[med-svn] r14909 - trunk/packages/logol/trunk/debian
Author: osallou-guest
Date: 2013-10-22 06:37:27 + (Tue, 22 Oct 2013)
New Revision: 14909
Modified:
trunk/packages/logol/trunk/debian/changelog
trunk/packages/logol/trunk/debian/control
Log:
new usptream release 1.6.4
Modified: trunk/packages/logol/trunk/debian/changelog
===
--- trunk/packages/logol/trunk/debian/changelog 2013-10-21 22:57:06 UTC (rev
14908)
+++ trunk/packages/logol/trunk/debian/changelog 2013-10-22 06:37:27 UTC (rev
14909)
@@ -1,3 +1,9 @@
+logol (1.6.4-1) unstable; urgency=low
+
+ * New upstream release fixing bugs
+
+ -- Olivier Sallou osal...@debian.org Tue, 22 Oct 2013 08:35:45 +0200
+
logol (1.6.3-1) unstable; urgency=low
* New upstream release fixing important bugs on distance search
Modified: trunk/packages/logol/trunk/debian/control
===
--- trunk/packages/logol/trunk/debian/control 2013-10-21 22:57:06 UTC (rev
14908)
+++ trunk/packages/logol/trunk/debian/control 2013-10-22 06:37:27 UTC (rev
14909)
@@ -8,7 +8,7 @@
Build-Depends: debhelper (= 8.0.0),default-jdk (= 1:1.6),ant,ruby
(=1.8),rubygems, gawk, swi-prolog (=6.4.1-3),
libbiojava-java, libdrmaa-java, antlr3, libcommons-cli-java,
libcommons-collections3-java, libcommons-configuration-java,
libcommons-lang-java, libcommons-logging-java, libxalan2-java,
libxerces2-java, junit4, libgnumail-java,
- liblog4j1.2-java,texlive, texlive-latex-extra, tex4ht, libncursesw5-dev,
ruby-cassiopee, ant-optional
+ liblog4j1.2-java,texlive, texlive-latex-extra, tex4ht, libncursesw5-dev,
ruby-cassiopee (=0.1.12), ant-optional
Standards-Version: 3.9.4
Homepage: http://logol.genouest.org
@@ -17,7 +17,7 @@
Depends: ${shlibs:Depends}, ${misc:Depends}, default-jre | java6-runtime, ruby
(=1.8),rubygems, gawk,
libbiojava-java, libdrmaa-java, antlr3, libcommons-cli-java,
libcommons-collections3-java, libcommons-configuration-java,
libcommons-lang-java, libcommons-logging-java, libxalan2-java,
libxerces2-java, libgnumail-java, liblog4j1.2-java,
- ruby-cassiopee, logol-bin
+ ruby-cassiopee (=0.1.12), logol-bin
Description: Pattern matching tool using Logol language
Logol is a pattern matching tool using the Logol language.
It searches with a specific grammar a pattern in small
___
debian-med-commit mailing list
debian-med-commit@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [picard-tools] 02/02: set java home
This is an automated email from the git hooks/post-receive script. osallou pushed a commit to branch master in repository picard-tools. commit b08c054a703e79b237e76edbf047e46fcab6471a Author: Olivier Sallou olivier.sal...@debian.org Date: Tue Oct 22 09:11:03 2013 +0200 set java home --- debian/rules |3 +++ 1 file changed, 3 insertions(+) diff --git a/debian/rules b/debian/rules index f672a76..161db85 100755 --- a/debian/rules +++ b/debian/rules @@ -2,6 +2,9 @@ export DH_OPTIONS +export ANT_HOME=/usr/share/ant +export JAVA_HOME=$(readlink -f /usr/bin/javac | sed s:/bin/javac::) + %: dh $@ --with javahelper,python2 -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/picard-tools.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [picard-tools] 01/02: use JAVA_HOME
This is an automated email from the git hooks/post-receive script.
osallou pushed a commit to branch master
in repository picard-tools.
commit 22cc843acc87c8357c2f4193a56952be739ff7cf
Author: Olivier Sallou olivier.sal...@debian.org
Date: Tue Oct 22 09:06:48 2013 +0200
use JAVA_HOME
---
debian/patches/01-build.xml | 15 ---
1 file changed, 12 insertions(+), 3 deletions(-)
diff --git a/debian/patches/01-build.xml b/debian/patches/01-build.xml
index d8f7ab3..b663c6d 100644
--- a/debian/patches/01-build.xml
+++ b/debian/patches/01-build.xml
@@ -16,7 +16,16 @@ Forwarded: no
property name=src value=src/java/
property name=src.scripts value=src/scripts/
-@@ -70,6 +70,11 @@
+@@ -53,7 +53,7 @@
+ property name=test.debug.port value=5005 / !-- override on the
command line if desired --
+
+ property environment=env/
+-property name=java6.home value=${env.JAVA6_HOME}/
++property name=java6.home value=${env.JAVA_HOME}/
+
+ condition property=isUnix
+ os family=unix/
+@@ -72,6 +72,11 @@
fileset dir=${lib}
include name=**/*.jar/
/fileset
@@ -28,7 +37,7 @@ Forwarded: no
/path
path id=metrics.classpath
pathelement path=${classpath}/
-@@ -194,8 +199,9 @@
+@@ -205,8 +210,9 @@
mkdir dir=${dist}/
jar destfile=${dist}/picard-${picard-version}.jar compress=no
fileset dir=${classes} includes =net/sf/picard/**/*.*/
@@ -39,7 +48,7 @@ Forwarded: no
manifest
attribute name=Implementation-Version
value=${picard-version}(${repository.revision})/
attribute name=Implementation-Vendor value=Broad
Institute/
-@@ -225,6 +231,8 @@
+@@ -236,6 +242,8 @@
/copy
/target
--
Alioth's /git/debian-med/git-commit-notice on
/srv/git.debian.org/git/debian-med/picard-tools.git
___
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] [picard-tools] branch master updated (9232c97 - b08c054)
This is an automated email from the git hooks/post-receive script. osallou pushed a change to branch master in repository picard-tools. from 9232c97 New upstream release, no new copyright nor license file. new 22cc843 use JAVA_HOME new b08c054 set java home The 2 revisions listed above as new are entirely new to this repository and will be described in separate emails. The revisions listed as adds were already present in the repository and have only been added to this reference. Summary of changes: debian/patches/01-build.xml | 15 --- debian/rules|3 +++ 2 files changed, 15 insertions(+), 3 deletions(-) -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/picard-tools.git ___ 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] r14910 - in trunk/packages/R: . r-cran-dosefinding r-cran-dosefinding/trunk r-cran-dosefinding/trunk/debian r-cran-dosefinding/trunk/debian/source
Author: tille
Date: 2013-10-22 07:29:39 + (Tue, 22 Oct 2013)
New Revision: 14910
Added:
trunk/packages/R/r-cran-dosefinding/
trunk/packages/R/r-cran-dosefinding/trunk/
trunk/packages/R/r-cran-dosefinding/trunk/debian/
trunk/packages/R/r-cran-dosefinding/trunk/debian/README.test
trunk/packages/R/r-cran-dosefinding/trunk/debian/changelog
trunk/packages/R/r-cran-dosefinding/trunk/debian/compat
trunk/packages/R/r-cran-dosefinding/trunk/debian/control
trunk/packages/R/r-cran-dosefinding/trunk/debian/copyright
trunk/packages/R/r-cran-dosefinding/trunk/debian/docs
trunk/packages/R/r-cran-dosefinding/trunk/debian/rules
trunk/packages/R/r-cran-dosefinding/trunk/debian/source/
trunk/packages/R/r-cran-dosefinding/trunk/debian/source/format
trunk/packages/R/r-cran-dosefinding/trunk/debian/upstream
trunk/packages/R/r-cran-dosefinding/trunk/debian/watch
Log:
Inject R DoseFinding
Added: trunk/packages/R/r-cran-dosefinding/trunk/debian/README.test
===
--- trunk/packages/R/r-cran-dosefinding/trunk/debian/README.test
(rev 0)
+++ trunk/packages/R/r-cran-dosefinding/trunk/debian/README.test
2013-10-22 07:29:39 UTC (rev 14910)
@@ -0,0 +1,5 @@
+Notes on how this package can be tested.
+
+
+This package can be tested by loading it into R with the command
+‘library(DoseFinding)’ in order to confirm its integrity.
Added: trunk/packages/R/r-cran-dosefinding/trunk/debian/changelog
===
--- trunk/packages/R/r-cran-dosefinding/trunk/debian/changelog
(rev 0)
+++ trunk/packages/R/r-cran-dosefinding/trunk/debian/changelog 2013-10-22
07:29:39 UTC (rev 14910)
@@ -0,0 +1,6 @@
+r-cran-dosefinding (0.9-9-1) UNRELEASED; urgency=low
+
+ * Initial release (closes: #???)
+TODO: Clarify nature of *.rda files with authors
+
+ -- Andreas Tille ti...@debian.org Tue, 22 Oct 2013 09:03:24 +0200
Added: trunk/packages/R/r-cran-dosefinding/trunk/debian/compat
===
--- trunk/packages/R/r-cran-dosefinding/trunk/debian/compat
(rev 0)
+++ trunk/packages/R/r-cran-dosefinding/trunk/debian/compat 2013-10-22
07:29:39 UTC (rev 14910)
@@ -0,0 +1 @@
+9
Added: trunk/packages/R/r-cran-dosefinding/trunk/debian/control
===
--- trunk/packages/R/r-cran-dosefinding/trunk/debian/control
(rev 0)
+++ trunk/packages/R/r-cran-dosefinding/trunk/debian/control2013-10-22
07:29:39 UTC (rev 14910)
@@ -0,0 +1,28 @@
+Source: r-cran-dosefinding
+Maintainer: Debian Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
+Uploaders: Andreas Tille ti...@debian.org
+Section: gnu-r
+Priority: optional
+Build-Depends: debhelper (= 9),
+ cdbs,
+ r-base-dev,
+ r-cran-lattice,
+ r-cran-mvtnorm
+Standards-Version: 3.9.4
+Vcs-Browser:
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-cran-dosefinding/trunk/
+Vcs-Svn:
svn://anonscm.debian.org/debian-med/trunk/packages/R/r-cran-dosefinding/trunk/
+Homepage: http://cran.r-project.org/web/packages/DoseFinding
+
+Package: r-cran-dosefinding
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${R:Depends},
+ r-cran-lattice,
+ r-cran-mvtnorm
+Description: Planning and Analyzing Dose Finding experiments
+ The DoseFinding GNU R package provides functions for the design and
+ analysis of dose-finding experiments (with focus on pharmaceutical Phase
+ II clinical trials). It provides functions for: multiple contrast tests,
+ fitting non-linear dose-response models (using Bayesian and non-Bayesian
+ estimation), calculating optimal designs and an implementation of the
+ MCPMod methodology.
Added: trunk/packages/R/r-cran-dosefinding/trunk/debian/copyright
===
--- trunk/packages/R/r-cran-dosefinding/trunk/debian/copyright
(rev 0)
+++ trunk/packages/R/r-cran-dosefinding/trunk/debian/copyright 2013-10-22
07:29:39 UTC (rev 14910)
@@ -0,0 +1,30 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: DoseFinding
+Upstream-Contact: Bjoern Bornkamp bbn...@gmail.com
+Source: http://cran.r-project.org/src/contrib/
+
+Files: *
+Copyright: 2010-2013 Bjoern Bornkamp bbn...@gmail.com, Jose Pinheiro, Frank
Bretz
+License: GPL3+
+
+Files: debian/*
+Copyright: 2013 Andreas Tille ti...@debian.org
+License: GPL3+
+
+License: GPL3+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later
[med-svn] r14911 - trunk/packages/insighttoolkit/wrapitk/python/trunk
Author: tille
Date: 2013-10-22 07:41:51 + (Tue, 22 Oct 2013)
New Revision: 14911
Removed:
trunk/packages/insighttoolkit/wrapitk/python/trunk/CMakeLists.txt
trunk/packages/insighttoolkit/wrapitk/python/trunk/debian/
Log:
Remove from SVN because the package will be removed from Debian
Deleted: trunk/packages/insighttoolkit/wrapitk/python/trunk/CMakeLists.txt
===
--- trunk/packages/insighttoolkit/wrapitk/python/trunk/CMakeLists.txt
2013-10-22 07:29:39 UTC (rev 14910)
+++ trunk/packages/insighttoolkit/wrapitk/python/trunk/CMakeLists.txt
2013-10-22 07:41:51 UTC (rev 14911)
@@ -1,17 +0,0 @@
-CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
-PROJECT(DebianWrapITK)
-
-#-
-# ITK version number. An even minor number corresponds to releases.
-SET(ITK_VERSION_MAJOR 3)
-SET(ITK_VERSION_MINOR 20)
-SET(ITK_VERSION_PATCH 1)
-
- # This setting of SOVERSION assumes that any API change
- # will increment either the minor or major version number of ITK.
- SET(ITK_LIBRARY_PROPERTIES
- VERSION
${ITK_VERSION_MAJOR}.${ITK_VERSION_MINOR}.${ITK_VERSION_PATCH}
- SOVERSION ${ITK_VERSION_MAJOR}.${ITK_VERSION_MINOR}
- )
-
-SUBDIRS(/usr/src/WrapITK)
___
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] r14912 - trunk/packages/insighttoolkit/wrapitk/python/trunk
Author: tille Date: 2013-10-22 07:42:48 + (Tue, 22 Oct 2013) New Revision: 14912 Modified: trunk/packages/insighttoolkit/wrapitk/python/trunk/README.status Log: The packaging was removed in revision 14911 from this repository Modified: trunk/packages/insighttoolkit/wrapitk/python/trunk/README.status === --- trunk/packages/insighttoolkit/wrapitk/python/trunk/README.status 2013-10-22 07:41:51 UTC (rev 14911) +++ trunk/packages/insighttoolkit/wrapitk/python/trunk/README.status 2013-10-22 07:42:48 UTC (rev 14912) @@ -2,6 +2,7 @@ Format: 1 Status: active Source: unknown +Removed: The package was removed from Debian (ROM: #727081) Comment: - The source of this package does not seem to be available. + The packaging was removed in revision 14911 from this repository ___ 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] [picard-tools] annotated tag debian/1.100-1 created (now 8987f03)
This is an automated email from the git hooks/post-receive script. osallou pushed a change to annotated tag debian/1.100-1 in repository picard-tools. at 8987f03 (tag) tagging fa4a3a6d7f5830a742e2c7aaaea3be35364c020d (commit) replaces debian/1.95-1 tagged by Olivier Sallou on Tue Oct 22 10:05:40 2013 +0200 - Log - picard-tools Debian release 1.100-1 Charles Plessy (5): Compress the source archive with XZ. Mark the use of git-buildpackage and pristine-tar with a gbp.conf file. Imported Upstream version 1.100 Merge tag 'upstream/1.100' New upstream release, no new copyright nor license file. Olivier Sallou (3): use JAVA_HOME set java home Upload release 1.100 --- No new revisions were added by this update. -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/picard-tools.git ___ 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] [picard-tools] 01/01: Upload release 1.100
This is an automated email from the git hooks/post-receive script. osallou pushed a commit to branch master in repository picard-tools. commit fa4a3a6d7f5830a742e2c7aaaea3be35364c020d Author: Olivier Sallou olivier.sal...@debian.org Date: Tue Oct 22 10:03:07 2013 +0200 Upload release 1.100 --- debian/changelog |5 - 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/debian/changelog b/debian/changelog index a5e622f..6ad412b 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,8 +1,11 @@ -picard-tools (1.100-1) UNRELEASED; urgency=low +picard-tools (1.100-1) unstable; urgency=low + [Charles Plessy] * Imported Upstream version 1.100 * Compress the source archive with XZ. * Mark the use of git-buildpackage and pristine-tar with a gbp.conf file. + [Olivier Sallou] + * d/rules: fix build for release -- Charles Plessy ple...@debian.org Sun, 20 Oct 2013 10:38:11 +0900 -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/picard-tools.git ___ 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] [picard-tools] branch master updated (b08c054 - fa4a3a6)
This is an automated email from the git hooks/post-receive script. osallou pushed a change to branch master in repository picard-tools. from b08c054 set java home new fa4a3a6 Upload release 1.100 The 1 revisions listed above as new are entirely new to this repository and will be described in separate emails. The revisions listed as adds were already present in the repository and have only been added to this reference. Summary of changes: debian/changelog |5 - 1 file changed, 4 insertions(+), 1 deletion(-) -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/picard-tools.git ___ 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] r14914 - trunk/packages/R/r-cran-dosefinding/trunk/debian
Author: tille Date: 2013-10-22 08:37:23 + (Tue, 22 Oct 2013) New Revision: 14914 Added: trunk/packages/R/r-cran-dosefinding/trunk/debian/README.source Modified: trunk/packages/R/r-cran-dosefinding/trunk/debian/changelog Log: Every single RData file is just documented in detail inside the upstream source Added: trunk/packages/R/r-cran-dosefinding/trunk/debian/README.source === --- trunk/packages/R/r-cran-dosefinding/trunk/debian/README.source (rev 0) +++ trunk/packages/R/r-cran-dosefinding/trunk/debian/README.source 2013-10-22 08:37:23 UTC (rev 14914) @@ -0,0 +1,33 @@ +Explanation for binary files inside source package according to + http://lists.debian.org/debian-devel/2013/09/msg00332.html + +The source packages contains some binary RData files which are +documented inside the according manpages + +Files: data/IBScovars.rda +Documentation: man/IBScovars.Rd + Irritable Bowel Syndrome Dose Response data with covariates + Published in: Biesheuvel, E. and Hothorn, L. A. (2002). Many-to-one comparisons in stratified designs, Biometrical Journal, 44, 101--116 + +Files: data/biom.rda +Documentation: man/biom.Rd + Biometrics Dose Response data + Published in: Bretz, F., Pinheiro, J. C., and Branson, M. (2005), Combining multiple comparisons and modeling techniques in dose-response studies, Biometrics, 61, 738--748 + +Files: data/glycobrom.rda +Documentation: man/glycobrom.Rd + Glycopyrronium Bromide dose-response data + Published in: http://clinicaltrials.gov/ct2/show/results/NCT00501852 + +Files: data/migraine.rda +Documentation: man/migraine.Rd + Migraine Dose Response data + Published in: http://clinicaltrials.gov/ct2/show/results/NCT00712725 + +Files: data/neurodeg.rda +Documentation: man/neurodeg.Rd + Neurodegenerative disease simulated longitudinal dose-finding data set + Published in: Pinheiro, J. C., Bornkamp, B., Glimm, E. and Bretz, F. (2013). Multiple comparisons and modelling for dose-finding using general parametric models + + -- Andreas Tille ti...@debian.org Tue, 22 Oct 2013 09:03:24 +0200 + Modified: trunk/packages/R/r-cran-dosefinding/trunk/debian/changelog === --- trunk/packages/R/r-cran-dosefinding/trunk/debian/changelog 2013-10-22 07:43:20 UTC (rev 14913) +++ trunk/packages/R/r-cran-dosefinding/trunk/debian/changelog 2013-10-22 08:37:23 UTC (rev 14914) @@ -1,6 +1,5 @@ r-cran-dosefinding (0.9-9-1) UNRELEASED; urgency=low * Initial release (closes: #???) -TODO: Clarify nature of *.rda files with authors -- Andreas Tille ti...@debian.org Tue, 22 Oct 2013 09:03:24 +0200 ___ 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] r14915 - trunk/packages/R/r-cran-dosefinding/trunk/debian
Author: tille Date: 2013-10-22 09:21:43 + (Tue, 22 Oct 2013) New Revision: 14915 Modified: trunk/packages/R/r-cran-dosefinding/trunk/debian/changelog Log: Upload to new Modified: trunk/packages/R/r-cran-dosefinding/trunk/debian/changelog === --- trunk/packages/R/r-cran-dosefinding/trunk/debian/changelog 2013-10-22 08:37:23 UTC (rev 14914) +++ trunk/packages/R/r-cran-dosefinding/trunk/debian/changelog 2013-10-22 09:21:43 UTC (rev 14915) @@ -1,5 +1,5 @@ -r-cran-dosefinding (0.9-9-1) UNRELEASED; urgency=low +r-cran-dosefinding (0.9-9-1) unstable; urgency=low - * Initial release (closes: #???) + * Initial release (closes: #727090) -- Andreas Tille ti...@debian.org Tue, 22 Oct 2013 09:03:24 +0200 ___ 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] [libvistaio] branch master updated (53964e6 - fd827f5)
This is an automated email from the git hooks/post-receive script. gert-guest pushed a change to branch master in repository libvistaio. from 53964e6 update copyright file to correct lintian warning new fd827f5 change date for imminent upload The 1 revisions listed above as new are entirely new to this repository and will be described in separate emails. The revisions listed as adds were already present in the repository and have only been added to this reference. Summary of changes: debian/changelog |2 +- 1 file changed, 1 insertion(+), 1 deletion(-) -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/libvistaio.git ___ 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] [libvistaio] 01/01: change date for imminent upload
This is an automated email from the git hooks/post-receive script. gert-guest pushed a commit to branch master in repository libvistaio. commit fd827f5b660790879d1626f60157575c287d2d95 Author: Gert Wollny gw.foss...@gmail.com Date: Tue Oct 22 11:45:46 2013 +0200 change date for imminent upload --- debian/changelog |2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/debian/changelog b/debian/changelog index a32c3ae..baee5f8 100644 --- a/debian/changelog +++ b/debian/changelog @@ -3,7 +3,7 @@ libvistaio (1.2.16-1) UNRELEASED; urgency=low * new upstream release * corrected debian/copyright entries (Closes: #726778) - -- Gert Wollny gw.foss...@gmail.com Mon, 21 Oct 2013 16:30:11 +0200 + -- Gert Wollny gw.foss...@gmail.com Tue, 22 Oct 2013 11:30:11 +0200 libvistaio (1.2.15-1) unstable; urgency=low -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/libvistaio.git ___ 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] [Debian Wiki] Update of DebianMed/Meeting/Aberdeen2014 by DanielBarker
Dear Wiki user, You have subscribed to a wiki page or wiki category on Debian Wiki for change notification. The DebianMed/Meeting/Aberdeen2014 page has been changed by DanielBarker: https://wiki.debian.org/DebianMed/Meeting/Aberdeen2014?action=diffrev1=34rev2=35 || 5|| Olivier Sallou|| osallou || yes || yes || U. Rennes 1|| Rennes (F) || 31 Jan || 3 Feb|| || 6|| Luca Clivio || luca.cli...@marionegri.it || yes|| no || Mario Negri Institute || Milan (I)|| 31 Jan || 2 Feb|| || 7|| Jim Procter || j.proc...@dundee.ac.uk || yes || not yet || University of Dundee || Dundee (UK) || 31 Jan || 2 Feb|| + || 8|| Daniel Barker || d...@st-andrews.ac.uk || yes || yes || University of St Andrews || Fife (UK) || 31 Jan || 2 Feb|| == Agenda == * Packaging Galaxy for Bio-Linux - the Debian way [Tim, Steffen] @@ -63, +64 @@ * note [Matus]: preliminary brainstorming on this topic has been done by László, Jon Ison, Matúš (+Steffen, Hervé, Bertrand, Kristoffer Rapacki. Notes connected to attributes to annotate are in this section of the [[https://docs.google.com/document/d/19VpzwxZdlz1K4P1q1a-WYZUtiSXwUp2nafM716dzW8I/edit?pli=1#bookmark=id.v415n1pdyfl0|CodefestOntoDoc]]) - Let's get more people on board and decide and make concrete steps in Stonehaven! * Community development, licensing, and potentially packaging of standards (incl. ontologies, schemata, ...) - what are the good, sustainable ways? Interested: Matus * p2pDB [Luca] - beyond the web: a peer to peer approach to data sharing for clinical trials and bioinformatics research + * Bioinformatics education on the Raspberry Pi [Daniel] == Acknowledgements == ___ 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] r14916 - trunk/packages/staden-io-lib/trunk/debian
Author: alteholz Date: 2013-10-22 17:18:44 + (Tue, 22 Oct 2013) New Revision: 14916 Modified: trunk/packages/staden-io-lib/trunk/debian/changelog Log: update description Modified: trunk/packages/staden-io-lib/trunk/debian/changelog === --- trunk/packages/staden-io-lib/trunk/debian/changelog 2013-10-22 09:21:43 UTC (rev 14915) +++ trunk/packages/staden-io-lib/trunk/debian/changelog 2013-10-22 17:18:44 UTC (rev 14916) @@ -1,7 +1,7 @@ staden-io-lib (1.13.2-3) unstable; urgency=low * debian/patches: add patch to build on hurd_i386 - * no need to remove package from architecture anymore (Closes: #726875) + * no need to remove package from mips anymore (Closes: #726875) -- Thorsten Alteholz deb...@alteholz.de Mon, 21 Oct 2013 18:10:59 +0200 ___ 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] [sra-sdk] branch master updated (37af34e - 9244ef5)
This is an automated email from the git hooks/post-receive script. tille pushed a change to branch master in repository sra-sdk. from 37af34e Add DEP3 headers new c04cf0e Fix build problem (thanks to Gert Wollny gw.foss...@gmail.com for the patch) new 63307c1 There are neither mod?? nor wmod?? files shipped in this version any more new 9244ef5 Reactivate deletion of libs/krypto/*.pic.o.list files to get a really clean source The 3 revisions listed above as new are entirely new to this repository and will be described in separate emails. The revisions listed as adds were already present in the repository and have only been added to this reference. Summary of changes: debian/changelog |6 debian/patches/build-with-system-libbz2-libz.patch | 36 debian/patches/series |1 + debian/rules |3 +- debian/sra-toolkit.install |2 -- 5 files changed, 44 insertions(+), 4 deletions(-) create mode 100644 debian/patches/build-with-system-libbz2-libz.patch -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/sra-sdk.git ___ 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] [sra-sdk] 02/03: There are neither mod?? nor wmod?? files shipped in this version any more
This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository sra-sdk. commit 63307c15f9b24d3cd74b0aabe51f793e45418bfd Author: Andreas Tille ti...@debian.org Date: Tue Oct 22 20:30:32 2013 +0200 There are neither mod?? nor wmod?? files shipped in this version any more --- debian/changelog |2 ++ debian/sra-toolkit.install |2 -- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/debian/changelog b/debian/changelog index 52e964b..bf1222f 100644 --- a/debian/changelog +++ b/debian/changelog @@ -18,6 +18,8 @@ sra-sdk (2.3.3-4~dfsg-1) UNRELEASED; urgency=low * debian/doc: USAGE is not provided by upstream any more * debian/patches/build-with-system-libbz2-libz.patch: Fix build problem (thanks to Gert Wollny gw.foss...@gmail.com for the patch) + * debian/sra-toolkit.install: There are neither mod?? nor wmod?? files +shipped in this version any more - so remove these from dh_install -- Andreas Tille ti...@debian.org Tue, 13 Aug 2013 11:04:25 +0200 diff --git a/debian/sra-toolkit.install b/debian/sra-toolkit.install index 040c9cc..790e7d8 100644 --- a/debian/sra-toolkit.install +++ b/debian/sra-toolkit.install @@ -1,5 +1,3 @@ bin??/*usr/bin -mod??/* usr/lib/ncbi/mod -wmod??/* usr/lib/ncbi/wmod schema/*/*.vschema usr/lib/ncbi/schema lib??/ncbi/*.kfg /etc/ncbi -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/sra-sdk.git ___ 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] [sra-sdk] 03/03: Reactivate deletion of libs/krypto/*.pic.o.list files to get a really clean source
This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository sra-sdk. commit 9244ef5d8da96716ac06f13e6b019a8bf4a00ea2 Author: Andreas Tille ti...@debian.org Date: Tue Oct 22 20:32:29 2013 +0200 Reactivate deletion of libs/krypto/*.pic.o.list files to get a really clean source --- debian/changelog |2 ++ debian/rules |3 +-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/debian/changelog b/debian/changelog index bf1222f..f05eb98 100644 --- a/debian/changelog +++ b/debian/changelog @@ -15,6 +15,8 @@ sra-sdk (2.3.3-4~dfsg-1) UNRELEASED; urgency=low - remove override because upstream seems to do the correct thing now - libsra-schema seems to be not built any more in this version so drop the special handling of it + - Reactivate deletion of libs/krypto/*.pic.o.list files to get a + really clean source * debian/doc: USAGE is not provided by upstream any more * debian/patches/build-with-system-libbz2-libz.patch: Fix build problem (thanks to Gert Wollny gw.foss...@gmail.com for the patch) diff --git a/debian/rules b/debian/rules index 73254a5..71dcdfb 100755 --- a/debian/rules +++ b/debian/rules @@ -8,8 +8,7 @@ override_dh_auto_clean: override_dh_clean: dh_clean - # These files are changing in the build process - # find libs/krypto -name *.o.list -delete + find libs/krypto -name *.pic.o.list -delete rm -f build/OUTDIR.linux override_dh_auto_configure: -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/sra-sdk.git ___ 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] [sra-sdk] 01/03: Fix build problem (thanks to Gert Wollny gw.foss...@gmail.com for the patch)
This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository sra-sdk. commit c04cf0e977a7539c7c7f72764a3f0975f7dfcc0d Author: Andreas Tille ti...@debian.org Date: Tue Oct 22 20:29:25 2013 +0200 Fix build problem (thanks to Gert Wollny gw.foss...@gmail.com for the patch) --- debian/changelog |2 ++ debian/patches/build-with-system-libbz2-libz.patch | 36 debian/patches/series |1 + 3 files changed, 39 insertions(+) diff --git a/debian/changelog b/debian/changelog index 5072ad4..52e964b 100644 --- a/debian/changelog +++ b/debian/changelog @@ -16,6 +16,8 @@ sra-sdk (2.3.3-4~dfsg-1) UNRELEASED; urgency=low - libsra-schema seems to be not built any more in this version so drop the special handling of it * debian/doc: USAGE is not provided by upstream any more + * debian/patches/build-with-system-libbz2-libz.patch: Fix build problem +(thanks to Gert Wollny gw.foss...@gmail.com for the patch) -- Andreas Tille ti...@debian.org Tue, 13 Aug 2013 11:04:25 +0200 diff --git a/debian/patches/build-with-system-libbz2-libz.patch b/debian/patches/build-with-system-libbz2-libz.patch new file mode 100644 index 000..0477ae7 --- /dev/null +++ b/debian/patches/build-with-system-libbz2-libz.patch @@ -0,0 +1,36 @@ +Author: Gert Wollny gw.foss...@gmail.com +LastChanged: Tue, 22 Oct 2013 00:15:19 +0200 +Description: Fix issue when trying to build against Debian packaged + libbz2 + +diff --git a/libs/ncbi-vdb/Makefile b/libs/ncbi-vdb/Makefile +index 7b08def..a9c1618 100644 +--- a/libs/ncbi-vdb/Makefile b/libs/ncbi-vdb/Makefile +@@ -88,7 +88,6 @@ endif + + VDB_LIB_CMN = \ + align-access \ +- bz2 \ + kfg \ + kfs \ + klib \ +@@ -98,8 +97,7 @@ VDB_LIB_CMN = \ + ksrch \ + $(LIBKXML) \ + kurl \ +- vfs \ +- z ++ vfs + + VDB_LIB_RD = \ + $(VDB_LIB_CMN) \ +@@ -116,7 +114,7 @@ VDB_OBJ = \ + $(addprefix $(ILIBDIR)/lib,$(addsuffix .a,$(VDB_LIB_RD))) + + VDB_LIB = \ +- $(addprefix -s,$(VDB_LIB_RD)) ++ $(addprefix -s,$(VDB_LIB_RD)) -lbz2 -lz + + $(LIBDIR)/libncbi-vdb.$(SHLX): $(VDB_OBJ) + $(LD) --dlib --vers $(SRCDIR) -o $@ $(VDB_LIB) diff --git a/debian/patches/series b/debian/patches/series index 2d5a674..8bbe9de 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,2 +1,3 @@ do_not_build_external_libs.patch 10_portability.patch +build-with-system-libbz2-libz.patch -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/sra-sdk.git ___ 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] [fis-gtm] 03/04: Imported Upstream version 6.0-001
This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository fis-gtm. commit 5839702be1df54193f4d518375c5077f5d64b889 Author: Andreas Tille ti...@debian.org Date: Tue Oct 22 20:52:52 2013 +0200 Imported Upstream version 6.0-001 -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/fis-gtm.git ___ 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] [fis-gtm] 01/04: Lintian clean excep of an upstream spelling error.
This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository fis-gtm. commit 5cd64929012059aea9b9d23ba03cebefbebf3d49 Author: Andreas Tille ti...@debian.org Date: Sun Oct 20 21:42:41 2013 +0200 Lintian clean excep of an upstream spelling error. --- debian/rules |4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/debian/rules b/debian/rules index 4e0c28f..1bcee8a 100755 --- a/debian/rules +++ b/debian/rules @@ -38,7 +38,7 @@ override_dh_auto_install: --distrib . \ --installdir $(LOCAL_GTM_INSTALL_DIR) @echo I: Removing redundant license file. One is already available. - rm$(LOCAL_GTM_INSTALL_DIR)/COPYING + find $(LOCAL_GTM_INSTALL_DIR) -name COPYING -delete # remove empty directories find $(LOCAL_GTM_INSTALL_DIR) -type d -empty -delete # fix permissions of directories @@ -105,6 +105,8 @@ override_dh_lintian: echo # The following permissions are really set intentionally in override_dh_fixpermissions debian/$(BINPKG).lintian-overrides echo $(BINPKG): setuid-binary usr/lib/fis-gtm/*/gtmsecshrdir/gtmsecshr 4500 root/root debian/$(BINPKG).lintian-overrides echo $(BINPKG): executable-is-not-world-readable usr/lib/fis-gtm/*/gtmsecshrdir/gtmsecshr 4500 debian/$(BINPKG).lintian-overrides + echo $(BINPKG): setuid-binary usr/lib/fis-gtm/*/gtmsecshr 4755 root/root debian/$(BINPKG).lintian-overrides + echo $(BINPKG): non-standard-dir-perm usr/lib/fis-gtm/*/gtmsecshrdir/ 0500 != 0755 debian/$(BINPKG).lintian-overrides dh_lintian -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/fis-gtm.git ___ 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] [fis-gtm] 02/04: There is no point in changing the originally downloaded tarball
This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository fis-gtm. commit e98d165c7765951662e742c4b1847a35e1f37ddc Author: Andreas Tille ti...@debian.org Date: Tue Oct 22 20:51:21 2013 +0200 There is no point in changing the originally downloaded tarball --- debian/watch |4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/debian/watch b/debian/watch index c3e8460..63934a8 100644 --- a/debian/watch +++ b/debian/watch @@ -1,5 +1,3 @@ version=3 opts=uversionmangle=s/^([0-9]*)([0-9])([0-9][0-9][0-9][A-Z]*)/$1.$2-$3/g \ -http://sf.net/fis-gtm/gtm_V(.*)_linux_i686_src\.tar\.gz \ -debian debian/get-orig-source - +http://sf.net/fis-gtm/gtm_V(.*)_linux_i686_src\.tar\.gz -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/fis-gtm.git ___ 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] [sra-sdk] 02/02: Updated changelog.
This is an automated email from the git hooks/post-receive script. plessy pushed a commit to branch master in repository sra-sdk. commit bf88fd06fd1c8abdb083cc4d8ba6683b485bb445 Author: Charles Plessy ple...@debian.org Date: Wed Oct 23 09:39:40 2013 +0900 Updated changelog. --- debian/changelog |3 +++ 1 file changed, 3 insertions(+) diff --git a/debian/changelog b/debian/changelog index f05eb98..2cf0668 100644 --- a/debian/changelog +++ b/debian/changelog @@ -23,6 +23,9 @@ sra-sdk (2.3.3-4~dfsg-1) UNRELEASED; urgency=low * debian/sra-toolkit.install: There are neither mod?? nor wmod?? files shipped in this version any more - so remove these from dh_install + [ Charles Plessy ] + 32dd5cd Updated symbols file. + -- Andreas Tille ti...@debian.org Tue, 13 Aug 2013 11:04:25 +0200 sra-sdk (2.1.7a-1) unstable; urgency=low -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/sra-sdk.git ___ 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] [sra-sdk] branch master updated (9244ef5 - bf88fd0)
This is an automated email from the git hooks/post-receive script. plessy pushed a change to branch master in repository sra-sdk. from 9244ef5 Reactivate deletion of libs/krypto/*.pic.o.list files to get a really clean source new 32dd5cd Updated symbols file. new bf88fd0 Updated changelog. The 2 revisions listed above as new are entirely new to this repository and will be described in separate emails. The revisions listed as adds were already present in the repository and have only been added to this reference. Summary of changes: debian/changelog |3 + debian/sra-toolkit-libs0.symbols |10101 +++--- 2 files changed, 6088 insertions(+), 4016 deletions(-) -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/sra-sdk.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
