172 libkmc-dev_2.3+dfsg-3_armhf.deb
Checksums-Sha256:
8cfc584c86b9f363643fefa74395b22376b71b281f41cb2bbdc5ba299140d3fe 8104794 kmc-dbgsym_2.3+dfsg-3_armhf.deb
8b9bff1846ad22bbdcde95537f06361efd9bd2a8012425982e36010bd54e390e 436478 kmc_2.3+dfsg-3_armhf.deb
82285120aeea9a4df5ae0b967342cd4aae91f0aece7e69364ebe62188e8ebae2 25172 libkmc-dev_2.3+dfsg-3_armhf.deb
Files:
a81e4fbdbbf443a9aa209f4197af0eb8 8104794 debug extra kmc-dbgsym_2.3+dfsg-3_armhf.deb
5e73b2e7f8f22488885bc74554b38235 436478 science optional kmc_2.3+dfsg-3_armhf.deb
273193e1e425a71be808053f21072d3d 25172 libdevel optional libkmc-dev_2.3+dfsg-3_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
kmc-dbgsym_2.3+dfsg-3_armhf.deb
-------------------------------
new debian package, version 2.0.
size 8104794 bytes: control archive=602 bytes.
478 bytes, 13 lines control
318 bytes, 3 lines md5sums
Package: kmc-dbgsym
Source: kmc
Version: 2.3+dfsg-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 9010
Depends: kmc (= 2.3+dfsg-3)
Section: debug
Priority: extra
Homepage: http://sun.aei.polsl.pl/kmc
Description: Debug symbols for kmc
Auto-Built-Package: debug-symbols
Build-Ids: 2d1a3efd1f0c0d0ec2fc39431665ec6fe66a431c a718e71e5bc5fa2fd47d750fcf0a37e00ca88f19 f326785d383b3e9e1fcb7a34b8aecea8b794c437
drwxr-xr-x root/root 0 2016-03-16 05:18 ./
drwxr-xr-x root/root 0 2016-03-16 05:18 ./usr/
drwxr-xr-x root/root 0 2016-03-16 05:18 ./usr/lib/
drwxr-xr-x root/root 0 2016-03-16 05:18 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-03-16 05:18 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-03-16 05:18 ./usr/lib/debug/.build-id/2d/
-rw-r--r-- root/root 158360 2016-03-16 05:18 ./usr/lib/debug/.build-id/2d/1a3efd1f0c0d0ec2fc39431665ec6fe66a431c.debug
drwxr-xr-x root/root 0 2016-03-16 05:18 ./usr/lib/debug/.build-id/a7/
-rw-r--r-- root/root 3464100 2016-03-16 05:18 ./usr/lib/debug/.build-id/a7/18e71e5bc5fa2fd47d750fcf0a37e00ca88f19.debug
drwxr-xr-x root/root 0 2016-03-16 05:18 ./usr/lib/debug/.build-id/f3/
-rw-r--r-- root/root 5590080 2016-03-16 05:18 ./usr/lib/debug/.build-id/f3/26785d383b3e9e1fcb7a34b8aecea8b794c437.debug
drwxr-xr-x root/root 0 2016-03-16 05:18 ./usr/share/
drwxr-xr-x root/root 0 2016-03-16 05:18 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-03-16 05:18 ./usr/share/doc/kmc-dbgsym -> kmc
kmc_2.3+dfsg-3_armhf.deb
------------------------
new debian package, version 2.0.
size 436478 bytes: control archive=1641 bytes.
1610 bytes, 31 lines control
1240 bytes, 18 lines md5sums
Package: kmc
Version: 2.3+dfsg-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1981
Depends: libbz2-1.0, libc6 (>= 2.4), libgcc1 (>= 1:3.5), libgomp1 (>= 4.9), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.6)
Section: science
Priority: optional
Homepage: http://sun.aei.polsl.pl/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 sequencing.
Unfortunately, sequencing errors (frequent in practice)
result 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 on high-end servers (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 2016-03-16 05:18 ./
drwxr-xr-x root/root 0 2016-03-16 05:18 ./bin/
-rwxr-xr-x root/root 1338936 2016-03-16 05:18 ./bin/kmc
-rwxr-xr-x root/root 42976 2016-03-16 05:18 ./bin/kmc_dump
-rwxr-xr-x root/root 617328 2016-03-16 05:18 ./bin/kmc_tools
drwxr-xr-x root/root 0 2016-03-16 05:17 ./usr/
drwxr-xr-x root/root 0 2016-03-16 05:17 ./usr/share/
drwxr-xr-x root/root 0 2016-03-16 05:17 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-03-16 05:18 ./usr/share/doc/kmc/
-rw-r--r-- root/root 679 2016-03-10 22:04 ./usr/share/doc/kmc/changelog.Debian.gz
-rw-r--r-- root/root 1210 2015-12-22 22:42 ./usr/share/doc/kmc/copyright
drwxr-xr-x root/root 0 2016-03-16 05:17 ./usr/share/man/
drwxr-xr-x root/root 0 2016-03-16 05:18 ./usr/share/man/man1/
-rw-r--r-- root/root 1132 2016-03-16 05:17 ./usr/share/man/man1/kmc.1.gz
-rw-r--r-- root/root 611 2016-03-16 05:17 ./usr/share/man/man1/kmc_dump.1.gz
-rw-r--r-- root/root 815 2016-03-16 05:17 ./usr/share/man/man1/kmc_tools-compact.1.gz
-rw-r--r-- root/root 1293 2016-03-16 05:17 ./usr/share/man/man1/kmc_tools-complex.1.gz
-rw-r--r-- root/root 991 2016-03-16 05:17 ./usr/share/man/man1/kmc_tools-counters_subtract.1.gz
-rw-r--r-- root/root 839 2016-03-16 05:17 ./usr/share/man/man1/kmc_tools-dump.1.gz
-rw-r--r-- root/root 1006 2016-03-16 05:17 ./usr/share/man/man1/kmc_tools-filter.1.gz
-rw-r--r-- root/root 805 2016-03-16 05:17 ./usr/share/man/man1/kmc_tools-histogram.1.gz
-rw-r--r-- root/root 951 2016-03-16 05:17 ./usr/share/man/man1/kmc_tools-intersect.1.gz
-rw-r--r-- root/root 952 2016-03-16 05:17 ./usr/share/man/man1/kmc_tools-kmers_subtract.1.gz
-rw-r--r-- root/root 863 2016-03-16 05:17 ./usr/share/man/man1/kmc_tools-sort.1.gz
-rw-r--r-- root/root 930 2016-03-16 05:17 ./usr/share/man/man1/kmc_tools-union.1.gz
-rw-r--r-- root/root 1181 2016-03-16 05:17 ./usr/share/man/man1/kmc_tools.1.gz
libkmc-dev_2.3+dfsg-3_armhf.deb
-------------------------------
new debian package, version 2.0.
size 25172 bytes: control archive=851 bytes.
614 bytes, 17 lines control
519 bytes, 8 lines md5sums
Package: libkmc-dev
Source: kmc
Version: 2.3+dfsg-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 92
Section: libdevel
Priority: optional
Homepage: http://sun.aei.polsl.pl/kmc
Description: library to access KMC k-mer count files
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.
.
This package contains the C++ library headers for accessing kmc's output
file format.
drwxr-xr-x root/root 0 2016-03-16 05:18 ./
drwxr-xr-x root/root 0 2016-03-16 05:17 ./usr/
drwxr-xr-x root/root 0 2016-03-16 05:17 ./usr/include/
drwxr-xr-x root/root 0 2016-03-16 05:17 ./usr/include/kmc/
-rw-r--r-- root/root 5781 2015-09-10 15:25 ./usr/include/kmc/kmc_file.h
-rw-r--r-- root/root 18341 2015-09-10 15:25 ./usr/include/kmc/kmer_api.h
-rw-r--r-- root/root 1022 2015-09-10 15:25 ./usr/include/kmc/kmer_defs.h
-rw-r--r-- root/root 4163 2015-09-10 15:25 ./usr/include/kmc/mmer.h
-rw-r--r-- root/root 85 2015-09-10 15:25 ./usr/include/kmc/stdafx.h
drwxr-xr-x root/root 0 2016-03-16 05:17 ./usr/lib/
drwxr-xr-x root/root 0 2016-03-16 05:18 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 48336 2016-03-16 05:18 ./usr/lib/arm-linux-gnueabihf/libkmc.a
drwxr-xr-x root/root 0 2016-03-16 05:17 ./usr/share/
drwxr-xr-x root/root 0 2016-03-16 05:17 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-03-16 05:18 ./usr/share/doc/libkmc-dev/
-rw-r--r-- root/root 679 2016-03-10 22:04 ./usr/share/doc/libkmc-dev/changelog.Debian.gz
-rw-r--r-- root/root 1210 2015-12-22 22:42 ./usr/share/doc/libkmc-dev/copyright
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 103384
Build-Time: 1201
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 284
Job: kmc_2.3+dfsg-3
Machine Architecture: armhf
Package: kmc
Package-Time: 1526
Source-Version: 2.3+dfsg-3
Space: 103384
Status: successful
Version: 2.3+dfsg-3
--------------------------------------------------------------------------------
Finished at 20160316-0519
Build needed 00:25:26, 103384k disc space