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 <[email protected]> -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 <[email protected]> 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 <[email protected]> Tue, 05 Jun 2012 14:38:11 +0200 + -- Andreas Tille <[email protected]> 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 <[email protected]> +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 <[email protected]> +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 @@ _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
