[med-svn] r13836 - in trunk/packages/microbiomeutil: . tags
Author: tille Date: 2013-06-05 08:14:33 + (Wed, 05 Jun 2013) New Revision: 13836 Added: trunk/packages/microbiomeutil/tags/ trunk/packages/microbiomeutil/tags/20101212-2/ Log: Tagged just uploaded version 20101212-2 ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13835 - trunk/packages/microbiomeutil/trunk/debian
Author: tille Date: 2013-06-05 08:13:29 + (Wed, 05 Jun 2013) New Revision: 13835 Modified: trunk/packages/microbiomeutil/trunk/debian/changelog Log: Initial upload to unstable as version *-2 to get a higher version number than previous changelog entries. Modified: trunk/packages/microbiomeutil/trunk/debian/changelog === --- trunk/packages/microbiomeutil/trunk/debian/changelog2013-06-04 15:19:40 UTC (rev 13834) +++ trunk/packages/microbiomeutil/trunk/debian/changelog2013-06-05 08:13:29 UTC (rev 13835) @@ -1,4 +1,4 @@ -microbiomeutil (20101212-1) UNRELEASED; urgency=low +microbiomeutil (20101212-2) unstable; urgency=low * Initial release to Debian (Closes: #711086) * debian/copyright: DEP5 copyright ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] jellyfish branch, master, updated. upstream/1.1.5-21-gf7eb6f0
The following commit has been merged in the master branch:
commit 22b775bef657023f14cbc3e1bf11f91ad7ee4120
Author: Andreas Tille ti...@debian.org
Date: Wed Jun 5 13:42:06 2013 +0200
Make sure dynamic library will be installed
diff --git a/debian/changelog b/debian/changelog
index 8a10582..48bf58d 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,6 +1,7 @@
jellyfish (1.1.10-1) UNRELEASED; urgency=low
* New upstream version
+ * debian/{rules,install}: Make sure dynamic library will be installed
-- Andreas Tille ti...@debian.org Wed, 05 Jun 2013 11:58:53 +0200
diff --git a/debian/install b/debian/install
index e772481..527b78f 100644
--- a/debian/install
+++ b/debian/install
@@ -1 +1,2 @@
usr/bin
+usr/lib
diff --git a/debian/rules b/debian/rules
index 31b9e46..4c9a9ae 100755
--- a/debian/rules
+++ b/debian/rules
@@ -10,3 +10,6 @@ override_dh_auto_configure:
override_dh_auto_install:
dh_auto_install --destdir=debian/tmp
+
+override_dh_install:
+ dh_install -X*.a -X*.la -Xpkgconfig
--
count k-mers of DNA
___
debian-med-commit mailing list
debian-med-commit@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] jellyfish branch, pristine-tar, updated. 77e4307ae538e8eb852a680227738a9f29f8ec36
The following commit has been merged in the pristine-tar branch: commit 77e4307ae538e8eb852a680227738a9f29f8ec36 Author: Andreas Tille ti...@debian.org Date: Wed Jun 5 11:58:49 2013 +0200 pristine-tar data for jellyfish_1.1.10.orig.tar.gz diff --git a/jellyfish_1.1.10.orig.tar.gz.delta b/jellyfish_1.1.10.orig.tar.gz.delta new file mode 100644 index 000..3057d00 Binary files /dev/null and b/jellyfish_1.1.10.orig.tar.gz.delta differ diff --git a/jellyfish_1.1.10.orig.tar.gz.id b/jellyfish_1.1.10.orig.tar.gz.id new file mode 100644 index 000..beb6fef --- /dev/null +++ b/jellyfish_1.1.10.orig.tar.gz.id @@ -0,0 +1 @@ +8cc16a515c86b3d4051ffa8cd4197d52de7e1bf8 -- count k-mers of DNA ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] jellyfish branch, master, updated. upstream/1.1.5-21-gf7eb6f0
The following commit has been merged in the master branch:
commit f7eb6f0071550895880b3e65490f60faca56685b
Author: Andreas Tille ti...@debian.org
Date: Wed Jun 5 13:43:07 2013 +0200
New upstream closes #701423
diff --git a/debian/changelog b/debian/changelog
index 48bf58d..1529192 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,6 +1,7 @@
jellyfish (1.1.10-1) UNRELEASED; urgency=low
* New upstream version
+Closes: #701423
* debian/{rules,install}: Make sure dynamic library will be installed
-- Andreas Tille ti...@debian.org Wed, 05 Jun 2013 11:58:53 +0200
--
count k-mers of DNA
___
debian-med-commit mailing list
debian-med-commit@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] jellyfish branch, master, updated. upstream/1.1.5-21-gf7eb6f0
The following commit has been merged in the master branch: commit 3a3ecd9bdfe783380478a0593f642ac3d71cef78 Author: Andreas Tille ti...@debian.org Date: Wed Jun 5 12:00:02 2013 +0200 New upstream version diff --git a/debian/changelog b/debian/changelog index 7141ca3..8a10582 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +jellyfish (1.1.10-1) UNRELEASED; urgency=low + + * New upstream version + + -- Andreas Tille ti...@debian.org Wed, 05 Jun 2013 11:58:53 +0200 + jellyfish (1.1.5-1) unstable; urgency=low * New upstream version fixing the FTBFS with gcc-4.7 bug -- count k-mers of DNA ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] jellyfish branch, master, updated. upstream/1.1.5-21-gf7eb6f0
The following commit has been merged in the master branch: commit d34f71a334b44c864a44a0543f2c427cc390b4b6 Merge: 8e7aa50262175fe031bce17d111a2995a4f62590 a3cc522fd6708d67c7d0dbc77f34c7457086f3d8 Author: Andreas Tille ti...@debian.org Date: Wed Jun 5 11:58:49 2013 +0200 Merge tag 'upstream/1.1.10' Upstream version 1.1.10 -- count k-mers of DNA ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] jellyfish branch, master, updated. upstream/1.1.5-23-g709917a
The following commit has been merged in the master branch:
commit 709917a789bea24650c453cf2923fea53d1fbe42
Author: Andreas Tille ti...@debian.org
Date: Wed Jun 5 13:44:44 2013 +0200
Standards-Version: 3.9.4 (no changes needed)
diff --git a/debian/changelog b/debian/changelog
index 2711a8a..0b139d0 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -5,6 +5,7 @@ jellyfish (1.1.10-1) UNRELEASED; urgency=low
* debian/{rules,install}: Make sure dynamic library will be installed
* debian/control:
- Removed DM-Upload-Allowed
+ - Standards-Version: 3.9.4 (no changes needed)
-- Andreas Tille ti...@debian.org Wed, 05 Jun 2013 11:58:53 +0200
diff --git a/debian/control b/debian/control
index e180621..f90a7e1 100644
--- a/debian/control
+++ b/debian/control
@@ -5,7 +5,7 @@ Maintainer: Debian Med Packaging Team
debian-med-packaging@lists.alioth.debian.
Uploaders: Shaun Jackman sjack...@debian.org,
Andreas Tille ti...@debian.org
Build-Depends: debhelper (= 9)
-Standards-Version: 3.9.3
+Standards-Version: 3.9.4
Homepage: http://www.cbcb.umd.edu/software/jellyfish/
Vcs-Git: git://git.debian.org/git/debian-med/jellyfish.git
Vcs-Browser: http://git.debian.org/?p=debian-med/jellyfish.git
--
count k-mers of DNA
___
debian-med-commit mailing list
debian-med-commit@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] jellyfish branch, master, updated. upstream/1.1.5-23-g709917a
The following commit has been merged in the master branch:
commit 58c57eb2142ed6b96cc99855acbb5cd672c72168
Author: Andreas Tille ti...@debian.org
Date: Wed Jun 5 13:44:09 2013 +0200
Removed DM-Upload-Allowed
diff --git a/debian/changelog b/debian/changelog
index 1529192..2711a8a 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -3,6 +3,8 @@ jellyfish (1.1.10-1) UNRELEASED; urgency=low
* New upstream version
Closes: #701423
* debian/{rules,install}: Make sure dynamic library will be installed
+ * debian/control:
+ - Removed DM-Upload-Allowed
-- Andreas Tille ti...@debian.org Wed, 05 Jun 2013 11:58:53 +0200
diff --git a/debian/control b/debian/control
index 087a02f..e180621 100644
--- a/debian/control
+++ b/debian/control
@@ -2,7 +2,6 @@ Source: jellyfish
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
-DM-Upload-Allowed: yes
Uploaders: Shaun Jackman sjack...@debian.org,
Andreas Tille ti...@debian.org
Build-Depends: debhelper (= 9)
--
count k-mers of DNA
___
debian-med-commit mailing list
debian-med-commit@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] jellyfish branch, master, updated. upstream/1.1.5-25-g5e2ed3e
The following commit has been merged in the master branch: commit 5e2ed3effc428dcded56cef0b4b9f1b29f5f258d Author: Andreas Tille ti...@debian.org Date: Wed Jun 5 14:03:13 2013 +0200 debian/lintian-overrides: Upstream decided to use a dynamic library without really intending to make this a development package diff --git a/debian/changelog b/debian/changelog index 9b342b7..7f8a016 100644 --- a/debian/changelog +++ b/debian/changelog @@ -7,6 +7,8 @@ jellyfish (1.1.10-1) UNRELEASED; urgency=low - Removed DM-Upload-Allowed - Standards-Version: 3.9.4 (no changes needed) - Build-Depends autotools-dev + * debian/lintian-overrides: Upstream decided to use a dynamic library +without really intending to make this a development package -- Andreas Tille ti...@debian.org Wed, 05 Jun 2013 11:58:53 +0200 diff --git a/debian/lintian-overrides b/debian/lintian-overrides new file mode 100644 index 000..3a502fa --- /dev/null +++ b/debian/lintian-overrides @@ -0,0 +1,4 @@ +# Upstream decided to use a dynamic library without really intending to make this a development package +jellyfish: package-name-doesnt-match-sonames libjellyfish-.* +jellyfish: non-dev-pkg-with-shlib-symlink .* + -- count k-mers of DNA ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] jellyfish branch, master, updated. upstream/1.1.5-25-g5e2ed3e
The following commit has been merged in the master branch: commit d04e4df75075c6ab3a40fcc881e65a275239e3ad Author: Andreas Tille ti...@debian.org Date: Wed Jun 5 14:02:19 2013 +0200 Build-Depends autotools-dev diff --git a/debian/changelog b/debian/changelog index 0b139d0..9b342b7 100644 --- a/debian/changelog +++ b/debian/changelog @@ -6,6 +6,7 @@ jellyfish (1.1.10-1) UNRELEASED; urgency=low * debian/control: - Removed DM-Upload-Allowed - Standards-Version: 3.9.4 (no changes needed) + - Build-Depends autotools-dev -- Andreas Tille ti...@debian.org Wed, 05 Jun 2013 11:58:53 +0200 diff --git a/debian/control b/debian/control index f90a7e1..90bc688 100644 --- a/debian/control +++ b/debian/control @@ -4,7 +4,8 @@ Priority: optional Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org Uploaders: Shaun Jackman sjack...@debian.org, Andreas Tille ti...@debian.org -Build-Depends: debhelper (= 9) +Build-Depends: debhelper (= 9), + autotools-dev Standards-Version: 3.9.4 Homepage: http://www.cbcb.umd.edu/software/jellyfish/ Vcs-Git: git://git.debian.org/git/debian-med/jellyfish.git -- count k-mers of DNA ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13837 - trunk/packages/microbiomeutil/trunk/debian
Author: tbooth-guest
Date: 2013-06-05 12:14:06 + (Wed, 05 Jun 2013)
New Revision: 13837
Modified:
trunk/packages/microbiomeutil/trunk/debian/changelog
trunk/packages/microbiomeutil/trunk/debian/control
trunk/packages/microbiomeutil/trunk/debian/rules
Log:
Pre-compute some necessary index files (ChimeraSlayer would do this anyway on
the
first run if it could write to the relevant dir)
Please fold my latest changelog entry into the entry for -3
Modified: trunk/packages/microbiomeutil/trunk/debian/changelog
===
--- trunk/packages/microbiomeutil/trunk/debian/changelog2013-06-05
08:14:33 UTC (rev 13836)
+++ trunk/packages/microbiomeutil/trunk/debian/changelog2013-06-05
12:14:06 UTC (rev 13837)
@@ -1,3 +1,12 @@
+microbiomeutil (20101212-1ubuntu8) precise; urgency=low
+
+ * Bio-Linux rebuild with Andreas' fixes
+ * ChimeraSlayer run from QIIME was not working. Need to pre-compute
+index files and add them to RESOURCES directory
+ * Also added missing direct dep on blast2
+
+ -- Tim Booth tbo...@ceh.ac.uk Wed, 05 Jun 2013 12:50:22 +0100
+
microbiomeutil (20101212-2) unstable; urgency=low
* Initial release to Debian (Closes: #711086)
Modified: trunk/packages/microbiomeutil/trunk/debian/control
===
--- trunk/packages/microbiomeutil/trunk/debian/control 2013-06-05 08:14:33 UTC
(rev 13836)
+++ trunk/packages/microbiomeutil/trunk/debian/control 2013-06-05 12:14:06 UTC
(rev 13837)
@@ -6,7 +6,8 @@
Tim Booth tbo...@ceh.ac.uk,
Andreas Tille ti...@debian.org
Build-Depends: debhelper (= 9),
- cdbfasta
+ cdbfasta,
+ blast2
Standards-Version: 3.9.4
Homepage: http://microbiomeutil.sourceforge.net/
Vcs-Browser:
http://svn.debian.org/wsvn/debian-med/trunk/packages/microbiomeutil/trunk/
@@ -31,7 +32,8 @@
Architecture: all
Depends: ${misc:Depends},
microbiomeutil-data,
- cdbfasta
+ cdbfasta,
+ blast2
Recommends: nast-ier
Description: detects likely chimeras in PCR amplified DNA
ChimeraSlayer is a chimeric sequence detection utility, compatible with
Modified: trunk/packages/microbiomeutil/trunk/debian/rules
===
--- trunk/packages/microbiomeutil/trunk/debian/rules2013-06-05 08:14:33 UTC
(rev 13836)
+++ trunk/packages/microbiomeutil/trunk/debian/rules2013-06-05 12:14:06 UTC
(rev 13837)
@@ -11,6 +11,18 @@
override_dh_auto_test :
true
+override_dh_auto_build :
+ dh_auto_build
+ #Pre-make indexes for ChimeraSlayer, otherwise it tries to write them
+ #to the non-writeable dir on first run and blows up
+ formatdb -p F -i RESOURCES/rRNA16S.gold.fasta 2/dev/null
+ cdbfasta -C RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta
+
+override_dh_auto_clean:
+ dh_auto_clean
+ rm -f RESOURCES/rRNA16S.gold.fasta.n* RESOURCES/*.cidx
+ rm -f formatdb.log
+
override_dh_install:
dh_install -XMakefile -Xsample_data -XLICENSE -XNAST-iEr.c
___
debian-med-commit mailing list
debian-med-commit@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] jellyfish branch, master, updated. upstream/1.1.5-26-g016146d
The following commit has been merged in the master branch:
commit 016146dc813cb5374651853506cbcce81b6413a3
Author: Andreas Tille ti...@debian.org
Date: Wed Jun 5 14:19:40 2013 +0200
debian/doc-base: docbase control file
diff --git a/debian/changelog b/debian/changelog
index 7f8a016..6c5295c 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -9,6 +9,7 @@ jellyfish (1.1.10-1) UNRELEASED; urgency=low
- Build-Depends autotools-dev
* debian/lintian-overrides: Upstream decided to use a dynamic library
without really intending to make this a development package
+ * debian/doc-base: docbase control file
-- Andreas Tille ti...@debian.org Wed, 05 Jun 2013 11:58:53 +0200
diff --git a/debian/control b/debian/doc-base
similarity index 54%
copy from debian/control
copy to debian/doc-base
index 90bc688..1113ccd 100644
--- a/debian/control
+++ b/debian/doc-base
@@ -1,21 +1,7 @@
-Source: jellyfish
-Section: science
-Priority: optional
-Maintainer: Debian Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
-Uploaders: Shaun Jackman sjack...@debian.org,
- Andreas Tille ti...@debian.org
-Build-Depends: debhelper (= 9),
- autotools-dev
-Standards-Version: 3.9.4
-Homepage: http://www.cbcb.umd.edu/software/jellyfish/
-Vcs-Git: git://git.debian.org/git/debian-med/jellyfish.git
-Vcs-Browser: http://git.debian.org/?p=debian-med/jellyfish.git
-
-
-Package: jellyfish
-Architecture: any-amd64
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: count k-mers in DNA sequences
+Document: jellyfish
+Title: Jellyfish: A fast k-mer counter
+Author: G. Marcais and C. Kingsford
+Abstract: Jellyfish is a software to count k-mers in DNA sequences.
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
DNA. A k-mer is a substring of length k, and counting the occurrences
of all such substrings is a central step in many analyses of DNA
@@ -29,3 +15,7 @@ Description: count k-mers in DNA sequences
files containing DNA sequences. It outputs its k-mer counts in an
binary format, which can be translated into a human-readable text
format using the jellyfish dump command.
+Section: Science/Biology
+
+Format: pdf
+Files: /usr/share/doc/jellyfish/jellyfish.pdf.gz
--
count k-mers of DNA
___
debian-med-commit mailing list
debian-med-commit@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13838 - trunk/package_template
Author: tille Date: 2013-06-05 12:49:45 + (Wed, 05 Jun 2013) New Revision: 13838 Modified: trunk/package_template/control Log: Bumped standards-version in template Modified: trunk/package_template/control === --- trunk/package_template/control 2013-06-05 12:14:06 UTC (rev 13837) +++ trunk/package_template/control 2013-06-05 12:49:45 UTC (rev 13838) @@ -4,7 +4,7 @@ Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org Uploaders: Andreas Tille ti...@debian.org Build-Depends: debhelper (= 9) -Standards-Version: 3.9.3 +Standards-Version: 3.9.4 Homepage: homepage Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/pkg/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/pkg/trunk/ ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] jellyfish branch, master, updated. upstream/1.1.5-30-gfa1dfe3
The following commit has been merged in the master branch: commit a237c5b6a60ede98890261eb4ef3361a98f94070 Author: Andreas Tille ti...@debian.org Date: Wed Jun 5 14:31:55 2013 +0200 debian/patches/man: refreshed + DEP3 description diff --git a/debian/changelog b/debian/changelog index 725bd4a..5dc0647 100644 --- a/debian/changelog +++ b/debian/changelog @@ -11,6 +11,7 @@ jellyfish (1.1.10-1) UNRELEASED; urgency=low * debian/lintian-overrides: Upstream decided to use a dynamic library without really intending to make this a development package * debian/doc-base: docbase control file + * debian/patches/man: refreshed + DEP3 description -- Andreas Tille ti...@debian.org Wed, 05 Jun 2013 11:58:53 +0200 diff --git a/debian/patches/man b/debian/patches/man index 11dcb7d..d8e1760 100644 --- a/debian/patches/man +++ b/debian/patches/man @@ -1,5 +1,8 @@ jellyfish.orig/doc/jellyfish.man -+++ jellyfish/doc/jellyfish.man +Author: Andreas Tille +Description: Fix NAME section in manpage + +--- a/doc/jellyfish.man b/doc/jellyfish.man @@ -12,11 +12,7 @@ .. .TH JELLYFISH 1 2010/10/1 k\-mer counter k\-mer counter -- count k-mers of DNA ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] jellyfish annotated tag, upstream/1.1.10, created. upstream/1.1.10
The annotated tag, upstream/1.1.10 has been created at 0857690874eb8014664c65987b6c12ce4c0a4aa1 (tag) tagging a3cc522fd6708d67c7d0dbc77f34c7457086f3d8 (commit) replaces upstream/1.1.5 tagged by Andreas Tille on Wed Jun 5 11:58:49 2013 +0200 - Shortlog Upstream version 1.1.10 Andreas Tille (1): Imported Upstream version 1.1.10 --- -- count k-mers of DNA ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] jellyfish branch, master, updated. upstream/1.1.5-30-gfa1dfe3
The following commit has been merged in the master branch: commit f1154077fe7e49e4e11fde912dbf3c682d72e1e3 Author: Andreas Tille ti...@debian.org Date: Wed Jun 5 14:40:02 2013 +0200 Add remaining related lintian 'I'nformation to overrides diff --git a/debian/lintian-overrides b/debian/lintian-overrides index 3a502fa..c0c0d90 100644 --- a/debian/lintian-overrides +++ b/debian/lintian-overrides @@ -1,4 +1,4 @@ # Upstream decided to use a dynamic library without really intending to make this a development package jellyfish: package-name-doesnt-match-sonames libjellyfish-.* jellyfish: non-dev-pkg-with-shlib-symlink .* - +jellyfish: no-symbols-control-file .* -- count k-mers of DNA ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] jellyfish branch, master, updated. upstream/1.1.5-30-gfa1dfe3
The following commit has been merged in the master branch: commit fa1dfe3012c8a1324726faf5939fe746f1ebb084 Author: Andreas Tille ti...@debian.org Date: Wed Jun 5 14:40:35 2013 +0200 Upload to unstable diff --git a/debian/changelog b/debian/changelog index 5dc0647..53f8fbc 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,4 +1,4 @@ -jellyfish (1.1.10-1) UNRELEASED; urgency=low +jellyfish (1.1.10-1) unstable; urgency=low * New upstream version Closes: #701423 -- count k-mers of DNA ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] jellyfish branch, master, updated. upstream/1.1.5-30-gfa1dfe3
The following commit has been merged in the master branch: commit 40909bd330379d19caeda244a4691681c770fbc1 Author: Andreas Tille ti...@debian.org Date: Wed Jun 5 14:31:11 2013 +0200 canonical VCS URLs diff --git a/debian/changelog b/debian/changelog index 6c5295c..725bd4a 100644 --- a/debian/changelog +++ b/debian/changelog @@ -7,6 +7,7 @@ jellyfish (1.1.10-1) UNRELEASED; urgency=low - Removed DM-Upload-Allowed - Standards-Version: 3.9.4 (no changes needed) - Build-Depends autotools-dev + - canonical VCS URLs * debian/lintian-overrides: Upstream decided to use a dynamic library without really intending to make this a development package * debian/doc-base: docbase control file diff --git a/debian/control b/debian/control index 90bc688..999b269 100644 --- a/debian/control +++ b/debian/control @@ -8,8 +8,8 @@ Build-Depends: debhelper (= 9), autotools-dev Standards-Version: 3.9.4 Homepage: http://www.cbcb.umd.edu/software/jellyfish/ -Vcs-Git: git://git.debian.org/git/debian-med/jellyfish.git -Vcs-Browser: http://git.debian.org/?p=debian-med/jellyfish.git +Vcs-Git: git://anonscm.debian.org/debian-med/jellyfish.git +Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/jellyfish.git Package: jellyfish -- count k-mers of DNA ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] jellyfish tag, debian/1.1.10-1, created. upstream/1.1.10-29-gfa1dfe3
The tag, debian/1.1.10-1 has been created at fa1dfe3012c8a1324726faf5939fe746f1ebb084 (commit) - Shortlog commit fa1dfe3012c8a1324726faf5939fe746f1ebb084 Author: Andreas Tille ti...@debian.org Date: Wed Jun 5 14:40:35 2013 +0200 Upload to unstable --- -- count k-mers of DNA ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13839 - trunk/packages/metastudent/trunk/debian
Author: hampt-guest Date: 2013-06-05 14:43:13 + (Wed, 05 Jun 2013) New Revision: 13839 Modified: trunk/packages/metastudent/trunk/debian/changelog Log: 1.0.9-1 - new upstream release Modified: trunk/packages/metastudent/trunk/debian/changelog === --- trunk/packages/metastudent/trunk/debian/changelog 2013-06-05 12:49:45 UTC (rev 13838) +++ trunk/packages/metastudent/trunk/debian/changelog 2013-06-05 14:43:13 UTC (rev 13839) @@ -1,8 +1,8 @@ -metastudent (1.0.8-3) UNRELEASED; urgency=low +metastudent (1.0.9-1) UNRELEASED; urgency=low - * NOT RELEASED YET + * New upstream release. - -- Laszlo Kajan lka...@rostlab.org Thu, 16 May 2013 18:28:22 +0200 + -- Tobias Hamp ha...@rostlab.org Wed, 05 Jun 2013 16:41:08 +0200 metastudent (1.0.8-2) unstable; urgency=low ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13840 - in trunk/packages/babraham/fastqc/trunk/debian: . patches
Author: osallou-guest
Date: 2013-06-05 15:12:46 + (Wed, 05 Jun 2013)
New Revision: 13840
Added:
trunk/packages/babraham/fastqc/trunk/debian/patches/fix_icon_loading
Modified:
trunk/packages/babraham/fastqc/trunk/debian/changelog
trunk/packages/babraham/fastqc/trunk/debian/patches/series
Log:
Close bug 697604, give debian path to load resources
Modified: trunk/packages/babraham/fastqc/trunk/debian/changelog
===
--- trunk/packages/babraham/fastqc/trunk/debian/changelog 2013-06-05
14:43:13 UTC (rev 13839)
+++ trunk/packages/babraham/fastqc/trunk/debian/changelog 2013-06-05
15:12:46 UTC (rev 13840)
@@ -1,3 +1,10 @@
+fastqc (0.10.1+dfsg-2) unstable; urgency=low
+
+ * Add patch to fix Templates and Contaminants loading
+in non interactive mode (Closes: #697604)
+
+ -- Olivier Sallou osal...@debian.org Wed, 05 Jun 2013 17:08:44 +0200
+
fastqc (0.10.1+dfsg-1) unstable; urgency=low
* Initial release (Closes: #670353)
Added: trunk/packages/babraham/fastqc/trunk/debian/patches/fix_icon_loading
===
--- trunk/packages/babraham/fastqc/trunk/debian/patches/fix_icon_loading
(rev 0)
+++ trunk/packages/babraham/fastqc/trunk/debian/patches/fix_icon_loading
2013-06-05 15:12:46 UTC (rev 13840)
@@ -0,0 +1,44 @@
+Subject: issue when loading resources
+Description: in Debian, templates and other resources are not embedded in Jar
file.
+ This is a problem when app tries to access the resources.
+ This patch provides the path in Debian hierarcy to find resources.
+Author: Olivier Sallou osal...@debian.org
+Last-Updated: 2013-06-05
+Forwarded: no
+--- a/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java
b/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java
+@@ -167,12 +167,12 @@
+ data.append(\n);
+
+ // Add in the icon files for pass/fail/warn
+- File templatesDir = new
File(URLDecoder.decode(ClassLoader.getSystemResource(Templates/Icons).getFile(),UTF-8));
++ File templatesDir = new
File(/usr/share/fastqc/Templates/Icons);
+ String [] names = templatesDir.list();
+ for (int n=0;nnames.length;n++) {
+ if (names[n].toLowerCase().endsWith(.png) ||
names[n].toLowerCase().endsWith(.jpg) ||
names[n].toLowerCase().endsWith(.jpeg)) {
+ zip.putNextEntry(new
ZipEntry(folderName()+/Icons/+names[n]));
+- FileInputStream fileIn = new
FileInputStream(new
File(URLDecoder.decode(ClassLoader.getSystemResource(Templates/Icons/+names[n]).getFile(),UTF-8)));
++ FileInputStream fileIn = new
FileInputStream(new File(/usr/share/fastqc/Templates/Icons/+names[n]));
+ int len;
+ while ((len = fileIn.read(buffer)) 0) {
+ zip.write(buffer, 0, len);
+@@ -235,7 +235,7 @@
+
+ private void addTemplate (String filename, String date) throws
IOException {
+
+- BufferedReader br = new BufferedReader(new FileReader(new
File(URLDecoder.decode(ClassLoader.getSystemResource(Templates/header_template.html).getFile(),UTF-8;
++ BufferedReader br = new BufferedReader(new FileReader(new
File(/usr/share/fastqc/Templates/header_template.html)));
+ String line;
+ while ((line = br.readLine())!=null) {
+
+--- a/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminentFinder.java
b/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminentFinder.java
+@@ -60,7 +60,7 @@
+
+ try {
+
+- File contaminantFile = new File
(URLDecoder.decode(ClassLoader.getSystemResource(Contaminants/contaminant_list.txt).getFile(),UTF-8));
++ File contaminantFile = new File
(/usr/share/fastqc/Contaminants/contaminant_list.txt);
+
+ if (System.getProperty(fastqc.contaminant_file) !=
null System.getProperty(fastqc.contaminant_file).length()0) {
+ contaminantFile = new
File(System.getProperty(fastqc.contaminant_file));
Modified: trunk/packages/babraham/fastqc/trunk/debian/patches/series
===
--- trunk/packages/babraham/fastqc/trunk/debian/patches/series 2013-06-05
14:43:13 UTC (rev 13839)
+++ trunk/packages/babraham/fastqc/trunk/debian/patches/series 2013-06-05
15:12:46 UTC (rev 13840)
@@ -1,3 +1,4 @@
Makefile.patch
fastqc.patch
fix-help-call.patch
+fix_icon_loading
___
debian-med-commit mailing list
debian-med-commit@lists.alioth.debian.org
[med-svn] r13841 - trunk/packages/babraham/fastqc/trunk/debian/patches
Author: osallou-guest
Date: 2013-06-05 15:14:47 + (Wed, 05 Jun 2013)
New Revision: 13841
Modified:
trunk/packages/babraham/fastqc/trunk/debian/patches/fastqc.patch
Log:
remove fuzz
Modified: trunk/packages/babraham/fastqc/trunk/debian/patches/fastqc.patch
===
--- trunk/packages/babraham/fastqc/trunk/debian/patches/fastqc.patch
2013-06-05 15:12:46 UTC (rev 13840)
+++ trunk/packages/babraham/fastqc/trunk/debian/patches/fastqc.patch
2013-06-05 15:14:47 UTC (rev 13841)
@@ -3,7 +3,7 @@
--- a/fastqc
+++ b/fastqc
-@@ -17,12 +17,12 @@ if ($^O =~ /Win/) {
+@@ -17,12 +17,12 @@
$delimiter = ';';
}
@@ -20,7 +20,7 @@
my @java_args;
my @files;
-@@ -177,10 +177,10 @@ if (@files or $version or $help) {
+@@ -177,10 +177,10 @@
if ($java_bin ne 'java') {
@@ -33,7 +33,7 @@
}
__DATA__
-@@ -273,4 +273,4 @@ BUGS
+@@ -273,4 +273,4 @@
Any bugs in fastqc should be reported either to
simon.andr...@babraham.ac.uk
or in www.bioinformatics.babraham.ac.uk/bugzilla/
___
debian-med-commit mailing list
debian-med-commit@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13842 - trunk/packages/babraham/fastqc/trunk/debian/patches
Author: osallou-guest Date: 2013-06-05 15:17:35 + (Wed, 05 Jun 2013) New Revision: 13842 Modified: trunk/packages/babraham/fastqc/trunk/debian/patches/fastqc.patch Log: remove fuzz Modified: trunk/packages/babraham/fastqc/trunk/debian/patches/fastqc.patch === --- trunk/packages/babraham/fastqc/trunk/debian/patches/fastqc.patch 2013-06-05 15:14:47 UTC (rev 13841) +++ trunk/packages/babraham/fastqc/trunk/debian/patches/fastqc.patch 2013-06-05 15:17:35 UTC (rev 13842) @@ -39,4 +39,4 @@ - \ No newline at end of file -+ ++ ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13844 - in trunk/packages/babraham/fastqc: . tags
Author: tille Date: 2013-06-05 15:43:45 + (Wed, 05 Jun 2013) New Revision: 13844 Added: trunk/packages/babraham/fastqc/tags/ trunk/packages/babraham/fastqc/tags/0.10.1+dfsg-2/ Log: Tagged 0.10.1+dfsg-2 ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13843 - trunk/packages/babraham/fastqc/trunk/debian
Author: osallou-guest Date: 2013-06-05 15:21:34 + (Wed, 05 Jun 2013) New Revision: 13843 Modified: trunk/packages/babraham/fastqc/trunk/debian/control Log: add myself as uploaded, remove deprecated DM-upload Modified: trunk/packages/babraham/fastqc/trunk/debian/control === --- trunk/packages/babraham/fastqc/trunk/debian/control 2013-06-05 15:17:35 UTC (rev 13842) +++ trunk/packages/babraham/fastqc/trunk/debian/control 2013-06-05 15:21:34 UTC (rev 13843) @@ -2,9 +2,9 @@ Section: science Priority: optional Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org -DM-Upload-Allowed: yes Uploaders: Steffen Moeller moel...@debian.org, - Andreas Tille ti...@debian.org + Andreas Tille ti...@debian.org, + Olivier Sallou osal...@debian.org Build-Depends: debhelper (= 9), javahelper, default-jdk, libsam-java, libjbzip2-java Standards-Version: 3.9.4 Homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13845 - in trunk/packages: . profit profit/trunk profit/trunk/debian profit/trunk/debian/patches profit/trunk/debian/source
Author: moeller
Date: 2013-06-05 16:19:05 + (Wed, 05 Jun 2013)
New Revision: 13845
Added:
trunk/packages/profit/
trunk/packages/profit/trunk/
trunk/packages/profit/trunk/debian/
trunk/packages/profit/trunk/debian/README.Debian
trunk/packages/profit/trunk/debian/README.source
trunk/packages/profit/trunk/debian/changelog
trunk/packages/profit/trunk/debian/compat
trunk/packages/profit/trunk/debian/control
trunk/packages/profit/trunk/debian/copyright
trunk/packages/profit/trunk/debian/docs
trunk/packages/profit/trunk/debian/patches/
trunk/packages/profit/trunk/debian/patches/AllowReadline.patch
trunk/packages/profit/trunk/debian/patches/AllowRedundantCleans.patch
trunk/packages/profit/trunk/debian/patches/series
trunk/packages/profit/trunk/debian/profit-data.dirs
trunk/packages/profit/trunk/debian/profit-data.install
trunk/packages/profit/trunk/debian/profit.dirs
trunk/packages/profit/trunk/debian/profit.install
trunk/packages/profit/trunk/debian/profit.sh
trunk/packages/profit/trunk/debian/rules
trunk/packages/profit/trunk/debian/source/
trunk/packages/profit/trunk/debian/source/format
Log:
This package is nothing for Debian Med itself, it is just another
one of those that come with source code (and consequently should
be rebuildable with our distribution) but are not redistributable.
ProFit is (sadly) a common tool in structural biology to align
two proteins. If I recall correctly (and things have not changed)
then it all starts with the centers of gravity plus a three dimensional
turning along what a sequence alignment gives us.
Property changes on: trunk/packages/profit/trunk/debian
___
Added: mergeWithUpstream
+ 1
Added: trunk/packages/profit/trunk/debian/README.Debian
===
--- trunk/packages/profit/trunk/debian/README.Debian
(rev 0)
+++ trunk/packages/profit/trunk/debian/README.Debian2013-06-05 16:19:05 UTC
(rev 13845)
@@ -0,0 +1,9 @@
+profit for Debian
+-
+
+The license of ProFit does not allow a redistribution.
+
+The documentation is not built, since it demanded too much of LaTeX to be
installed,
+also for a conversion to HTML. It ships with the original source code.
+
+ -- Steffen Moeller moel...@debian.org Wed, 05 Jun 2013 17:38:14 +0200
Added: trunk/packages/profit/trunk/debian/README.source
===
--- trunk/packages/profit/trunk/debian/README.source
(rev 0)
+++ trunk/packages/profit/trunk/debian/README.source2013-06-05 16:19:05 UTC
(rev 13845)
@@ -0,0 +1,9 @@
+profit for Debian
+-
+
+this file describes information about the source package, see Debian policy
+manual section 4.14. You WILL either need to modify or delete this file
+
+
+
+
Added: trunk/packages/profit/trunk/debian/changelog
===
--- trunk/packages/profit/trunk/debian/changelog
(rev 0)
+++ trunk/packages/profit/trunk/debian/changelog2013-06-05 16:19:05 UTC
(rev 13845)
@@ -0,0 +1,5 @@
+profit (3.1-1) UNRELEASED; urgency=low
+
+ * The license does not allow a redistribution.
+
+ -- Steffen Moeller moel...@debian.org Wed, 05 Jun 2013 17:38:14 +0200
Added: trunk/packages/profit/trunk/debian/compat
===
--- trunk/packages/profit/trunk/debian/compat (rev 0)
+++ trunk/packages/profit/trunk/debian/compat 2013-06-05 16:19:05 UTC (rev
13845)
@@ -0,0 +1 @@
+8
Added: trunk/packages/profit/trunk/debian/control
===
--- trunk/packages/profit/trunk/debian/control (rev 0)
+++ trunk/packages/profit/trunk/debian/control 2013-06-05 16:19:05 UTC (rev
13845)
@@ -0,0 +1,21 @@
+Source: profit
+Section: non-free/science
+Priority: optional
+Maintainer: Steffen Moeller steffen_moel...@gmx.de
+Build-Depends: debhelper (= 8.0.0), libreadline-dev
+Standards-Version: 3.9.4
+Homepage: http://www.bioinf.org.uk/software/profit/
+#Vcs-Git: git://git.debian.org/collab-maint/profit.git
+#Vcs-Browser: http://git.debian.org/?p=collab-maint/profit.git;a=summary
+
+Package: profit
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, profit-data
+Description: Protein structure alignment
+ Nothing to be redistributed.
+
+Package: profit-data
+Architecture: all
+Recommends: profit
+Description: Help and data files for Profit
+ Nothing to be redistributed.
Added: trunk/packages/profit/trunk/debian/copyright
===
--- trunk/packages/profit/trunk/debian/copyright
(rev 0)
+++ trunk/packages/profit/trunk/debian/copyright
[med-svn] r13846 - trunk/packages/profit/trunk/debian
Author: moeller Date: 2013-06-05 16:21:14 + (Wed, 05 Jun 2013) New Revision: 13846 Modified: trunk/packages/profit/trunk/debian/README.source trunk/packages/profit/trunk/debian/control Log: Adjusting email address. Modified: trunk/packages/profit/trunk/debian/README.source === --- trunk/packages/profit/trunk/debian/README.source2013-06-05 16:19:05 UTC (rev 13845) +++ trunk/packages/profit/trunk/debian/README.source2013-06-05 16:21:14 UTC (rev 13846) @@ -1,9 +1,7 @@ profit for Debian - -this file describes information about the source package, see Debian policy -manual section 4.14. You WILL either need to modify or delete this file +No source should be redistributed. - Modified: trunk/packages/profit/trunk/debian/control === --- trunk/packages/profit/trunk/debian/control 2013-06-05 16:19:05 UTC (rev 13845) +++ trunk/packages/profit/trunk/debian/control 2013-06-05 16:21:14 UTC (rev 13846) @@ -1,7 +1,7 @@ Source: profit Section: non-free/science Priority: optional -Maintainer: Steffen Moeller steffen_moel...@gmx.de +Maintainer: Steffen Moeller moel...@debian.org Build-Depends: debhelper (= 8.0.0), libreadline-dev Standards-Version: 3.9.4 Homepage: http://www.bioinf.org.uk/software/profit/ ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13847 - in trunk/packages/rosetta/trunk/debian: . patches
Author: moeller
Date: 2013-06-05 16:22:11 + (Wed, 05 Jun 2013)
New Revision: 13847
Modified:
trunk/packages/rosetta/trunk/debian/changelog
trunk/packages/rosetta/trunk/debian/control
trunk/packages/rosetta/trunk/debian/patches/gcc4.6patch
Log:
Adjusted for Rosetta 3.5.
Modified: trunk/packages/rosetta/trunk/debian/changelog
===
--- trunk/packages/rosetta/trunk/debian/changelog 2013-06-05 16:21:14 UTC
(rev 13846)
+++ trunk/packages/rosetta/trunk/debian/changelog 2013-06-05 16:22:11 UTC
(rev 13847)
@@ -1,3 +1,9 @@
+rosetta (3.5-1) UNRELEASED; urgency=low
+
+ * New upstream release.
+
+ -- Steffen Moeller moel...@debian.org Wed, 05 Jun 2013 09:21:49 +0200
+
rosetta (3.4-1) UNRELEASED; urgency=low
* New upstream release.
Modified: trunk/packages/rosetta/trunk/debian/control
===
--- trunk/packages/rosetta/trunk/debian/control 2013-06-05 16:21:14 UTC (rev
13846)
+++ trunk/packages/rosetta/trunk/debian/control 2013-06-05 16:22:11 UTC (rev
13847)
@@ -2,12 +2,11 @@
Section: non-free/science
Priority: extra
Maintainer: Debian Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
-DM-Upload-Allowed: yes
Uploaders: Steffen Moeller moel...@debian.org
Build-Depends: debhelper (= 7.0.50~), scons, zlib1g-dev, libboost-dev
#cxxtest
#Build-Depends-Indep: doxygen
-Standards-Version: 3.9.2
+Standards-Version: 3.9.4
Homepage: http://www.rosettacommons.org
Vcs-Browser:
http://svn.debian.org/wsvn/debian-med/trunk/packages/rosetta/trunk/
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/rosetta/trunk/
Modified: trunk/packages/rosetta/trunk/debian/patches/gcc4.6patch
===
--- trunk/packages/rosetta/trunk/debian/patches/gcc4.6patch 2013-06-05
16:21:14 UTC (rev 13846)
+++ trunk/packages/rosetta/trunk/debian/patches/gcc4.6patch 2013-06-05
16:22:11 UTC (rev 13847)
@@ -1,8 +1,8 @@
-Index: rosetta-3.4/tools/build/basic.settings
+Index: rosetta_source/tools/build/basic.settings
===
rosetta-3.4.orig/tools/build/basic.settings2012-03-20
19:44:23.0 +0100
-+++ rosetta-3.4/tools/build/basic.settings 2012-04-23 16:58:16.491426801
+0200
-@@ -327,6 +327,12 @@
+--- rosetta_source.orig/tools/build/basic.settings
rosetta_source/tools/build/basic.settings
+@@ -372,6 +372,12 @@
cxx: g++-4.6,
},
},
@@ -15,16 +15,21 @@
gcc, macos : {
appends : {
flags : {
-Index: rosetta-3.4/tools/build/options.settings
+Index: rosetta_source/tools/build/options.settings
===
rosetta-3.4.orig/tools/build/options.settings 2012-03-20
19:44:23.0 +0100
-+++ rosetta-3.4/tools/build/options.settings 2012-04-23 16:58:35.675165901
+0200
-@@ -9,7 +9,7 @@
+--- rosetta_source.orig/tools/build/options.settings
rosetta_source/tools/build/options.settings
+@@ -9,11 +9,11 @@
options = {
cxx : {
--gcc : [ 3.3, 3.4, 4.0, 4.1, 4.2, 4.3,4.4,4.5,
4.6, * ],
-+gcc : [ 3.3, 3.4, 4.0, 4.1, 4.2, 4.3,4.4,4.5,
4.6, 4.7, * ],
+-gcc : [ 3.3, 3.4, 4.0, 4.1, 4.2, 4.3,4.4,4.5,
4.6,4.7, * ],
++gcc : [ 3.3, 3.4, 4.0, 4.1, 4.2, 4.3,4.4,4.5,
4.6,4.7, 4.8, * ],
icc : [ 8.0, 8.1, 9.0, 9.1, 10.0, 10.1, 11.1, *
], #PBHACK
msvc: [ 7.0, 7.1, 8.0, 8.1, * ],
xlc : [ 7.0, 8.0, 9.0, XL, * ],
+-clang : [ 1.7, 2.1, 2.0, 2.8, 2.9, 3.0, 3.1, 4.0,
3.0-6ubuntu3, 4.1, 4.2, * ],
++clang : [ 1.7, 2.1, 2.0, 2.8, 2.9, 3.0, 3.1, 4.0,
3.0-6ubuntu3, 4.1, 4.2, 4.3, * ],
+ },
+
+ os : {
___
debian-med-commit mailing list
debian-med-commit@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13848 - in trunk/packages/mira/trunk/debian: . patches
Author: alteholz Date: 2013-06-05 18:10:33 + (Wed, 05 Jun 2013) New Revision: 13848 Added: trunk/packages/mira/trunk/debian/obsolete.mira-assembler.install trunk/packages/mira/trunk/debian/patches/hardening-flags.patch Removed: trunk/packages/mira/trunk/debian/mira-assembler.install Modified: trunk/packages/mira/trunk/debian/changelog trunk/packages/mira/trunk/debian/compat trunk/packages/mira/trunk/debian/control trunk/packages/mira/trunk/debian/patches/series trunk/packages/mira/trunk/debian/patches/xsltproc_nonet_for_doc_build trunk/packages/mira/trunk/debian/rules trunk/packages/mira/trunk/debian/watch Log: some progress Modified: trunk/packages/mira/trunk/debian/changelog === --- trunk/packages/mira/trunk/debian/changelog 2013-06-05 16:22:11 UTC (rev 13847) +++ trunk/packages/mira/trunk/debian/changelog 2013-06-05 18:10:33 UTC (rev 13848) @@ -1,3 +1,23 @@ +mira (3.9.17-1) UNRELEASED; urgency=low + + * new upstream version + * debian/control: Standards-Version set to 3.9.4 (no changes) + * debian/control: DM-Upload-Allowed: removed + * debian/control: use dh 9 + * debian/control: add dependency to libboost-iostreams-dev + * debian/rules: get-orig-source added + * debian/watch: do not look at dev-versions + * TODO: RC bug (gcc4.8) + boost 1.53 + lintian stuff: manpages +spelling errors +hardening flags for fastatool +extended description +docbase +Up to now the new version builds with old gcc and old boost. + + -- Thorsten Alteholz deb...@alteholz.de Wed, 05 Jun 2013 18:00:01 +0200 + mira (3.4.0.1-3) unstable; urgency=low [ Charles Plessy ] Modified: trunk/packages/mira/trunk/debian/compat === --- trunk/packages/mira/trunk/debian/compat 2013-06-05 16:22:11 UTC (rev 13847) +++ trunk/packages/mira/trunk/debian/compat 2013-06-05 18:10:33 UTC (rev 13848) @@ -1 +1 @@ -7 +9 Modified: trunk/packages/mira/trunk/debian/control === --- trunk/packages/mira/trunk/debian/control2013-06-05 16:22:11 UTC (rev 13847) +++ trunk/packages/mira/trunk/debian/control2013-06-05 18:10:33 UTC (rev 13848) @@ -2,14 +2,25 @@ Section: science Priority: optional Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org -DM-Upload-Allowed: yes -Uploaders: Charles Plessy ple...@debian.org, Steffen Moeller moel...@debian.org, - Tim Booth tbo...@ceh.ac.uk, Andreas Tille ti...@debian.org -Build-Depends: debhelper (= 7.0.50~), autotools-dev, dblatex, docbook-xsl, - libboost-thread-dev, libboost-regex-dev, libexpat1-dev, - libgoogle-perftools-dev [i386 amd64], perl, flex, - vim-common, zlib1g-dev -Standards-Version: 3.9.3 +Uploaders: Charles Plessy ple...@debian.org, + Steffen Moeller moel...@debian.org, + Tim Booth tbo...@ceh.ac.uk, + Andreas Tille ti...@debian.org, + Thorsten Alteholz deb...@alteholz.de +Build-Depends: debhelper (= 9), + autotools-dev, + dblatex, + docbook-xsl, + libboost-thread-dev, + libboost-regex-dev, + libboost-iostreams-dev, + libexpat1-dev, + libgoogle-perftools-dev [i386 amd64], + perl, + flex, + vim-common, + zlib1g-dev +Standards-Version: 3.9.4 Homepage: http://chevreux.org/projects_mira.html Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mira/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mira/trunk/ Deleted: trunk/packages/mira/trunk/debian/mira-assembler.install === --- trunk/packages/mira/trunk/debian/mira-assembler.install 2013-06-05 16:22:11 UTC (rev 13847) +++ trunk/packages/mira/trunk/debian/mira-assembler.install 2013-06-05 18:10:33 UTC (rev 13848) @@ -1,8 +0,0 @@ -src/progs/fastatoolusr/bin/ -src/progs/mira usr/bin/ -src/progs/scftool usr/bin/ -src/progs/sw usr/bin/ -src/progs/convert_project usr/bin/ -src/scripts/fasta2frag.tcl usr/bin/ -src/scripts/fastaselect.tclusr/bin/ -src/scripts/fastqselect.tclusr/bin/ Copied: trunk/packages/mira/trunk/debian/obsolete.mira-assembler.install (from rev 13765, trunk/packages/mira/trunk/debian/mira-assembler.install) === --- trunk/packages/mira/trunk/debian/obsolete.mira-assembler.install (rev 0) +++ trunk/packages/mira/trunk/debian/obsolete.mira-assembler.install 2013-06-05 18:10:33 UTC (rev 13848) @@ -0,0 +1,8 @@ +#src/progs/fastatool usr/bin/ +#src/progs/mirausr/bin/ +#src/progs/scftool usr/bin/ +#src/progs/sw usr/bin/ +#src/progs/convert_project usr/bin/ +#src/scripts/fasta2frag.tclusr/bin/
[med-svn] r13849 - trunk/packages/libzeep/trunk/debian
Author: alteholz Date: 2013-06-05 20:08:47 + (Wed, 05 Jun 2013) New Revision: 13849 Modified: trunk/packages/libzeep/trunk/debian/changelog trunk/packages/libzeep/trunk/debian/control Log: close bug Modified: trunk/packages/libzeep/trunk/debian/changelog === --- trunk/packages/libzeep/trunk/debian/changelog 2013-06-05 18:10:33 UTC (rev 13848) +++ trunk/packages/libzeep/trunk/debian/changelog 2013-06-05 20:08:47 UTC (rev 13849) @@ -1,6 +1,6 @@ libzeep (3.0.1-1) unstable; urgency=low - * New upstream release with fix for IBM S/390 + * New upstream release with fix for IBM S/390 (Closes: #710543) -- Maarten L. Hekkelman m.hekkel...@cmbi.ru.nl Wed, 06 Jun 2013 10:00:00 +0200 Modified: trunk/packages/libzeep/trunk/debian/control === --- trunk/packages/libzeep/trunk/debian/control 2013-06-05 18:10:33 UTC (rev 13848) +++ trunk/packages/libzeep/trunk/debian/control 2013-06-05 20:08:47 UTC (rev 13849) @@ -13,7 +13,6 @@ Section: libs Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/libzeep/trunk/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/libzeep/trunk/ -DM-Upload-Allowed: yes Homepage: http://www.cmbi.ru.nl/libzeep/ Package: libzeep-dev ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13850 - trunk/packages/profit/trunk/debian
Author: tille
Date: 2013-06-05 21:05:26 + (Wed, 05 Jun 2013)
New Revision: 13850
Modified:
trunk/packages/profit/trunk/debian/changelog
trunk/packages/profit/trunk/debian/control
trunk/packages/profit/trunk/debian/copyright
Log:
Even if package is non-redistributable the metainformation should be correct
and helpful because prospective package gatherer grabs and uses this information
Modified: trunk/packages/profit/trunk/debian/changelog
===
--- trunk/packages/profit/trunk/debian/changelog2013-06-05 20:08:47 UTC
(rev 13849)
+++ trunk/packages/profit/trunk/debian/changelog2013-06-05 21:05:26 UTC
(rev 13850)
@@ -1,5 +1,6 @@
profit (3.1-1) UNRELEASED; urgency=low
+ * Initial packaging that would (closes: #525428) if package would be
redistributable
* The license does not allow a redistribution.
-- Steffen Moeller moel...@debian.org Wed, 05 Jun 2013 17:38:14 +0200
Modified: trunk/packages/profit/trunk/debian/control
===
--- trunk/packages/profit/trunk/debian/control 2013-06-05 20:08:47 UTC (rev
13849)
+++ trunk/packages/profit/trunk/debian/control 2013-06-05 21:05:26 UTC (rev
13850)
@@ -5,14 +5,17 @@
Build-Depends: debhelper (= 8.0.0), libreadline-dev
Standards-Version: 3.9.4
Homepage: http://www.bioinf.org.uk/software/profit/
-#Vcs-Git: git://git.debian.org/collab-maint/profit.git
-#Vcs-Browser: http://git.debian.org/?p=collab-maint/profit.git;a=summary
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/profit/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/profit/trunk/
Package: profit
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}, profit-data
Description: Protein structure alignment
- Nothing to be redistributed.
+ ProFit is designed to be the ultimate protein least squares fitting
+ program. It has many features including flexible specification of
+ fitting zones and atoms, calculation of RMS over different zones or
+ atoms, RMS-by-residue calculation, on-line help facility, etc.
Package: profit-data
Architecture: all
Modified: trunk/packages/profit/trunk/debian/copyright
===
--- trunk/packages/profit/trunk/debian/copyright2013-06-05 20:08:47 UTC
(rev 13849)
+++ trunk/packages/profit/trunk/debian/copyright2013-06-05 21:05:26 UTC
(rev 13850)
@@ -5,7 +5,7 @@
Files: *
Copyright: years put author's name and email here
years likewise for another author
-License: special license
+License: non-distributable
ProFit
.
Protein Least Squares Fitting
___
debian-med-commit mailing list
debian-med-commit@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
