[med-svn] r13465 - trunk/packages/R/r-cran-genabel/trunk/debian
Author: plessy Date: 2013-05-01 06:09:20 + (Wed, 01 May 2013) New Revision: 13465 Modified: trunk/packages/R/r-cran-genabel/trunk/debian/changelog Log: r-cran-genabel (1.7-4-1) unstable; urgency=low * New upstream version * Updated qvalue package name (moved from CRAN to Bioconductor). * Drop references to old name r-other-genabel. * Drop build-dependance on package only suggested. * Normalised VCS URLs following Lintian's standard. * Acquire R:Depends directly from r-base-dev. * Normalised control file with cme. -- Charles Plessy ple...@debian.org Wed, 01 May 2013 14:58:43 +0900 Modified: trunk/packages/R/r-cran-genabel/trunk/debian/changelog === --- trunk/packages/R/r-cran-genabel/trunk/debian/changelog 2013-05-01 05:57:53 UTC (rev 13464) +++ trunk/packages/R/r-cran-genabel/trunk/debian/changelog 2013-05-01 06:09:20 UTC (rev 13465) @@ -1,4 +1,4 @@ -r-cran-genabel (1.7-4-1) UNRELEASED; urgency=low +r-cran-genabel (1.7-4-1) unstable; urgency=low * New upstream version * Updated qvalue package name (moved from CRAN to Bioconductor). @@ -8,7 +8,7 @@ * Acquire R:Depends directly from r-base-dev. * Normalised control file with cme. - -- Charles Plessy ple...@debian.org Wed, 01 May 2013 14:34:36 +0900 + -- Charles Plessy ple...@debian.org Wed, 01 May 2013 14:58:43 +0900 r-cran-genabel (1.7-3-1) 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] r13466 - in trunk/packages/R/r-cran-genabel/tags: . 1.7-4-1/debian
Author: plessy
Date: 2013-05-01 06:09:53 + (Wed, 01 May 2013)
New Revision: 13466
Added:
trunk/packages/R/r-cran-genabel/tags/1.7-4-1/
trunk/packages/R/r-cran-genabel/tags/1.7-4-1/debian/changelog
trunk/packages/R/r-cran-genabel/tags/1.7-4-1/debian/control
trunk/packages/R/r-cran-genabel/tags/1.7-4-1/debian/copyright
trunk/packages/R/r-cran-genabel/tags/1.7-4-1/debian/rules
Removed:
trunk/packages/R/r-cran-genabel/tags/1.7-4-1/debian/changelog
trunk/packages/R/r-cran-genabel/tags/1.7-4-1/debian/control
trunk/packages/R/r-cran-genabel/tags/1.7-4-1/debian/copyright
trunk/packages/R/r-cran-genabel/tags/1.7-4-1/debian/rules
Log:
[svn-buildpackage] Tagging r-cran-genabel 1.7-4-1
Deleted: trunk/packages/R/r-cran-genabel/tags/1.7-4-1/debian/changelog
===
--- trunk/packages/R/r-cran-genabel/trunk/debian/changelog 2013-05-01
04:10:07 UTC (rev 13456)
+++ trunk/packages/R/r-cran-genabel/tags/1.7-4-1/debian/changelog
2013-05-01 06:09:53 UTC (rev 13466)
@@ -1,76 +0,0 @@
-r-cran-genabel (1.7-3-1) UNRELEASED; urgency=low
-
- * New upstream version
- * Replace debian/README.Debian by debian/README.test
- * DEP5 copyright
- * Standards-Version: 3.9.4 (no changes needed)
- * debhelper 9 (control+compat)
-
- -- Andreas Tille ti...@debian.org Sat, 02 Feb 2013 12:32:39 +0100
-
-r-cran-genabel (1.7-0-3) testing-proposed-updates; urgency=low
-
- * Upload to testing-proposed-updates
-
- -- Andreas Tille ti...@debian.org Sat, 02 Feb 2013 07:08:19 +
-
-r-cran-genabel (1.7-0-2) unstable; urgency=low
-
- * Fixing the problem which prevents the package from loading while
-checking the version on CRAN
-Closes: #699260
-
- -- Andreas Tille ti...@debian.org Wed, 30 Jan 2013 13:11:06 +0100
-
-r-cran-genabel (1.7-0-1) unstable; urgency=low
-
- * New upstream release.
- * Depends and Suggests packages according to DESCRIPTION (debian/control).
- * Corrected VCS URLs (debian/control).
- * Conforms with Policy 3.9.2 (debian/control, no other changes needed).
- * Build-Depend on r-cran-mass instead of the whole r-recommended.
-
- -- Charles Plessy ple...@debian.org Fri, 13 Jan 2012 13:56:32 +0900
-
-r-cran-genabel (1.6-5-1) unstable; urgency=low
-
- * New upstream release, buildable with R 2.12 (closes: #620269).
-
- [ Andreas Tille ]
- * debian/control:
-- added myself to uploaders
-- changed section to gnu-r
-- Depend on ${R:Depends}
- * debian/rules:
-- fix permissions of files that should not be executable
-- Require a number equal or superior than the R version the package
- was built with, using a R:Depends substvar
-
- [ Charles Plessy ]
- * debian/control:
-- Added myself to uploaders.
-- Use debhelper 8 (debian/compat).
-- Build-depend on R 2.10 according to DESCRIPTION.
-- Replaces r-other-genabel.
-- Added Vcs-Browser and Vcs-Svn fields.
-- Updated homepage.
- * Install CHANGES.LOG as upstream changelog (debian/rules).
- * Converted debian/copyright to DEP-5 format.
-
- -- Charles Plessy ple...@debian.org Fri, 01 Apr 2011 13:46:37 +0900
-
-r-cran-genabel (1.6-4-1) unstable; urgency=low
-
- * New upstream release.
- * The package has now arrived in CRAN and is taken from there,
-which according to the R policy is also reflected by the name change.
- * Switch to source/format 3.0 (quilt)
- * Bumped policy-standard to 3.9.1.
-
- -- Steffen Moeller moel...@debian.org Sat, 05 Feb 2011 18:06:24 +0100
-
-r-other-genabel (1.4-0-1) unstable; urgency=low
-
- * Initial release (Closes: #492044).
-
- -- Steffen Moeller moel...@debian.org Wed, 23 Jul 2008 15:43:37 +0200
Copied: trunk/packages/R/r-cran-genabel/tags/1.7-4-1/debian/changelog (from rev
13465, trunk/packages/R/r-cran-genabel/trunk/debian/changelog)
===
--- trunk/packages/R/r-cran-genabel/tags/1.7-4-1/debian/changelog
(rev 0)
+++ trunk/packages/R/r-cran-genabel/tags/1.7-4-1/debian/changelog
2013-05-01 06:09:53 UTC (rev 13466)
@@ -0,0 +1,88 @@
+r-cran-genabel (1.7-4-1) unstable; urgency=low
+
+ * New upstream version
+ * Updated qvalue package name (moved from CRAN to Bioconductor).
+ * Drop references to old name r-other-genabel.
+ * Drop build-dependance on package only suggested.
+ * Normalised VCS URLs following Lintian's standard.
+ * Acquire R:Depends directly from r-base-dev.
+ * Normalised control file with cme.
+
+ -- Charles Plessy ple...@debian.org Wed, 01 May 2013 14:58:43 +0900
+
+r-cran-genabel (1.7-3-1) unstable; urgency=low
+
+ * New upstream version
+ * Replace debian/README.Debian by debian/README.test
+ * DEP5 copyright
+ * Standards-Version: 3.9.4 (no changes needed)
+ * debhelper 9 (control+compat)
+
+ -- Andreas Tille ti...@debian.org Sat, 02 Feb 2013 12:32:39 +0100
+
+r-cran-genabel (1.7-0-3) testing-proposed-updates; urgency=low
+
+ *
[med-svn] [SCM] picard-tools branch, master, updated. debian/1.82-2-18-ge2c1be2
The following commit has been merged in the master branch:
commit 9bfa34c77dd41ed10f39bb5276c5047003ec7040
Author: Olivier Sallou olivier.sal...@debian.org
Date: Wed May 1 09:19:57 2013 +0200
add JEXL2 dependency
diff --git a/debian/control b/debian/control
index 343498b..3506320 100644
--- a/debian/control
+++ b/debian/control
@@ -7,7 +7,8 @@ Uploaders: Shaun Jackman sjack...@debian.org,
Charles Plessy ple...@debian.org,
Olivier Sallou osal...@debian.org
Build-Depends: ant, default-jdk, testng, libsnappy1.0.3-java,
- debhelper (= 7.0.50~), libjbzip2-java, libcofoja-java
+ debhelper (= 7.0.50~), libjbzip2-java, libcofoja-java,
+ libcommons-jexl2-java
Standards-Version: 3.9.3
Homepage: http://picard.sourceforge.net/
Vcs-Git: git://git.debian.org/git/debian-med/picard-tools.git
@@ -27,7 +28,8 @@ Architecture: all
Depends: default-jre | java6-runtime, ${misc:Depends},
libsam-java (= ${source:Version}), ${python:Depends},
libjbzip2-java,
- libcofoja-java
+ libcofoja-java,
+ libcommons-jexl2-java
Suggests: python, r-base-core
Description: Command line tools to manipulate SAM and BAM files
SAM (Sequence Alignment/Map) format is a generic format for storing
--
manipulate SAM and BAM files
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[med-svn] [SCM] picard-tools branch, master, updated. debian/1.82-2-18-ge2c1be2
The following commit has been merged in the master branch:
commit 2c251dce1e623c989930810936bc6a1bfeb98a33
Author: Olivier Sallou olivier.sal...@debian.org
Date: Wed May 1 09:17:08 2013 +0200
add cofoja dependency
diff --git a/debian/control b/debian/control
index 7e7f521..343498b 100644
--- a/debian/control
+++ b/debian/control
@@ -7,7 +7,7 @@ Uploaders: Shaun Jackman sjack...@debian.org,
Charles Plessy ple...@debian.org,
Olivier Sallou osal...@debian.org
Build-Depends: ant, default-jdk, testng, libsnappy1.0.3-java,
- debhelper (= 7.0.50~), libjbzip2-java
+ debhelper (= 7.0.50~), libjbzip2-java, libcofoja-java
Standards-Version: 3.9.3
Homepage: http://picard.sourceforge.net/
Vcs-Git: git://git.debian.org/git/debian-med/picard-tools.git
@@ -26,7 +26,8 @@ Package: picard-tools
Architecture: all
Depends: default-jre | java6-runtime, ${misc:Depends},
libsam-java (= ${source:Version}), ${python:Depends},
- libjbzip2-java
+ libjbzip2-java,
+ libcofoja-java
Suggests: python, r-base-core
Description: Command line tools to manipulate SAM and BAM files
SAM (Sequence Alignment/Map) format is a generic format for storing
--
manipulate SAM and BAM files
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[med-svn] [SCM] picard-tools branch, master, updated. debian/1.82-2-18-ge2c1be2
The following commit has been merged in the master branch:
commit d8c95d8fc0e89707525569400a54e260a27227b9
Author: Olivier Sallou olivier.sal...@debian.org
Date: Wed May 1 09:22:10 2013 +0200
add jexl2 to classpath
diff --git a/debian/patches/01-build.xml b/debian/patches/01-build.xml
index 615f631..ffa30a1 100644
--- a/debian/patches/01-build.xml
+++ b/debian/patches/01-build.xml
@@ -25,7 +25,7 @@ Forwarded: no
property environment=env/
-@@ -72,6 +72,10 @@
+@@ -72,6 +72,11 @@
fileset dir=${lib}
include name=**/*.jar/
/fileset
@@ -33,10 +33,11 @@ Forwarded: no
+pathelement path=/usr/share/java/snappy1.0.3-java.jar/
+pathelement path=/usr/share/java/jbzip2.jar/
+pathelement path=/usr/share/java/cofoja.jar/
++pathelement path=/usr/share/java/commons-jexl2.jar/
/path
path id=metrics.classpath
pathelement path=${classpath}/
-@@ -209,7 +213,7 @@
+@@ -209,7 +214,7 @@
mkdir dir=${dist}/
jar destfile=${dist}/picard-${picard-version}.jar compress=no
fileset dir=${classes} includes =net/sf/picard/**/*.*/
@@ -45,7 +46,7 @@ Forwarded: no
manifest
attribute name=Implementation-Version
value=${picard-version}(${repository.revision})/
attribute name=Implementation-Vendor value=Broad
Institute/
-@@ -239,6 +243,8 @@
+@@ -239,6 +244,8 @@
/copy
/target
--
manipulate SAM and BAM files
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[med-svn] [SCM] picard-tools branch, master, updated. debian/1.82-2-18-ge2c1be2
The following commit has been merged in the master branch: commit a29b7931e5a0f9265fb0fed49290d3b1b5c908cd Author: Olivier Sallou olivier.sal...@debian.org Date: Wed May 1 09:33:23 2013 +0200 add/update classpath diff --git a/debian/bin/picard-tools b/debian/bin/picard-tools index 2bd95d5..e892287 100755 --- a/debian/bin/picard-tools +++ b/debian/bin/picard-tools @@ -62,4 +62,4 @@ EOF esac p=/usr/share/java -exec java -XX:MaxPermSize=256m -cp $p/jbzip2.jar:$p/picard.jar:$p/sam.jar $main $@ +exec java -XX:MaxPermSize=256m -cp $p/jbzip2.jar:$p/picard.jar:$p/sam.jar:$p/cofoja.jar:$p/commons-jexl2.jar $main $@ diff --git a/debian/picard-tools.classpath b/debian/picard-tools.classpath new file mode 100644 index 000..7034c2e --- /dev/null +++ b/debian/picard-tools.classpath @@ -0,0 +1 @@ +usr/share/java/commons-jexl2.jar usr/share/java/cofoja.jar usr/share/java/jbzip2.jar usr/share/java/sam.jar -- manipulate SAM and BAM files ___ 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] picard-tools branch, master, updated. debian/1.82-2-18-ge2c1be2
The following commit has been merged in the master branch: commit 99ea5121699b25181b631b639c63236c99d5df08 Author: Olivier Sallou olivier.sal...@debian.org Date: Wed May 1 09:40:30 2013 +0200 fix classpath in manifest diff --git a/debian/picard-tools.classpath b/debian/picard-tools.classpath index 7034c2e..72b7b96 100644 --- a/debian/picard-tools.classpath +++ b/debian/picard-tools.classpath @@ -1 +1 @@ -usr/share/java/commons-jexl2.jar usr/share/java/cofoja.jar usr/share/java/jbzip2.jar usr/share/java/sam.jar +/usr/share/java/commons-jexl2.jar /usr/share/java/cofoja.jar /usr/share/java/jbzip2.jar /usr/share/java/sam.jar -- manipulate SAM and BAM files ___ 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] picard-tools branch, master, updated. debian/1.82-2-18-ge2c1be2
The following commit has been merged in the master branch: commit d15d8322b40a0d74234aaac83428cf9f038c0680 Author: Olivier Sallou olivier.sal...@debian.org Date: Wed May 1 09:37:57 2013 +0200 add javahelper diff --git a/debian/control b/debian/control index 3506320..3cdbab4 100644 --- a/debian/control +++ b/debian/control @@ -8,7 +8,8 @@ Uploaders: Shaun Jackman sjack...@debian.org, Olivier Sallou osal...@debian.org Build-Depends: ant, default-jdk, testng, libsnappy1.0.3-java, debhelper (= 7.0.50~), libjbzip2-java, libcofoja-java, - libcommons-jexl2-java + libcommons-jexl2-java, + javahelper (=0.25) Standards-Version: 3.9.3 Homepage: http://picard.sourceforge.net/ Vcs-Git: git://git.debian.org/git/debian-med/picard-tools.git diff --git a/debian/rules b/debian/rules index 125a6d4..11140b7 100755 --- a/debian/rules +++ b/debian/rules @@ -3,7 +3,7 @@ export DH_OPTIONS %: - dh $@ + dh $@ --with javahelper override_dh_auto_build: dh_auto_build -- -Dant.build.javac.source=1.5 -Dant.build.javac.target=1.5 -- manipulate SAM and BAM files ___ 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] picard-tools branch, master, updated. debian/1.82-2-18-ge2c1be2
The following commit has been merged in the master branch: commit e2c1be2095c3896691974df34d9dcd2f04cb5d86 Author: Olivier Sallou olivier.sal...@debian.org Date: Wed May 1 09:48:29 2013 +0200 upload to experimental diff --git a/debian/changelog b/debian/changelog index d871205..da787cb 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,9 +1,6 @@ -picard-tools (1.87-1) UNRELEASED; urgency=low +picard-tools (1.87-1) experimental; urgency=low * New upstream release - TODO: need additional library cofoja (https://code.google.com/p/cofoja/) -- packaging in progress by O. Sallou - - Needs JEXL2 (java lib) -- Olivier Sallou osal...@debian.org Thu, 21 Mar 2013 15:14:04 +0100 -- manipulate SAM and BAM files ___ 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] picard-tools branch, master, updated. debian/1.82-2-18-ge2c1be2
The following commit has been merged in the master branch: commit 3562d629b9843d706b630bd566047c49f5ba9d25 Author: Olivier Sallou olivier.sal...@debian.org Date: Wed May 1 09:44:05 2013 +0200 add missing jar origin file diff --git a/debian/picard-tools.classpath b/debian/picard-tools.classpath index 72b7b96..947e7e2 100644 --- a/debian/picard-tools.classpath +++ b/debian/picard-tools.classpath @@ -1 +1 @@ -/usr/share/java/commons-jexl2.jar /usr/share/java/cofoja.jar /usr/share/java/jbzip2.jar /usr/share/java/sam.jar +usr/share/java/picard.jar /usr/share/java/commons-jexl2.jar /usr/share/java/cofoja.jar /usr/share/java/jbzip2.jar /usr/share/java/sam.jar -- manipulate SAM and BAM files ___ 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] picard-tools annotated tag, debian/1.87-1, created. debian/1.87-1
The annotated tag, debian/1.87-1 has been created at 3ba069a6a825a57478c2b7c2686233612ae7f1ad (tag) tagging e2c1be2095c3896691974df34d9dcd2f04cb5d86 (commit) replaces debian/1.82-2 tagged by Olivier Sallou on Wed May 1 09:50:56 2013 +0200 - Shortlog picard-tools Debian release 1.87-1 Olivier Sallou (18): Update SVN url Imported Upstream version 1.87 Imported Upstream version 1.87 Merge tag 'upstream/1.87' new upstream release 1.87 add todo, require new dependency packaging update pathc to new release add cofoja to classpath add status on deps merge fix 705686 add cofoja dependency add JEXL2 dependency add jexl2 to classpath add/update classpath add javahelper fix classpath in manifest add missing jar origin file upload to experimental --- -- manipulate SAM and BAM files ___ 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] aghermann branch, master, updated. 37a0de8357bfecc4e7f7ec7b402c4c4b73d7cac6
The following commit has been merged in the master branch: commit 37a0de8357bfecc4e7f7ec7b402c4c4b73d7cac6 Author: Andrei Zavada johnhom...@gmail.com Date: Wed May 1 12:43:54 2013 +0300 amend debian/changelog diff --git a/debian/changelog b/debian/changelog index d7f9dc9..4e13fe8 100644 --- a/debian/changelog +++ b/debian/changelog @@ -7,7 +7,7 @@ aghermann (0.9.0-1) experimental; urgency=low aghermann (0.8.1-1) experimental; urgency=low * New upstream version. - * Compiles with g++4-8 (Closes: #701241). +- fixed compatibility issues with g++-4.8 (Closes: #701241). -- Andrei Zavada johnhom...@gmail.com Tue, 26 Jan 2013 01:15:08 +0200 -- Sleep experiment manager ___ 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] picard-tools branch, master, updated. debian/1.87-1-6-g0504974
The following commit has been merged in the master branch: commit 66593c73cebf892d5e31ad2bb51251b670ddda87 Author: Olivier Sallou olivier.sal...@debian.org Date: Wed May 1 11:30:45 2013 +0200 update llast log date diff --git a/debian/changelog b/debian/changelog index da787cb..c5788ec 100644 --- a/debian/changelog +++ b/debian/changelog @@ -2,7 +2,7 @@ picard-tools (1.87-1) experimental; urgency=low * New upstream release - -- Olivier Sallou osal...@debian.org Thu, 21 Mar 2013 15:14:04 +0100 + -- Olivier Sallou osal...@debian.org Web, 01 May 2013 15:14:04 +0100 picard-tools (1.82-2) unstable; urgency=low -- manipulate SAM and BAM files ___ 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] picard-tools branch, master, updated. debian/1.87-1-6-g0504974
The following commit has been merged in the master branch: commit fd6a74be20d7267e3b0d2752b660db66cd7c44f9 Author: Olivier Sallou olivier.sal...@debian.org Date: Wed May 1 11:31:45 2013 +0200 update last log date diff --git a/debian/changelog b/debian/changelog index c5788ec..41b09ae 100644 --- a/debian/changelog +++ b/debian/changelog @@ -2,7 +2,7 @@ picard-tools (1.87-1) experimental; urgency=low * New upstream release - -- Olivier Sallou osal...@debian.org Web, 01 May 2013 15:14:04 +0100 + -- Olivier Sallou osal...@debian.org Wed, 01 May 2013 15:14:04 +0100 picard-tools (1.82-2) unstable; urgency=low -- manipulate SAM and BAM files ___ 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] picard-tools branch, master, updated. debian/1.87-1-6-g0504974
The following commit has been merged in the master branch: commit cf023503d97308f22c6fc0676fbcda311a4eaad4 Author: Olivier Sallou olivier.sal...@debian.org Date: Wed May 1 13:57:48 2013 +0200 new upstream 1.90 diff --git a/debian/changelog b/debian/changelog index 41b09ae..79ea434 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +picard-tools (1.90-1) UNRELEASED; urgency=low + + * New upstream release + + -- Olivier Sallou osal...@debian.org Wed, 01 May 2013 13:57:05 +0200 + picard-tools (1.87-1) experimental; urgency=low * New upstream release -- manipulate SAM and BAM files ___ 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] picard-tools branch, pristine-tar, updated. 5f44675aa0b8f5e9d512db7b3000c84e72657a0f
The following commit has been merged in the pristine-tar branch: commit 5f44675aa0b8f5e9d512db7b3000c84e72657a0f Author: Olivier Sallou olivier.sal...@debian.org Date: Wed May 1 14:05:15 2013 +0200 pristine-tar data for picard-tools_1.90.orig.tar.bz2 diff --git a/picard-tools_1.90.orig.tar.bz2.delta b/picard-tools_1.90.orig.tar.bz2.delta new file mode 100644 index 000..1fe0d99 Binary files /dev/null and b/picard-tools_1.90.orig.tar.bz2.delta differ diff --git a/picard-tools_1.90.orig.tar.bz2.id b/picard-tools_1.90.orig.tar.bz2.id new file mode 100644 index 000..c49b61b --- /dev/null +++ b/picard-tools_1.90.orig.tar.bz2.id @@ -0,0 +1 @@ +119faebd8495ded25bd00a0d95be708fc4b97232 -- manipulate SAM and BAM files ___ 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] picard-tools branch, master, updated. debian/1.87-1-6-g0504974
The following commit has been merged in the master branch: commit 050497440235ff670a08e41236ceebf502b8fafa Author: Olivier Sallou olivier.sal...@debian.org Date: Wed May 1 14:11:47 2013 +0200 upload to experimental diff --git a/debian/changelog b/debian/changelog index 79ea434..4a26dd3 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,4 +1,4 @@ -picard-tools (1.90-1) UNRELEASED; urgency=low +picard-tools (1.90-1) experimental; urgency=low * New upstream release -- manipulate SAM and BAM files ___ 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] picard-tools branch, master, updated. debian/1.87-1-6-g0504974
The following commit has been merged in the master branch: commit f2bdbe715d1312dde24031982eff4fd2dc57d9b5 Merge: cf023503d97308f22c6fc0676fbcda311a4eaad4 67202adf442e0bdc7a2cad85cd330cec855b8580 Author: Olivier Sallou olivier.sal...@debian.org Date: Wed May 1 14:05:17 2013 +0200 Merge tag 'upstream/1.90' Upstream version 1.90 -- manipulate SAM and BAM files ___ 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] picard-tools annotated tag, upstream/1.90, created. upstream/1.90
The annotated tag, upstream/1.90 has been created at 5ff8f1a7f401fec8f0c5259fb646be5195a43156 (tag) tagging 67202adf442e0bdc7a2cad85cd330cec855b8580 (commit) replaces upstream/1.87 tagged by Olivier Sallou on Wed May 1 14:05:16 2013 +0200 - Shortlog Upstream version 1.90 Olivier Sallou (1): Imported Upstream version 1.90 --- -- manipulate SAM and BAM files ___ 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] picard-tools annotated tag, debian/1.90-1, created. debian/1.90-1
The annotated tag, debian/1.90-1 has been created at 072568ff29cf13e9c6969902eb42bbabada28da8 (tag) tagging 050497440235ff670a08e41236ceebf502b8fafa (commit) replaces debian/1.87-1 tagged by Olivier Sallou on Wed May 1 14:19:37 2013 +0200 - Shortlog picard-tools Debian release 1.90-1 Olivier Sallou (6): update llast log date update last log date new upstream 1.90 Imported Upstream version 1.90 Merge tag 'upstream/1.90' upload to experimental --- -- manipulate SAM and BAM files ___ 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] r13468 - in trunk/packages/proalign/trunk/debian: . scripts source
Author: alteholz Date: 2013-05-01 20:09:53 + (Wed, 01 May 2013) New Revision: 13468 Added: trunk/packages/proalign/trunk/debian/manifest.txt trunk/packages/proalign/trunk/debian/proalign.install trunk/packages/proalign/trunk/debian/rules trunk/packages/proalign/trunk/debian/scripts/ trunk/packages/proalign/trunk/debian/scripts/proalign trunk/packages/proalign/trunk/debian/source/ trunk/packages/proalign/trunk/debian/source/format Modified: trunk/packages/proalign/trunk/debian/ trunk/packages/proalign/trunk/debian/changelog trunk/packages/proalign/trunk/debian/control trunk/packages/proalign/trunk/debian/watch Log: proalign almost ready, just needs a manpage and some tests Property changes on: trunk/packages/proalign/trunk/debian ___ Added: mergeWithUpstream + 1 Modified: trunk/packages/proalign/trunk/debian/changelog === --- trunk/packages/proalign/trunk/debian/changelog 2013-05-01 13:31:42 UTC (rev 13467) +++ trunk/packages/proalign/trunk/debian/changelog 2013-05-01 20:09:53 UTC (rev 13468) @@ -1,5 +1,5 @@ -proalign (0.603-1) unstable; urgency=low +proalign (0.603-1) UNRELEASED; urgency=low * Initial release (Closes: #378290) - -- Andreas Tille ti...@debian.org Thu, 24 May 2012 14:30:13 +0200 + -- Thorsten Alteholz deb...@alteholz.de Tue, 01 May 2013 18:00:00 +0200 Modified: trunk/packages/proalign/trunk/debian/control === --- trunk/packages/proalign/trunk/debian/control2013-05-01 13:31:42 UTC (rev 13467) +++ trunk/packages/proalign/trunk/debian/control2013-05-01 20:09:53 UTC (rev 13468) @@ -3,9 +3,10 @@ Priority: optional Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org DM-Upload-Allowed: yes -Uploaders: Andreas Tille ti...@debian.org +Uploaders: Andreas Tille ti...@debian.org, + Thorsten Alteholz deb...@alteholz.de Build-Depends: debhelper (= 9) -Standards-Version: 3.9.3 +Standards-Version: 3.9.4 Homepage: http://ueg.ulb.ac.be/ProAlign/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/proalign/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/proalign/trunk/ @@ -18,11 +19,11 @@ models (HMM). It includes a graphical interface (GUI) allowing to (i) perform alignments of nucleotide or amino-acid sequences, (ii) view the quality of solutions, (iii) filter the unreliable alignment regions and - (iv) export alignments to other softwares. + (iv) export alignments to other software. . ProAlign uses a progressive method, such that multiple alignment is created stepwise by performing pairwise alignments in the nodes of a guide tree. Sequences are described with vectors of character probabilities, and each pairwise alignment reconstructs the ancestral (parent) sequence by computing the probabilities of different - characters according to an evolutionary model. \ No newline at end of file + characters according to an evolutionary model. Added: trunk/packages/proalign/trunk/debian/manifest.txt === --- trunk/packages/proalign/trunk/debian/manifest.txt (rev 0) +++ trunk/packages/proalign/trunk/debian/manifest.txt 2013-05-01 20:09:53 UTC (rev 13468) @@ -0,0 +1,3 @@ +Manifest-version: 1.0 +Main-Class: proalign.ProAlign + Added: trunk/packages/proalign/trunk/debian/proalign.install === --- trunk/packages/proalign/trunk/debian/proalign.install (rev 0) +++ trunk/packages/proalign/trunk/debian/proalign.install 2013-05-01 20:09:53 UTC (rev 13468) @@ -0,0 +1,3 @@ +debian/scripts/proalign usr/bin +build/ProAlign.jar usr/share/proalign + Added: trunk/packages/proalign/trunk/debian/rules === --- trunk/packages/proalign/trunk/debian/rules (rev 0) +++ trunk/packages/proalign/trunk/debian/rules 2013-05-01 20:09:53 UTC (rev 13468) @@ -0,0 +1,23 @@ +#!/usr/bin/make -f + +# DH_VERBOSE := 1 + +%: + dh $@ + +override_dh_auto_build: + mkdir -p build + javac -d ./build *.java + find + (cd build; jar cmvf ../debian/manifest.txt ProAlign.jar *) + #(cd build; jar cmvf ../debian/manifest.txt ProAlign.jar proalign/ProAlign.class proalign/OutFile.class) + +override_dh_auto_install: + find + dh_auto_install + #dh_installchangelogs README + +get-orig-source: + mkdir -p ../tarballs + uscan --verbose --force-download --destdir=../tarballs + Property changes on: trunk/packages/proalign/trunk/debian/rules ___ Added: svn:executable + * Added:
