[Debian-med-packaging] [med-svn] r5639 - trunk/packages/probcons/trunk/debian
Charles Plessy
plessy at debian.org
Mon Jan 3 22:27:07 UTC 2011
Le Mon, Jan 03, 2011 at 10:25:07PM +0000, Charles Plessy a écrit :
> Author: plessy
> Date: 2011-01-03 22:25:07 +0000 (Mon, 03 Jan 2011)
> New Revision: 5639
>
> Modified:
> trunk/packages/probcons/trunk/debian/changelog
> Log:
> Uploaded.
Just for the record, here is the build log.
--
Charles
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sbuild (Debian sbuild) 0.59.0 (02 Aug 2009) on illkix.dunkklar.org
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? probcons 1.12-7 (amd64) 04 jan 2011 07:09 ?
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Package: probcons
Version: 1.12-7
Architecture: amd64
Start Time: 20110104-0709
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? Fetch source files ?
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Local sources
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probcons_1.12-7.dsc exists in .; copying to chroot
Check arch
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** Using build dependencies supplied by package:
Build-Depends: debhelper (>= 8), quilt
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? Install build dependencies ?
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Checking for already installed source dependencies...
debhelper: already installed (8.0.0 >= 8 is satisfied)
quilt: already installed (0.48-7)
Checking for source dependency conflicts...
Installing positive dependencies:
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: Linux 2.6.33.1hagenix amd64 (x86_64)
Toolchain package versions: libc6-dev_2.9-23 linux-libc-dev_2.6.32-29 g++-4.4_ =*=NOT INSTALLED=*= gcc-4.4_ =*=NOT INSTALLED=*= binutils_2.19.51.20090805-1 libstdc++6-4.4-dev_ =*=NOT INSTALLED=*= libstdc++6_4.4.5-10
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? Build ?
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Unpack source
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dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
dpkg-source: warning: extracting unsigned source package (probcons_1.12-7.dsc)
dpkg-source: info: extracting probcons in probcons-1.12
dpkg-source: info: unpacking probcons_1.12.orig.tar.gz
dpkg-source: info: unpacking probcons_1.12-7.debian.tar.gz
dpkg-source: info: applying 10_add-RNA-in-Makefile.diff
dpkg-source: info: applying 11-Rename-programs-in-Makefile.diff
dpkg-source: info: applying fix-gcc-4.5-headers
Check disc space
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dpkg-buildpackage
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dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package probcons
dpkg-buildpackage: source version 1.12-7
dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
dpkg-source --before-build probcons-1.12
dpkg-buildpackage: host architecture amd64
/usr/bin/fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
make[1]: Entering directory `/build/karl-probcons_1.12-7-amd64-BNO64G/probcons-1.12'
rm -f probcons probcons-RNA pc-compare pc-project pc-makegnuplot
make[1]: Leaving directory `/build/karl-probcons_1.12-7-amd64-BNO64G/probcons-1.12'
debian/rules override_dh_clean
make[1]: Entering directory `/build/karl-probcons_1.12-7-amd64-BNO64G/probcons-1.12'
dh_clean probcons probcons-RNA pc-project pc-compare pc-makegnuplot Main-RNA.cc Defaults-RNA.h
make[1]: Leaving directory `/build/karl-probcons_1.12-7-amd64-BNO64G/probcons-1.12'
dpkg-source -b probcons-1.12
dpkg-source: info: using source format `3.0 (quilt)'
dpkg-source: info: building probcons using existing ./probcons_1.12.orig.tar.gz
dpkg-source: info: building probcons in probcons_1.12-7.debian.tar.gz
dpkg-source: info: building probcons in probcons_1.12-7.dsc
debian/rules build
dh build
dh_testdir
dh_auto_configure
debian/rules override_dh_auto_build
make[1]: Entering directory `/build/karl-probcons_1.12-7-amd64-BNO64G/probcons-1.12'
cp Main.cc Main-RNA.cc
sed -i s/Defaults.h/Defaults-RNA.h/ Main-RNA.cc
cp debian/Defaults-RNA.h Defaults-RNA.h
dh_auto_build
make[2]: Entering directory `/build/karl-probcons_1.12-7-amd64-BNO64G/probcons-1.12'
g++ -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=2 -DVERSION="1.12" -funroll-loops -lm -o probcons Main.cc
In file included from Main.cc:11:
ProbabilisticModel.h: In member function 'void ProbabilisticModel::ComputeNewParameters(Sequence*, Sequence*, const VF&, const VF&, VF&, VF&, VF&, VVF&, VF&, bool) const':
ProbabilisticModel.h:493: warning: suggest parentheses around && within ||
g++ -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=1 -DVERSION="1.12" -funroll-loops -lm -o probcons-RNA Main-RNA.cc
In file included from Main-RNA.cc:11:
ProbabilisticModel.h: In member function 'void ProbabilisticModel::ComputeNewParameters(Sequence*, Sequence*, const VF&, const VF&, VF&, VF&, VF&, VVF&, VF&, bool) const':
ProbabilisticModel.h:493: warning: suggest parentheses around && within ||
g++ -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=2 -DVERSION="1.12" -funroll-loops -o pc-compare CompareToRef.cc
g++ -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=2 -DVERSION="1.12" -funroll-loops -o pc-project ProjectPairwise.cc
g++ -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=2 -DVERSION="1.12" -funroll-loops -o pc-makegnuplot MakeGnuPlot.cc
make[2]: Leaving directory `/build/karl-probcons_1.12-7-amd64-BNO64G/probcons-1.12'
make[1]: Leaving directory `/build/karl-probcons_1.12-7-amd64-BNO64G/probcons-1.12'
dh_auto_test
/usr/bin/fakeroot debian/rules binary
dh binary
dh_testroot
dh_prep
dh_installdirs
dh_auto_install
dh_install
dh_installdocs
dh_installchangelogs
dh_installexamples
dh_installman
dh_installcatalogs
dh_installcron
dh_installdebconf
dh_installemacsen
dh_installifupdown
dh_installinfo
dh_installinit
dh_installmenu
dh_installmime
dh_installmodules
dh_installlogcheck
dh_installlogrotate
dh_installpam
dh_installppp
dh_installudev
dh_installwm
dh_installxfonts
dh_bugfiles
dh_lintian
dh_gconf
dh_icons
dh_perl
dh_usrlocal
debian/rules override_dh_link
make[1]: Entering directory `/build/karl-probcons_1.12-7-amd64-BNO64G/probcons-1.12'
rm -rf /build/karl-probcons_1.12-7-amd64-BNO64G/probcons-1.12/debian/probcons-extra/usr/share/doc/probcons-extra
dh_link -p probcons-extra usr/share/doc/probcons usr/share/doc/probcons-extra
make[1]: Leaving directory `/build/karl-probcons_1.12-7-amd64-BNO64G/probcons-1.12'
dh_compress
dh_fixperms
dh_strip
dh_makeshlibs
dh_shlibdeps
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package `probcons' in `../probcons_1.12-7_amd64.deb'.
dpkg-deb: building package `probcons-extra' in `../probcons-extra_1.12-7_amd64.deb'.
dpkg-genchanges >../probcons_1.12-7_amd64.changes
dpkg-genchanges: not including original source code in upload
dpkg-source --after-build probcons-1.12
dpkg-buildpackage: binary and diff upload (original source NOT included)
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Build finished at 20110104-0711
probcons_1.12-7_amd64.changes:
Format: 1.8
Date: Tue, 04 Jan 2011 06:57:45 +0900
Source: probcons
Binary: probcons probcons-extra
Architecture: source amd64
Version: 1.12-7
Distribution: sid-amd64-sbuild
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
probcons - PROBabilistic CONSistency-based multiple sequence alignment
probcons-extra - Extra programs from the probcons package
Closes: 607729 608710
Changes:
probcons (1.12-7) unstable; urgency=low
.
* Use dh for debian/rules, which will also switch off parallel building
(Closes: #607729, #608710).
* Switch to Debhelper 8 (debian/control, debian/compat).
Checksums-Sha1:
334236c568973ee211d7f4075c194cc4ad652aa1 1097 probcons_1.12-7.dsc
2124b8d9b4c8d9cc8bb80ba02e72ddba732f45a6 11289 probcons_1.12-7.debian.tar.gz
b38ad18461f56a3597eb94352930b63c38d22f94 216544 probcons_1.12-7_amd64.deb
818c6e329c468015aa751460c0c4eee2d5924a34 57470 probcons-extra_1.12-7_amd64.deb
Checksums-Sha256:
b8c8b9d30392f37272175f55b6f1ac5493e83ae917d174013e5d9edc7941c700 1097 probcons_1.12-7.dsc
b5a5949abffb6e6955f538ebb7d05f9a19aacdc83c29b33a6aebfe5566a7e70a 11289 probcons_1.12-7.debian.tar.gz
d078ccc63c33ec6ddbfc4a6013e64ecb41c53cd33c53d44d76200ab9241e5dad 216544 probcons_1.12-7_amd64.deb
f54c81b50713c5eedd286001068e0770a8176ad7b18bfd8a46421897ceafbcb6 57470 probcons-extra_1.12-7_amd64.deb
Files:
7bea6869e1104a3a8450b70b3ada2b8c 1097 science optional probcons_1.12-7.dsc
29bd79790566da7c237d7c4faf3493ca 11289 science optional probcons_1.12-7.debian.tar.gz
6996729897d7141a6b3355718727968b 216544 science optional probcons_1.12-7_amd64.deb
b421c99c4954f814489a24ddd02ec9d9 57470 science extra probcons-extra_1.12-7_amd64.deb
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? Package contents ?
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probcons_1.12-7_amd64.deb
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nouveau paquet Debian, version 2.0.
taille 216544 octets : archive de contrôle = 996 octets.
1011 octets, 20 lignes control
526 octets, 8 lignes md5sums
Package: probcons
Version: 1.12-7
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 508
Depends: libc6 (>= 2.2.5), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.2.1)
Suggests: probcons-extra
Enhances: t-coffee
Section: science
Priority: optional
Homepage: http://probcons.stanford.edu/
Description: PROBabilistic CONSistency-based multiple sequence alignment
Tool for generating multiple alignments of protein sequences. Using a
combination of probabilistic modeling and consistency-based alignment
techniques, PROBCONS has achieved the highest accuracies of all alignment
methods to date. On the BAliBASE benchmark alignment database, alignments
produced by PROBCONS show statistically significant improvement over current
programs, containing an average of 7% more correctly aligned columns than
those of T-Coffee, 11% more correctly aligned columns than those of CLUSTAL W,
and 14% more correctly aligned columns than those of DIALIGN.
drwxr-xr-x root/root 0 2011-01-04 07:10 ./
drwxr-xr-x root/root 0 2011-01-04 07:10 ./usr/
drwxr-xr-x root/root 0 2011-01-04 07:10 ./usr/share/
drwxr-xr-x root/root 0 2011-01-04 07:10 ./usr/share/man/
drwxr-xr-x root/root 0 2011-01-04 07:10 ./usr/share/man/man1/
-rw-r--r-- root/root 1801 2011-01-04 07:10 ./usr/share/man/man1/probcons.1.gz
-rw-r--r-- root/root 866 2011-01-04 07:10 ./usr/share/man/man1/probcons-RNA.1.gz
drwxr-xr-x root/root 0 2011-01-04 07:10 ./usr/share/doc/
drwxr-xr-x root/root 0 2011-01-04 07:10 ./usr/share/doc/probcons/
-rw-r--r-- root/root 995 2008-01-05 00:58 ./usr/share/doc/probcons/copyright
-rw-r--r-- root/root 1499 2011-01-04 06:58 ./usr/share/doc/probcons/changelog.Debian.gz
-rw-r--r-- root/root 1764 2007-04-04 02:39 ./usr/share/doc/probcons/README.gz
-rw-r--r-- root/root 750 2007-04-18 22:39 ./usr/share/doc/probcons/README.Debian
drwxr-xr-x root/root 0 2011-01-04 07:11 ./usr/bin/
-rwxr-xr-x root/root 229792 2011-01-04 07:11 ./usr/bin/probcons
-rwxr-xr-x root/root 217008 2011-01-04 07:11 ./usr/bin/probcons-RNA
probcons-extra_1.12-7_amd64.deb
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nouveau paquet Debian, version 2.0.
taille 57470 octets : archive de contrôle = 851 octets.
841 octets, 20 lignes control
374 octets, 6 lignes md5sums
Package: probcons-extra
Source: probcons
Version: 1.12-7
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 168
Depends: probcons (= 1.12-7), libc6 (>= 2.2.5), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.2.1)
Suggests: gnuplot-nox | gnuplot-x11
Section: science
Priority: extra
Homepage: http://probcons.stanford.edu/
Description: Extra programs from the probcons package
Contains the convert, project and makgnuplot programs from the probcons
package, which have been renamed to pc-compare, pc-project and pc-makegnuplot
respectively to avoid collisions with other program names. These programs are
mostly useful for testing purposes and are not required for the normal usage of
Probcons.
.
Probcons is a tool for generating multiple alignments of protein
sequences.
drwxr-xr-x root/root 0 2011-01-04 07:10 ./
drwxr-xr-x root/root 0 2011-01-04 07:10 ./usr/
drwxr-xr-x root/root 0 2011-01-04 07:10 ./usr/share/
drwxr-xr-x root/root 0 2011-01-04 07:10 ./usr/share/man/
drwxr-xr-x root/root 0 2011-01-04 07:10 ./usr/share/man/man1/
-rw-r--r-- root/root 965 2011-01-04 07:10 ./usr/share/man/man1/pc-compare.1.gz
-rw-r--r-- root/root 878 2011-01-04 07:10 ./usr/share/man/man1/pc-makegnuplot.1.gz
-rw-r--r-- root/root 884 2011-01-04 07:10 ./usr/share/man/man1/pc-project.1.gz
drwxr-xr-x root/root 0 2011-01-04 07:10 ./usr/share/doc/
drwxr-xr-x root/root 0 2011-01-04 07:11 ./usr/bin/
-rwxr-xr-x root/root 15208 2011-01-04 07:11 ./usr/bin/pc-makegnuplot
-rwxr-xr-x root/root 64640 2011-01-04 07:11 ./usr/bin/pc-compare
-rwxr-xr-x root/root 40864 2011-01-04 07:11 ./usr/bin/pc-project
lrwxrwxrwx root/root 0 2011-01-04 07:10 ./usr/share/doc/probcons-extra -> probcons
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? Finished ?
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Built successfully
Purging /var/lib/schroot/mount/sid-amd64-sbuild-efff348e-c13a-4db3-83ac-29e0ad88cfee/build/karl-probcons_1.12-7-amd64-BNO64G
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Finished at 20110104-0711
Build needed 00:02:06, 2312k disc space
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