[Debian-med-packaging] Bug#789880: murasaki: FTBFS on mipsel "debian/rules:24: recipe for target 'override_dh_installman' failed"
Gustavo Prado Alkmim
alkmim at ic.unicamp.br
Thu Jun 25 04:24:24 UTC 2015
Package: murasaki
Version: 1.68.6-1
Severity: serious
Justification: fails to build from source (but built successfully in the past)
Dear Maintainer,
Package is failing to build on buildd. I'm working on a fix and I will attach it as soon as possible. Full log is attached.
Build Log tail:
dh_installman
# create manpages for PL files
mkdir -p debian/murasaki-common/usr/share/man/man1
for pscript in debian/murasaki-common/usr/lib/debian-med/bin/* ; do \
pod2man ${pscript} > debian/murasaki-common/usr/share/man/man1/`basename ${pscript}`.1 ; \
done
Can't open debian/murasaki-common/usr/lib/debian-med/bin/*: No such file or directory at /usr/bin/pod2man line 71.
make[1]: *** [override_dh_installman] Error 2
debian/rules:24: recipe for target 'override_dh_installman' failed
make[1]: Leaving directory '/«PKGBUILDDIR»'
make: *** [binary-arch] Error 2
debian/rules:13: recipe for target 'binary-arch' failed
dpkg-buildpackage: error: fakeroot debian/rules binary-arch gave error exit status 2
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sbuild (Debian sbuild) 0.64.0 (17 May 2013) on mipsel-manda-02.debian.org
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� murasaki 1.68.6-1 (mipsel) 22 Jun 2015 15:38 �
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Package: murasaki
Version: 1.68.6-1
Source Version: 1.68.6-1
Distribution: sid
Machine Architecture: mipsel
Host Architecture: mipsel
Build Architecture: mipsel
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I: NOTICE: Log filtering will replace 'build/murasaki-FaaXSQ/murasaki-1.68.6' with '�PKGBUILDDIR�'
I: NOTICE: Log filtering will replace 'build/murasaki-FaaXSQ' with '�BUILDDIR�'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-mipsel-sbuild-4a4978e5-063f-4ea4-add2-46ac86e5f19f' with '�CHROOT�'
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� Update chroot �
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Get:1 http://debian.netcologne.de unstable InRelease [204 kB]
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Get:18 http://ftp.debian.org unstable/contrib mipsel Packages [42.7 kB]
Fetched 31.4 MB in 47s (657 kB/s)
Reading package lists...
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� Fetch source files �
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Check APT
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Checking available source versions...
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Download source files with APT
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Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'murasaki' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/murasaki/trunk/
Need to get 316 kB of source archives.
Get:1 http://ftp.debian.org/debian/ unstable/main murasaki 1.68.6-1 (dsc) [2244 B]
Get:2 http://ftp.debian.org/debian/ unstable/main murasaki 1.68.6-1 (tar) [308 kB]
Get:3 http://ftp.debian.org/debian/ unstable/main murasaki 1.68.6-1 (diff) [5680 B]
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Download complete and in download only mode
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
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dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/�BUILDDIR�/resolver-zsmmRY/apt_archive/sbuild-build-depends-core-dummy.deb'.
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OK
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Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), libboost-regex-dev, libboost-iostreams-dev, libboost-filesystem-dev, libterm-readkey-perl, libtext-wrapper-perl, libcrypto++-dev, libpstreams-dev, libopenmpi-dev
Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), libboost-regex-dev, libboost-iostreams-dev, libboost-filesystem-dev, libterm-readkey-perl, libtext-wrapper-perl, libcrypto++-dev, libpstreams-dev, libopenmpi-dev
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dpkg-deb: building package `sbuild-build-depends-murasaki-dummy' in `/�BUILDDIR�/resolver-ZJAlNW/apt_archive/sbuild-build-depends-murasaki-dummy.deb'.
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OK
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W: line 16 [wheezy-backports-sloppy-mipsel-sbuild] aliases: Alias �stable-backports-mipsel-sbuild� already associated with �unknown� chroot
W: line 16 [wheezy-backports-sloppy-mipsel-sbuild] aliases: Alias �stable-backports-mipsel-sbuild� already associated with �unknown� chroot
W: line 16 [wheezy-backports-sloppy-mipsel-sbuild] aliases: Alias �stable-backports-mipsel-sbuild� already associated with �unknown� chroot
W: line 16 [wheezy-backports-sloppy-mipsel-sbuild] aliases: Alias �stable-backports-mipsel-sbuild� already associated with �unknown� chroot
Reading package lists...
+------------------------------------------------------------------------------+
� Install murasaki build dependencies (apt-based resolver) �
+------------------------------------------------------------------------------+
Installing build dependencies
W: line 16 [wheezy-backports-sloppy-mipsel-sbuild] aliases: Alias �stable-backports-mipsel-sbuild� already associated with �unknown� chroot
W: line 16 [wheezy-backports-sloppy-mipsel-sbuild] aliases: Alias �stable-backports-mipsel-sbuild� already associated with �unknown� chroot
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
adduser bsdmainutils debhelper file gcc-5-base gettext gettext-base
groff-base icu-devtools intltool-debian libasprintf0c2
libboost-filesystem-dev libboost-filesystem1.55-dev
libboost-filesystem1.55.0 libboost-iostreams-dev libboost-iostreams1.55-dev
libboost-iostreams1.55.0 libboost-regex-dev libboost-regex1.55-dev
libboost-regex1.55.0 libboost-system1.55-dev libboost-system1.55.0
libboost1.55-dev libcroco3 libcrypto++-dev libcrypto++9 libffi6 libgfortran3
libglib2.0-0 libhwloc-dev libhwloc5 libibverbs-dev libibverbs1 libicu-dev
libicu52 libltdl-dev libltdl7 libmagic1 libnuma-dev libnuma1 libopenmpi-dev
libopenmpi1.6 libpipeline1 libpstreams-dev libterm-readkey-perl
libtext-wrapper-perl libunistring0 libxml2 man-db openmpi-common perl
perl-base perl-modules po-debconf
Suggested packages:
liblocale-gettext-perl wamerican wordlist whois vacation dh-make gettext-doc
groff libboost1.55-doc libboost-atomic1.55-dev libboost-chrono1.55-dev
libboost-context1.55-dev libboost-coroutine1.55-dev
libboost-date-time1.55-dev libboost-exception1.55-dev libboost-graph1.55-dev
libboost-graph-parallel1.55-dev libboost-locale1.55-dev libboost-log1.55-dev
libboost-math1.55-dev libboost-mpi1.55-dev libboost-mpi-python1.55-dev
libboost-program-options1.55-dev libboost-python1.55-dev
libboost-random1.55-dev libboost-serialization1.55-dev
libboost-signals1.55-dev libboost-test1.55-dev libboost-thread1.55-dev
libboost-timer1.55-dev libboost-wave1.55-dev libboost1.55-tools-dev
libmpfrc++-dev libntl-dev libhwloc-contrib-plugins icu-doc libtool-doc less
www-browser perl-doc libterm-readline-gnu-perl libterm-readline-perl-perl
libb-lint-perl libcpanplus-dist-build-perl libcpanplus-perl
libfile-checktree-perl liblog-message-simple-perl liblog-message-perl
libobject-accessor-perl libmail-box-perl
Recommended packages:
curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
libglib2.0-data shared-mime-info xdg-user-dirs libhwloc-plugins libtool
xml-core netbase rename libarchive-extract-perl libmodule-pluggable-perl
libpod-latex-perl libterm-ui-perl libtext-soundex-perl libcgi-pm-perl
libmodule-build-perl libpackage-constants-perl libmail-sendmail-perl
The following NEW packages will be installed:
adduser bsdmainutils debhelper file gcc-5-base gettext gettext-base
groff-base icu-devtools intltool-debian libasprintf0c2
libboost-filesystem-dev libboost-filesystem1.55-dev
libboost-filesystem1.55.0 libboost-iostreams-dev libboost-iostreams1.55-dev
libboost-iostreams1.55.0 libboost-regex-dev libboost-regex1.55-dev
libboost-regex1.55.0 libboost-system1.55-dev libboost-system1.55.0
libboost1.55-dev libcroco3 libcrypto++-dev libcrypto++9 libffi6 libgfortran3
libglib2.0-0 libhwloc-dev libhwloc5 libibverbs-dev libibverbs1 libicu-dev
libicu52 libltdl-dev libltdl7 libmagic1 libnuma-dev libnuma1 libopenmpi-dev
libopenmpi1.6 libpipeline1 libpstreams-dev libterm-readkey-perl
libtext-wrapper-perl libunistring0 libxml2 man-db openmpi-common po-debconf
sbuild-build-depends-murasaki-dummy
The following packages will be upgraded:
perl perl-base perl-modules
3 upgraded, 52 newly installed, 0 to remove and 70 not upgraded.
Need to get 43.1 MB/43.1 MB of archives.
After this operation, 228 MB of additional disk space will be used.
Get:1 http://debian.netcologne.de/debian/ unstable/main perl mipsel 5.20.2-6 [2090 kB]
Get:2 http://debian.netcologne.de/debian/ unstable/main perl-base mipsel 5.20.2-6 [1118 kB]
Get:3 http://debian.netcologne.de/debian/ unstable/main perl-modules all 5.20.2-6 [2540 kB]
Get:4 http://debian.netcologne.de/debian/ unstable/main libboost-iostreams1.55.0 mipsel 1.55.0+dfsg-3 [46.9 kB]
Get:5 http://debian.netcologne.de/debian/ unstable/main libpipeline1 mipsel 1.4.0-1 [26.6 kB]
Get:6 http://debian.netcologne.de/debian/ unstable/main groff-base mipsel 1.22.3-1 [1218 kB]
Get:7 http://debian.netcologne.de/debian/ unstable/main bsdmainutils mipsel 9.0.6 [184 kB]
Get:8 http://debian.netcologne.de/debian/ unstable/main man-db mipsel 2.7.0.2-5 [984 kB]
Get:9 http://debian.netcologne.de/debian/ unstable/main libasprintf0c2 mipsel 0.19.4-1 [31.7 kB]
Get:10 http://debian.netcologne.de/debian/ unstable/main libmagic1 mipsel 1:5.22+15-2 [249 kB]
Get:11 http://debian.netcologne.de/debian/ unstable/main libicu52 mipsel 52.1-9 [6691 kB]
Get:12 http://debian.netcologne.de/debian/ unstable/main libxml2 mipsel 2.9.2+dfsg1-3 [815 kB]
Get:13 http://debian.netcologne.de/debian/ unstable/main libboost-system1.55.0 mipsel 1.55.0+dfsg-3 [30.2 kB]
Get:14 http://debian.netcologne.de/debian/ unstable/main libboost-filesystem1.55.0 mipsel 1.55.0+dfsg-3 [55.3 kB]
Get:15 http://debian.netcologne.de/debian/ unstable/main libboost-regex1.55.0 mipsel 1.55.0+dfsg-3 [248 kB]
Get:16 http://debian.netcologne.de/debian/ unstable/main libffi6 mipsel 3.1-2+b2 [18.4 kB]
Get:17 http://debian.netcologne.de/debian/ unstable/main libglib2.0-0 mipsel 2.44.1-1 [2293 kB]
Get:18 http://debian.netcologne.de/debian/ unstable/main libcroco3 mipsel 0.6.8-3+b1 [119 kB]
Get:19 http://debian.netcologne.de/debian/ unstable/main gcc-5-base mipsel 5.1.1-11 [165 kB]
Get:20 http://debian.netcologne.de/debian/ unstable/main libgfortran3 mipsel 5.1.1-11 [170 kB]
Get:21 http://debian.netcologne.de/debian/ unstable/main libltdl7 mipsel 2.4.2-1.11 [42.8 kB]
Get:22 http://debian.netcologne.de/debian/ unstable/main libnuma1 mipsel 2.0.10-1 [29.9 kB]
Get:23 http://debian.netcologne.de/debian/ unstable/main libunistring0 mipsel 0.9.3-5.2+b1 [257 kB]
Get:24 http://debian.netcologne.de/debian/ unstable/main libhwloc5 mipsel 1.11.0-1 [70.5 kB]
Get:25 http://debian.netcologne.de/debian/ unstable/main adduser all 3.113+nmu3 [264 kB]
Get:26 http://debian.netcologne.de/debian/ unstable/main file mipsel 1:5.22+15-2 [60.1 kB]
Get:27 http://debian.netcologne.de/debian/ unstable/main gettext-base mipsel 0.19.4-1 [121 kB]
Get:28 http://debian.netcologne.de/debian/ unstable/main gettext mipsel 0.19.4-1 [1189 kB]
Get:29 http://debian.netcologne.de/debian/ unstable/main intltool-debian all 0.35.0+20060710.2 [25.9 kB]
Get:30 http://debian.netcologne.de/debian/ unstable/main po-debconf all 1.0.18 [248 kB]
Get:31 http://debian.netcologne.de/debian/ unstable/main debhelper all 9.20150507 [824 kB]
Get:32 http://debian.netcologne.de/debian/ unstable/main icu-devtools mipsel 52.1-9 [167 kB]
Get:33 http://debian.netcologne.de/debian/ unstable/main libboost1.55-dev mipsel 1.55.0+dfsg-3 [5813 kB]
Get:34 http://debian.netcologne.de/debian/ unstable/main libboost-system1.55-dev mipsel 1.55.0+dfsg-3 [32.4 kB]
Get:35 http://debian.netcologne.de/debian/ unstable/main libboost-filesystem1.55-dev mipsel 1.55.0+dfsg-3 [69.7 kB]
Get:36 http://debian.netcologne.de/debian/ unstable/main libboost-filesystem-dev mipsel 1.55.0.2 [3046 B]
Get:37 http://debian.netcologne.de/debian/ unstable/main libicu-dev mipsel 52.1-9 [7700 kB]
Get:38 http://debian.netcologne.de/debian/ unstable/main libboost-regex1.55-dev mipsel 1.55.0+dfsg-3 [335 kB]
Get:39 http://debian.netcologne.de/debian/ unstable/main libboost-iostreams1.55-dev mipsel 1.55.0+dfsg-3 [57.9 kB]
Get:40 http://debian.netcologne.de/debian/ unstable/main libboost-iostreams-dev mipsel 1.55.0.2 [3012 B]
Get:41 http://debian.netcologne.de/debian/ unstable/main libboost-regex-dev mipsel 1.55.0.2 [3284 B]
Get:42 http://debian.netcologne.de/debian/ unstable/main libcrypto++9 mipsel 5.6.1-6 [1314 kB]
Get:43 http://debian.netcologne.de/debian/ unstable/main libcrypto++-dev mipsel 5.6.1-6 [3032 kB]
Get:44 http://debian.netcologne.de/debian/ unstable/main libltdl-dev mipsel 2.4.2-1.11 [158 kB]
Get:45 http://debian.netcologne.de/debian/ unstable/main libpstreams-dev all 0.8.0-2 [125 kB]
Get:46 http://debian.netcologne.de/debian/ unstable/main libterm-readkey-perl mipsel 2.32-2 [26.1 kB]
Get:47 http://debian.netcologne.de/debian/ unstable/main libtext-wrapper-perl all 1.05-1 [11.6 kB]
Get:48 http://debian.netcologne.de/debian/ unstable/main libnuma-dev mipsel 2.0.10-1 [45.9 kB]
Get:49 http://debian.netcologne.de/debian/ unstable/main libhwloc-dev mipsel 1.11.0-1 [141 kB]
Get:50 http://debian.netcologne.de/debian/ unstable/main libibverbs1 mipsel 1.1.8-1.1 [30.4 kB]
Get:51 http://debian.netcologne.de/debian/ unstable/main libibverbs-dev mipsel 1.1.8-1.1 [86.7 kB]
Get:52 http://debian.netcologne.de/debian/ unstable/main libopenmpi1.6 mipsel 1.6.5-9.2 [1141 kB]
Get:53 http://debian.netcologne.de/debian/ unstable/main openmpi-common all 1.6.5-9.2 [110 kB]
Get:54 http://debian.netcologne.de/debian/ unstable/main libopenmpi-dev mipsel 1.6.5-9.2 [448 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 43.1 MB in 9s (4679 kB/s)
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Preparing to unpack .../perl-modules_5.20.2-6_all.deb ...
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Preparing to unpack .../libopenmpi-dev_1.6.5-9.2_mipsel.deb ...
Unpacking libopenmpi-dev (1.6.5-9.2) ...
Selecting previously unselected package sbuild-build-depends-murasaki-dummy.
Preparing to unpack .../sbuild-build-depends-murasaki-dummy.deb ...
Unpacking sbuild-build-depends-murasaki-dummy (0.invalid.0) ...
Setting up perl-modules (5.20.2-6) ...
Setting up perl (5.20.2-6) ...
Setting up libboost-iostreams1.55.0:mipsel (1.55.0+dfsg-3) ...
Setting up libpipeline1:mipsel (1.4.0-1) ...
Setting up groff-base (1.22.3-1) ...
Setting up bsdmainutils (9.0.6) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up man-db (2.7.0.2-5) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libasprintf0c2:mipsel (0.19.4-1) ...
Setting up libmagic1:mipsel (1:5.22+15-2) ...
Setting up libicu52:mipsel (52.1-9) ...
Setting up libxml2:mipsel (2.9.2+dfsg1-3) ...
Setting up libboost-system1.55.0:mipsel (1.55.0+dfsg-3) ...
Setting up libboost-filesystem1.55.0:mipsel (1.55.0+dfsg-3) ...
Setting up libboost-regex1.55.0:mipsel (1.55.0+dfsg-3) ...
Setting up libffi6:mipsel (3.1-2+b2) ...
Setting up libglib2.0-0:mipsel (2.44.1-1) ...
No schema files found: doing nothing.
Setting up libcroco3:mipsel (0.6.8-3+b1) ...
Setting up gcc-5-base:mipsel (5.1.1-11) ...
Setting up libgfortran3:mipsel (5.1.1-11) ...
Setting up libltdl7:mipsel (2.4.2-1.11) ...
Setting up libnuma1:mipsel (2.0.10-1) ...
Setting up libunistring0:mipsel (0.9.3-5.2+b1) ...
Setting up libhwloc5:mipsel (1.11.0-1) ...
Setting up adduser (3.113+nmu3) ...
Setting up file (1:5.22+15-2) ...
Setting up gettext-base (0.19.4-1) ...
Setting up gettext (0.19.4-1) ...
Setting up intltool-debian (0.35.0+20060710.2) ...
Setting up po-debconf (1.0.18) ...
Setting up debhelper (9.20150507) ...
Setting up icu-devtools (52.1-9) ...
Setting up libboost1.55-dev:mipsel (1.55.0+dfsg-3) ...
Setting up libboost-system1.55-dev:mipsel (1.55.0+dfsg-3) ...
Setting up libboost-filesystem1.55-dev:mipsel (1.55.0+dfsg-3) ...
Setting up libboost-filesystem-dev:mipsel (1.55.0.2) ...
Setting up libicu-dev:mipsel (52.1-9) ...
Setting up libboost-regex1.55-dev:mipsel (1.55.0+dfsg-3) ...
Setting up libboost-iostreams1.55-dev:mipsel (1.55.0+dfsg-3) ...
Setting up libboost-iostreams-dev:mipsel (1.55.0.2) ...
Setting up libboost-regex-dev:mipsel (1.55.0.2) ...
Setting up libcrypto++9 (5.6.1-6) ...
Setting up libcrypto++-dev (5.6.1-6) ...
Setting up libltdl-dev:mipsel (2.4.2-1.11) ...
Setting up libpstreams-dev (0.8.0-2) ...
Setting up libterm-readkey-perl (2.32-2) ...
Setting up libtext-wrapper-perl (1.05-1) ...
Setting up libnuma-dev:mipsel (2.0.10-1) ...
Setting up libhwloc-dev:mipsel (1.11.0-1) ...
Setting up libibverbs1 (1.1.8-1.1) ...
Setting up libibverbs-dev (1.1.8-1.1) ...
Setting up libopenmpi1.6 (1.6.5-9.2) ...
Setting up openmpi-common (1.6.5-9.2) ...
Setting up libopenmpi-dev (1.6.5-9.2) ...
update-alternatives: using /usr/lib/openmpi/include to provide /usr/include/mpi (mpi) in auto mode
Setting up sbuild-build-depends-murasaki-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.19-15) ...
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+------------------------------------------------------------------------------+
� Build environment �
+------------------------------------------------------------------------------+
Kernel: Linux 3.16.0-0.bpo.4-loongson-3 mipsel (mips64)
Toolchain package versions: binutils_2.25-5 dpkg-dev_1.17.24 g++-4.9_4.9.2-10 gcc-4.9_4.9.2-10 libc6-dev_2.19-15 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 linux-libc-dev_3.16.7-ckt4-3
Package versions: adduser_3.113+nmu3 apt_1.0.9.7 base-files_8 base-passwd_3.5.37 bash_4.3-12 binutils_2.25-5 bsdmainutils_9.0.6 bsdutils_1:2.25.2-5 build-essential_11.7 bzip2_1.0.6-7+b2 coreutils_8.23-3 cpp_4:4.9.2-2 cpp-4.9_4.9.2-10 dash_0.5.7-4+b1 debconf_1.5.55 debfoster_2.7-2 debhelper_9.20150507 debian-archive-keyring_2014.3 debianutils_4.4+b1 diffutils_1:3.3-1+b1 dpkg_1.17.24 dpkg-dev_1.17.24 e2fslibs_1.42.12-1.1 e2fsprogs_1.42.12-1.1 fakeroot_1.20.2-1 file_1:5.22+15-2 findutils_4.4.2-9+b1 g++_4:4.9.2-2 g++-4.9_4.9.2-10 gcc_4:4.9.2-2 gcc-4.9_4.9.2-10 gcc-4.9-base_4.9.2-10 gcc-5-base_5.1.1-11 gettext_0.19.4-1 gettext-base_0.19.4-1 gnupg_1.4.18-6 gpgv_1.4.18-6 grep_2.20-4.1 groff-base_1.22.3-1 gzip_1.6-4 hostname_3.15 icu-devtools_52.1-9 init_1.22 initscripts_2.88dsf-58 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.2 libacl1_2.2.52-2 libapt-pkg4.12_1.0.9.7 libasprintf0c2_0.19.4-1 libatomic1_4.9.2-10 libattr1_1:2.4.47-2 libaudit-common_1:2.4-1 libaudit1_1:2.4-1+b1 libblkid1_2.25.2-5 libboost-filesystem-dev_1.55.0.2 libboost-filesystem1.55-dev_1.55.0+dfsg-3 libboost-filesystem1.55.0_1.55.0+dfsg-3 libboost-iostreams-dev_1.55.0.2 libboost-iostreams1.55-dev_1.55.0+dfsg-3 libboost-iostreams1.55.0_1.55.0+dfsg-3 libboost-regex-dev_1.55.0.2 libboost-regex1.55-dev_1.55.0+dfsg-3 libboost-regex1.55.0_1.55.0+dfsg-3 libboost-system1.55-dev_1.55.0+dfsg-3 libboost-system1.55.0_1.55.0+dfsg-3 libboost1.55-dev_1.55.0+dfsg-3 libbz2-1.0_1.0.6-7+b2 libc-bin_2.19-15 libc-dev-bin_2.19-15 libc6_2.19-15 libc6-dev_2.19-15 libcap2_1:2.24-6 libcloog-isl4_0.18.2-1+b2 libcomerr2_1.42.12-1.1 libcroco3_0.6.8-3+b1 libcrypto++-dev_5.6.1-6 libcrypto++9_5.6.1-6 libdb5.3_5.3.28-9 libdebconfclient0_0.192 libdpkg-perl_1.17.24 libfakeroot_1.20.2-1 libffi6_3.1-2+b2 libgc1c2_1:7.2d-6.4 libgcc-4.9-dev_4.9.2-10 libgcc1_1:4.9.2-10 libgcrypt20_1.6.2-4+b1 libgdbm3_1.8.3-13.1 libgfortran3_5.1.1-11 libglib2.0-0_2.44.1-1 libgmp10_2:6.0.0+dfsg-6 libgomp1_4.9.2-10 libgpg-error0_1.17-3 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_52.1-9 libicu52_52.1-9 libisl10_0.12.2-2 libltdl-dev_2.4.2-1.11 libltdl7_2.4.2-1.11 liblzma5_5.1.1alpha+20120614-2+b3 libmagic1_1:5.22+15-2 libmount1_2.25.2-5 libmpc3_1.0.3-1 libmpfr4_3.1.2-3 libncurses5_5.9+20140913-1+b1 libnuma-dev_2.0.10-1 libnuma1_2.0.10-1 libopenmpi-dev_1.6.5-9.2 libopenmpi1.6_1.6.5-9.2 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_2:8.35-3.3 libpipeline1_1.4.0-1 libpstreams-dev_0.8.0-2 libreadline6_6.3-8+b3 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1+b1 libsepol1_2.3-2 libslang2_2.3.0-2 libsmartcols1_2.25.2-5 libss2_1.42.12-1.1 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 libsystemd0_215-12 libterm-readkey-perl_2.32-2 libtext-wrapper-perl_1.05-1 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140913-1+b1 libunistring0_0.9.3-5.2+b1 libusb-0.1-4_2:0.1.12-25 libustr-1.0-1_1.0.4-3+b2 libuuid1_2.25.2-5 libxml2_2.9.2+dfsg1-3 linux-libc-dev_3.16.7-ckt4-3 login_1:4.2-3 lsb-base_4.1+Debian13+nmu1 make_4.0-8.1 man-db_2.7.0.2-5 mawk_1.3.3-17 mount_2.25.2-5 multiarch-support_2.19-15 ncurses-base_5.9+20140913-1 ncurses-bin_5.9+20140913-1+b1 openmpi-common_1.6.5-9.2 passwd_1:4.2-3 patch_2.7.4-2 perl_5.20.2-6 perl-base_5.20.2-6 perl-modules_5.20.2-6 po-debconf_1.0.18 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-murasaki-dummy_0.invalid.0 sed_4.2.2-4+b1 sensible-utils_0.0.9 startpar_0.59-3 sudo_1.8.12-1 sysv-rc_2.88dsf-58 sysvinit-core_2.88dsf-58 sysvinit-utils_2.88dsf-58 tar_1.27.1-2+b1 tzdata_2015a-1 util-linux_2.25.2-5 xz-utils_5.1.1alpha+20120614-2+b3 zlib1g_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
� Build �
+------------------------------------------------------------------------------+
Unpack source
-------------
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W: line 16 [wheezy-backports-sloppy-mipsel-sbuild] aliases: Alias �stable-backports-mipsel-sbuild� already associated with �unknown� chroot
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Thu Apr 16 12:06:40 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./murasaki_1.68.6-1.dsc
dpkg-source: info: extracting murasaki in murasaki-1.68.6
dpkg-source: info: unpacking murasaki_1.68.6.orig.tar.gz
dpkg-source: info: unpacking murasaki_1.68.6-1.debian.tar.xz
dpkg-source: info: applying use_proper_libboost_names.patch
dpkg-source: info: applying include_libpstream.patch
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying man_syntax.patch
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Check disc space
----------------
Sufficient free space for build
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User Environment
----------------
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DEB_BUILD_OPTIONS=parallel=5
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=sid-mipsel-sbuild
SCHROOT_CHROOT_NAME=sid-mipsel-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=sid-mipsel-sbuild-4a4978e5-063f-4ea4-add2-46ac86e5f19f
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
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dpkg-buildpackage: source package murasaki
dpkg-buildpackage: source version 1.68.6-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build murasaki-1.68.6
dpkg-buildpackage: host architecture mipsel
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
make -j1 clean
make[1]: Entering directory '/�PKGBUILDDIR�'
rm -rf *.o *~ .*~ core
make -C src clean
make[2]: Entering directory '/�PKGBUILDDIR�/src'
rm -rf *.o *~ .*~ core ../murasaki ../cgr-image ../cgr-compare ../cgr-random ../cgr-sample ../testeco ../align-compare ../align-or ../geneparse ../align-and ../align-best ../align-coverage ../getsegments ../mbfa
make[2]: Leaving directory '/�PKGBUILDDIR�/src'
make[1]: Leaving directory '/�PKGBUILDDIR�'
dh_clean
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/�PKGBUILDDIR�'
dh_auto_build -- USE_MPI=YES
make -j1 USE_MPI=YES
make[2]: Entering directory '/�PKGBUILDDIR�'
make -C src all
make[3]: Entering directory '/�PKGBUILDDIR�/src'
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c murasaki.cc
murasaki.cc: In function 'void procLocs(LocList&, std::list<Location>&, int, int)':
murasaki.cc:1008:8: warning: variable 'revZero' set but not used [-Wunused-but-set-variable]
bool revZero=false;
^
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c timing.cc
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c dinkymath.cc
dinkymath.cc: In function 'std::string littleEndianStr(unsigned int, int)':
dinkymath.cc:40:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
int last=0;
^
dinkymath.cc: In function 'std::string littleEndianPat(unsigned int, int)':
dinkymath.cc:53:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
int last=0;
^
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c sequence.cc
sequence.cc: In member function 'std::pair<double, long int> IntervalSet::entropy() const':
sequence.cc:3330:10: warning: variable 'shortest' set but not used [-Wunused-but-set-variable]
SeqPos shortest=0,shortlen=length(spaces[0]);
^
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c msethash.cc
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c options.cc
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c ecohash.cc
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c ecolist.cc
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c murasaki_mpi.cc
murasaki_mpi.cc: In function 'void mpi_hasher_client_mode(BitSequence*)':
murasaki_mpi.cc:561:9: warning: variable 'send_done' set but not used [-Wunused-but-set-variable]
int send_done;
^
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c arrayhash.cc
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c seqread.cc
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c scoring.cc
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c openhash.cc
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c genopts.cc
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c binseq.cc
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../murasaki murasaki.o timing.o dinkymath.o sequence.o msethash.o options.o ecohash.o ecolist.o murasaki_mpi.o arrayhash.o seqread.o scoring.o openhash.o genopts.o binseq.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-image.cc
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr.cc
cgr.cc: In member function 'void Cgr::merge(Cgr&)':
cgr.cc:140:7: warning: variable 'redist' set but not used [-Wunused-but-set-variable]
int redist=(unsigned long)(rez*rez)<=seedcount;
^
cgr.cc: In member function 'bool Cgr::savePNG(std::string)':
cgr.cc:288:7: warning: variable 'res' set but not used [-Wunused-but-set-variable]
int res;
^
cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)':
cgr.cc:435:7: warning: variable 'wordwidth' set but not used [-Wunused-but-set-variable]
int wordwidth=1;
^
cgr.cc: In member function 'int PgmBuffer::loadBinaryPGM(std::string)':
cgr.cc:551:36: warning: 'maxval' may be used uninitialized in this function [-Wmaybe-uninitialized]
default: data.back()*=(maxout/maxval);break;//ugly, but it'll work
^
cgr.cc:557:31: warning: 'height' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(data.size()<(uint)(height*width))
^
cgr.cc:557:31: warning: 'width' may be used uninitialized in this function [-Wmaybe-uninitialized]
cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)':
cgr.cc:485:31: warning: 'height' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(data.size()<(uint)(height*width))
^
cgr.cc:485:31: warning: 'width' may be used uninitialized in this function [-Wmaybe-uninitialized]
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-image cgr-image.o cgr.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-compare.cc
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-compare cgr-compare.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-random.cc
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-sample.cc
cgr-sample.cc: In function 'int main(int, char**)':
cgr-sample.cc:54:8: warning: variable 'repeatmask' set but not used [-Wunused-but-set-variable]
bool repeatmask=false,save=false;
^
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-sample cgr.o cgr-sample.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c testeco.cc
testeco.cc:42:3: warning: this decimal constant is unsigned only in ISO C90
const long genomesize=3221225472;
^
testeco.cc: In function 'long int bigrand()':
testeco.cc:29:43: warning: left shift count >= width of type
return (long)(((unsigned long)(rand())<<32) + ((unsigned long)(rand())));
^
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-compare.cc
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c alignments.cc
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-or.cc
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c geneparse.cc
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-and.cc
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-best.cc
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-coverage.cc
align-coverage.cc: In function 'int main(int, char**)':
align-coverage.cc:148:10: warning: variable 'seqStats' set but not used [-Wunused-but-set-variable]
bool seqStats=true;
^
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c getsegments.cc
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c mbfa.cc
mpicxx -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
make[3]: Leaving directory '/�PKGBUILDDIR�/src'
make[2]: Leaving directory '/�PKGBUILDDIR�'
for bin in geneparse mbfa murasaki cgr-* testeco align-* ; do \
mv ${bin} ${bin}-mpi ; \
done
make clean
make[2]: Entering directory '/�PKGBUILDDIR�'
rm -rf *.o *~ .*~ core
make -C src clean
make[3]: Entering directory '/�PKGBUILDDIR�/src'
rm -rf *.o *~ .*~ core ../murasaki ../cgr-image ../cgr-compare ../cgr-random ../cgr-sample ../testeco ../align-compare ../align-or ../geneparse ../align-and ../align-best ../align-coverage ../getsegments ../mbfa
make[3]: Leaving directory '/�PKGBUILDDIR�/src'
make[2]: Leaving directory '/�PKGBUILDDIR�'
dh_auto_build -- USE_MPI=NO
make -j1 USE_MPI=NO
make[2]: Entering directory '/�PKGBUILDDIR�'
make -C src all
make[3]: Entering directory '/�PKGBUILDDIR�/src'
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c murasaki.cc
murasaki.cc: In function 'void procLocs(LocList&, std::list<Location>&, int, int)':
murasaki.cc:1008:8: warning: variable 'revZero' set but not used [-Wunused-but-set-variable]
bool revZero=false;
^
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c timing.cc
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c dinkymath.cc
dinkymath.cc: In function 'std::string littleEndianStr(unsigned int, int)':
dinkymath.cc:40:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
int last=0;
^
dinkymath.cc: In function 'std::string littleEndianPat(unsigned int, int)':
dinkymath.cc:53:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
int last=0;
^
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c sequence.cc
sequence.cc: In member function 'std::pair<double, long int> IntervalSet::entropy() const':
sequence.cc:3330:10: warning: variable 'shortest' set but not used [-Wunused-but-set-variable]
SeqPos shortest=0,shortlen=length(spaces[0]);
^
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c msethash.cc
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c options.cc
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c ecohash.cc
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c ecolist.cc
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c murasaki_mpi.cc
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c arrayhash.cc
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c seqread.cc
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c scoring.cc
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c openhash.cc
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c genopts.cc
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c binseq.cc
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../murasaki murasaki.o timing.o dinkymath.o sequence.o msethash.o options.o ecohash.o ecolist.o murasaki_mpi.o arrayhash.o seqread.o scoring.o openhash.o genopts.o binseq.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-image.cc
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr.cc
cgr.cc: In member function 'void Cgr::merge(Cgr&)':
cgr.cc:140:7: warning: variable 'redist' set but not used [-Wunused-but-set-variable]
int redist=(unsigned long)(rez*rez)<=seedcount;
^
cgr.cc: In member function 'bool Cgr::savePNG(std::string)':
cgr.cc:288:7: warning: variable 'res' set but not used [-Wunused-but-set-variable]
int res;
^
cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)':
cgr.cc:435:7: warning: variable 'wordwidth' set but not used [-Wunused-but-set-variable]
int wordwidth=1;
^
cgr.cc: In member function 'int PgmBuffer::loadBinaryPGM(std::string)':
cgr.cc:551:36: warning: 'maxval' may be used uninitialized in this function [-Wmaybe-uninitialized]
default: data.back()*=(maxout/maxval);break;//ugly, but it'll work
^
cgr.cc:557:31: warning: 'height' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(data.size()<(uint)(height*width))
^
cgr.cc:557:31: warning: 'width' may be used uninitialized in this function [-Wmaybe-uninitialized]
cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)':
cgr.cc:485:31: warning: 'height' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(data.size()<(uint)(height*width))
^
cgr.cc:485:31: warning: 'width' may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-image cgr-image.o cgr.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-compare.cc
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-compare cgr-compare.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-random.cc
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-sample.cc
cgr-sample.cc: In function 'int main(int, char**)':
cgr-sample.cc:54:8: warning: variable 'repeatmask' set but not used [-Wunused-but-set-variable]
bool repeatmask=false,save=false;
^
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-sample cgr.o cgr-sample.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c testeco.cc
testeco.cc:42:3: warning: this decimal constant is unsigned only in ISO C90
const long genomesize=3221225472;
^
testeco.cc: In function 'long int bigrand()':
testeco.cc:29:43: warning: left shift count >= width of type
return (long)(((unsigned long)(rand())<<32) + ((unsigned long)(rand())));
^
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-compare.cc
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c alignments.cc
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-or.cc
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c geneparse.cc
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-and.cc
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-best.cc
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-coverage.cc
align-coverage.cc: In function 'int main(int, char**)':
align-coverage.cc:148:10: warning: variable 'seqStats' set but not used [-Wunused-but-set-variable]
bool seqStats=true;
^
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c getsegments.cc
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c mbfa.cc
g++ -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -lcryptopp -pthread
make[3]: Leaving directory '/�PKGBUILDDIR�/src'
make[2]: Leaving directory '/�PKGBUILDDIR�'
make[1]: Leaving directory '/�PKGBUILDDIR�'
dh_auto_test -a
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
debian/rules override_dh_install
make[1]: Entering directory '/�PKGBUILDDIR�'
dh_install
# using wildcards in install files is practical but it duplicates some files
find debian/murasaki/usr -name "*-mpi" -delete
make[1]: Leaving directory '/�PKGBUILDDIR�'
dh_installdocs -a
dh_installchangelogs -a
debian/rules override_dh_installman
make[1]: Entering directory '/�PKGBUILDDIR�'
dh_installman
# create manpages for PL files
mkdir -p debian/murasaki-common/usr/share/man/man1
for pscript in debian/murasaki-common/usr/lib/debian-med/bin/* ; do \
pod2man ${pscript} > debian/murasaki-common/usr/share/man/man1/`basename ${pscript}`.1 ; \
done
Can't open debian/murasaki-common/usr/lib/debian-med/bin/*: No such file or directory at /usr/bin/pod2man line 71.
make[1]: *** [override_dh_installman] Error 2
debian/rules:24: recipe for target 'override_dh_installman' failed
make[1]: Leaving directory '/�PKGBUILDDIR�'
make: *** [binary-arch] Error 2
debian/rules:13: recipe for target 'binary-arch' failed
dpkg-buildpackage: error: fakeroot debian/rules binary-arch gave error exit status 2
--------------------------------------------------------------------------------
Build finished at 20150622-1619
Finished
--------
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
� Cleanup �
+------------------------------------------------------------------------------+
Purging /�BUILDDIR�
W: line 16 [wheezy-backports-sloppy-mipsel-sbuild] aliases: Alias �stable-backports-mipsel-sbuild� already associated with �unknown� chroot
W: line 16 [wheezy-backports-sloppy-mipsel-sbuild] aliases: Alias �stable-backports-mipsel-sbuild� already associated with �unknown� chroot
Not cleaning session: cloned chroot in use
W: line 16 [wheezy-backports-sloppy-mipsel-sbuild] aliases: Alias �stable-backports-mipsel-sbuild� already associated with �unknown� chroot
W: line 16 [wheezy-backports-sloppy-mipsel-sbuild] aliases: Alias �stable-backports-mipsel-sbuild� already associated with �unknown� chroot
W: line 16 [wheezy-backports-sloppy-mipsel-sbuild] aliases: Alias �stable-backports-mipsel-sbuild� already associated with �unknown� chroot
W: line 16 [wheezy-backports-sloppy-mipsel-sbuild] aliases: Alias �stable-backports-mipsel-sbuild� already associated with �unknown� chroot
W: line 16 [wheezy-backports-sloppy-mipsel-sbuild] aliases: Alias �stable-backports-mipsel-sbuild� already associated with �unknown� chroot
W: line 16 [wheezy-backports-sloppy-mipsel-sbuild] aliases: Alias �stable-backports-mipsel-sbuild� already associated with �unknown� chroot
+------------------------------------------------------------------------------+
� Summary �
+------------------------------------------------------------------------------+
Build Architecture: mipsel
Build-Space: 162944
Build-Time: 2278
Distribution: sid
Fail-Stage: build
Host Architecture: mipsel
Install-Time: 94
Job: murasaki_1.68.6-1
Machine Architecture: mipsel
Package: murasaki
Package-Time: 2471
Source-Version: 1.68.6-1
Space: 162944
Status: attempted
Version: 1.68.6-1
--------------------------------------------------------------------------------
Finished at 20150622-1619
Build needed 00:41:11, 162944k disc space
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