[med-svn] r12664 - in trunk/packages/beast-mcmc/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Mon Dec 17 16:36:32 UTC 2012
Author: tille
Date: 2012-12-17 16:36:32 +0000 (Mon, 17 Dec 2012)
New Revision: 12664
Added:
trunk/packages/beast-mcmc/trunk/debian/libnucleotidelikelihoodcore0.install
trunk/packages/beast-mcmc/trunk/debian/libnucleotidelikelihoodcore0.links
Removed:
trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.install
trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.links
trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.lintian-overrides
trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.lintian-overrides
Modified:
trunk/packages/beast-mcmc/trunk/debian/changelog
trunk/packages/beast-mcmc/trunk/debian/control
trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_tracer_xml.patch
trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch
Log:
rename beast-mcmc-lib to libnucleotidelikelihoodcore0
Deleted: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.install
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.install 2012-12-17 15:35:22 UTC (rev 12663)
+++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.install 2012-12-17 16:36:32 UTC (rev 12664)
@@ -1 +0,0 @@
-native/*.so* usr/lib
Deleted: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.links
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.links 2012-12-17 15:35:22 UTC (rev 12663)
+++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.links 2012-12-17 16:36:32 UTC (rev 12664)
@@ -1,2 +0,0 @@
-usr/lib/libNucleotideLikelihoodCore.so.0 usr/lib/libNucleotideLikelihoodCore.so
-usr/lib/libAminoAcidLikelihoodCore.so.0 usr/lib/libAminoAcidLikelihoodCore.so
Deleted: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.lintian-overrides
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.lintian-overrides 2012-12-17 15:35:22 UTC (rev 12663)
+++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.lintian-overrides 2012-12-17 16:36:32 UTC (rev 12664)
@@ -1,5 +0,0 @@
-# The libraries are rather private to beast-mcmc and naming the package differently or
-# splitting them into two packages does not make any practical sense
-# Andreas Tille <tille at debian.org>
-beast-mcmc-lib: package-name-doesnt-match-sonames libAminoAcidLikelihoodCore0 libNucleotideLikelihoodCore0
-
Deleted: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.lintian-overrides
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.lintian-overrides 2012-12-17 15:35:22 UTC (rev 12663)
+++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.lintian-overrides 2012-12-17 16:36:32 UTC (rev 12664)
@@ -1,2 +0,0 @@
-# The menu is calling x-terminal-emulator which is provided via dependencies
-beast-mcmc: menu-command-not-in-package /usr/share/menu/beast-mcmc:7 x-terminal-emulator
Modified: trunk/packages/beast-mcmc/trunk/debian/changelog
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/changelog 2012-12-17 15:35:22 UTC (rev 12663)
+++ trunk/packages/beast-mcmc/trunk/debian/changelog 2012-12-17 16:36:32 UTC (rev 12664)
@@ -4,8 +4,13 @@
* debian/{control,rules}: use default java implementation
thanks for the patch to James Page <james.page at ubuntu.com>
Closes: #683509
+ * debian/control:
+ - rename beast-mcmc-lib to libnucleotidelikelihoodcore0
+ - Standards-Version: 3.9.4 (no changes needed)
+ - do not depend from xterm any more
+ * Remove now unneeded lintian overrides
- -- Andreas Tille <tille at debian.org> Tue, 05 Jun 2012 14:38:11 +0200
+ -- Andreas Tille <tille at debian.org> Mon, 17 Dec 2012 16:43:17 +0100
beast-mcmc (1.6.2-3) unstable; urgency=low
Modified: trunk/packages/beast-mcmc/trunk/debian/control
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/control 2012-12-17 15:35:22 UTC (rev 12663)
+++ trunk/packages/beast-mcmc/trunk/debian/control 2012-12-17 16:36:32 UTC (rev 12664)
@@ -9,7 +9,7 @@
libjebl2-java, libjam-java, figtree, liboptions-java, libhmsbeagle-java (>= 1.1r1092),
libcolt-java, libmpj-java, r-cran-rjava, libcommons-math-java (>= 2.2),
libjdom1-java, junit4, libmtj-java, libitext1-java, texlive-latex-base
-Standards-Version: 3.9.3
+Standards-Version: 3.9.4
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/beast-mcmc/trunk/
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/beast-mcmc/trunk/
XS-Autobuild: yes
@@ -18,7 +18,7 @@
Package: beast-mcmc
Architecture: all
Depends: ${shlibs:Depends}, ${misc:Depends}, ${java:Depends}, openjdk-6-jre | java-jre,
- beast-mcmc-lib, xterm | x-terminal-emulator
+ libnucleotidelikelihoodcore0 (>= ${source:Version})
Suggests: beast-mcmc-doc
Description: Bayesian MCMC phylogenetic inference
BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
@@ -31,11 +31,14 @@
is a simple to use user-interface program for setting up standard
analyses and a suit of programs for analysing the results.
-Package: beast-mcmc-lib
+Package: libnucleotidelikelihoodcore0
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
-Suggests: beast-mcmc-doc
-Description: Bayesian MCMC phylogenetic inference
+Replaces: beast-mcmc-lib
+Conflicts: beast-mcmc-lib
+Provides: beast-mcmc-lib
+Section: contrib/libs
+Description: implementation of LikelihoodCore for nucleotides used by beast-mcmc
BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
sequences. It is entirely orientated towards rooted, time-measured
phylogenies inferred using strict or relaxed molecular clock models. It
@@ -46,7 +49,8 @@
is a simple to use user-interface program for setting up standard
analyses and a suit of programs for analysing the results.
.
- This package contains an architecture dependent library.
+ This package an implementation of LikelihoodCore for nucleotides that calls
+ native methods for maximum speed.
Package: beast-mcmc-examples
Architecture: all
Copied: trunk/packages/beast-mcmc/trunk/debian/libnucleotidelikelihoodcore0.install (from rev 12662, trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.install)
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/libnucleotidelikelihoodcore0.install (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/libnucleotidelikelihoodcore0.install 2012-12-17 16:36:32 UTC (rev 12664)
@@ -0,0 +1 @@
+native/*.so* usr/lib
Copied: trunk/packages/beast-mcmc/trunk/debian/libnucleotidelikelihoodcore0.links (from rev 12662, trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.links)
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/libnucleotidelikelihoodcore0.links (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/libnucleotidelikelihoodcore0.links 2012-12-17 16:36:32 UTC (rev 12664)
@@ -0,0 +1,2 @@
+usr/lib/libNucleotideLikelihoodCore.so.0 usr/lib/libNucleotideLikelihoodCore.so
+usr/lib/libAminoAcidLikelihoodCore.so.0 usr/lib/libAminoAcidLikelihoodCore.so
Modified: trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_tracer_xml.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_tracer_xml.patch 2012-12-17 15:35:22 UTC (rev 12663)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_tracer_xml.patch 2012-12-17 16:36:32 UTC (rev 12664)
@@ -1,3 +1,7 @@
+Author: Andreas Tille <tille at debian.org>
+Date: Tue, 10 Jan 2012 22:29:24 +0100
+Description: Make sure also tracer is builded with Debian packages JARs
+
--- a/build_tracer.xml
+++ b/build_tracer.xml
@@ -32,6 +32,7 @@
Modified: trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch 2012-12-17 15:35:22 UTC (rev 12663)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch 2012-12-17 16:36:32 UTC (rev 12664)
@@ -1,3 +1,8 @@
+Description: Fix some latex error that are preventing proper creation of docs
+Author: Andreas Tille <tille at debian.org>
+Date: Tue, 05 Jun 2012 14:38:11 +0200
+LastUpdated: Mon, 17 Dec 2012 16:43:17 +0100
+
--- a/doc/Yule.tex
+++ b/doc/Yule.tex
@@ -35,6 +35,7 @@
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