[med-svn] r5879 - in trunk/packages/mrbayes/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Thu Feb 3 22:05:24 UTC 2011
Author: tille
Date: 2011-02-03 22:05:22 +0000 (Thu, 03 Feb 2011)
New Revision: 5879
Added:
trunk/packages/mrbayes/trunk/debian/README.source
trunk/packages/mrbayes/trunk/debian/mb-mpi.1
trunk/packages/mrbayes/trunk/debian/mrbayes-mpi.README.Debian
trunk/packages/mrbayes/trunk/debian/mrbayes-mpi.install
trunk/packages/mrbayes/trunk/debian/mrbayes-mpi.manpages
trunk/packages/mrbayes/trunk/debian/mrbayes.README.Debian
trunk/packages/mrbayes/trunk/debian/mrbayes.install
trunk/packages/mrbayes/trunk/debian/mrbayes.manpages
trunk/packages/mrbayes/trunk/debian/patches/
trunk/packages/mrbayes/trunk/debian/patches/no_ncurses.patch
trunk/packages/mrbayes/trunk/debian/patches/series
Removed:
trunk/packages/mrbayes/trunk/debian/README.Debian
Modified:
trunk/packages/mrbayes/trunk/debian/changelog
trunk/packages/mrbayes/trunk/debian/control
trunk/packages/mrbayes/trunk/debian/rules
Log:
Some polishing, dropped useless libncurses dependency, provide better docs for MPI package
Deleted: trunk/packages/mrbayes/trunk/debian/README.Debian
===================================================================
--- trunk/packages/mrbayes/trunk/debian/README.Debian 2011-02-03 16:03:01 UTC (rev 5878)
+++ trunk/packages/mrbayes/trunk/debian/README.Debian 2011-02-03 22:05:22 UTC (rev 5879)
@@ -1,10 +0,0 @@
-MrBayes for Debian
-------------------
-
-You can download the Manual for MrBayes as PDF from
- http://mrbayes.sourceforge.net/mb3.1_manual.pdf
-
-The command reference can be downloaded here
- http://mrbayes.sourceforge.net/commref_mb3.1.pdf
-
- -- Andreas Tille <tille at debian.org> Sat, 10 Jul 2010 19:03:40 +0200
Added: trunk/packages/mrbayes/trunk/debian/README.source
===================================================================
--- trunk/packages/mrbayes/trunk/debian/README.source (rev 0)
+++ trunk/packages/mrbayes/trunk/debian/README.source 2011-02-03 22:05:22 UTC (rev 5879)
@@ -0,0 +1,4 @@
+This packages uses the quilt patch system. Please read
+/usr/share/doc/quilt/README.source for more information.
+
+ -- Andreas Tille <tille at debian.org> Thu, 03 Feb 2011 16:39:19 +0100
Modified: trunk/packages/mrbayes/trunk/debian/changelog
===================================================================
--- trunk/packages/mrbayes/trunk/debian/changelog 2011-02-03 16:03:01 UTC (rev 5878)
+++ trunk/packages/mrbayes/trunk/debian/changelog 2011-02-03 22:05:22 UTC (rev 5879)
@@ -1,15 +1,8 @@
mrbayes (3.1.2-1) UNRELEASED; urgency=low
- * ITP IS MISSING
- * Adjustments for latest Debian policy.
- - build dependencies
- - Debian source code management with Debian Med
- * Added mrbayes-mpi package
- * Added mb-mpi binary
- * Using debhelper
- * Initial upload to Debian.
+ * Initial release in Debian (Closes: #611928)
- -- Steffen Moeller <moeller at debian.org> Mon, 01 Nov 2010 01:32:14 +0100
+ -- Andreas Tille <tille at debian.org> Thu, 03 Feb 2011 22:23:31 +0100
mrbayes (3.1.2-0ubuntu1) feisty; urgency=low
Modified: trunk/packages/mrbayes/trunk/debian/control
===================================================================
--- trunk/packages/mrbayes/trunk/debian/control 2011-02-03 16:03:01 UTC (rev 5878)
+++ trunk/packages/mrbayes/trunk/debian/control 2011-02-03 22:05:22 UTC (rev 5879)
@@ -9,7 +9,7 @@
Pjotr Prins <pjotr.debian at thebird.nl>,
Andreas Tille <tille at debian.org>
Standards-Version: 3.9.1
-Build-Depends: debhelper (>= 7), libncurses-dev, libreadline-dev, mpi-default-dev, quilt
+Build-Depends: debhelper (>= 7.1), libreadline-dev, mpi-default-dev, quilt (>=0.47)
Homepage: http://mrbayes.csit.fsu.edu/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mrbayes/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mrbayes/trunk/
@@ -18,7 +18,7 @@
Package: mrbayes
Architecture: any
Depends: ${shlibs:Depends}, bash (>=3.1), ${misc:Depends}
-Description: A program for the Bayesian estimation of phylogeny
+Description: Bayesian Inference of Phylogeny
Bayesian inference of phylogeny is based upon a quantity called the posterior
probability distribution of trees, which is the probability of a tree
conditioned on the observations. The conditioning is accomplished using
@@ -31,7 +31,7 @@
Architecture: any
Depends: ${shlibs:Depends}, bash (>=3.1), ${misc:Depends}
Suggests: mpi-default
-Description: A program for the Bayesian estimation of phylogeny - mpi version
+Description: Bayesian Inference of Phylogeny - mpi version
Bayesian inference of phylogeny is based upon a quantity called the posterior
probability distribution of trees, which is the probability of a tree
conditioned on the observations. The conditioning is accomplished using
Added: trunk/packages/mrbayes/trunk/debian/mb-mpi.1
===================================================================
--- trunk/packages/mrbayes/trunk/debian/mb-mpi.1 (rev 0)
+++ trunk/packages/mrbayes/trunk/debian/mb-mpi.1 2011-02-03 22:05:22 UTC (rev 5879)
@@ -0,0 +1,11 @@
+.TH mrbayes "1" "Nov 2006" "mrbayes 3.1.2" "User Commands"
+.SH NAME
+mb-mpi \- A program for the Bayesian estimation (parallel version)
+.SH SYNOPSIS
+.B mb-mpi [OPTION]... [FILE]...
+.SH DESCRIPTION
+A program for the Bayesian estimation of phylogeny Bayesian inference of phylogeny
+.SH OPTIONS
+.B \-i
+interactive mode
+
Added: trunk/packages/mrbayes/trunk/debian/mrbayes-mpi.README.Debian
===================================================================
--- trunk/packages/mrbayes/trunk/debian/mrbayes-mpi.README.Debian (rev 0)
+++ trunk/packages/mrbayes/trunk/debian/mrbayes-mpi.README.Debian 2011-02-03 22:05:22 UTC (rev 5879)
@@ -0,0 +1,12 @@
+MrBayes for Debian
+------------------
+
+This is the MPI version of MrBayes.
+
+You can download the Manual for MrBayes as PDF from
+ http://mrbayes.sourceforge.net/mb3.1_manual.pdf
+
+The command reference can be downloaded here
+ http://mrbayes.sourceforge.net/commref_mb3.1.pdf
+
+ -- Andreas Tille <tille at debian.org> Thu, 03 Feb 2011 22:23:31 +0100
Added: trunk/packages/mrbayes/trunk/debian/mrbayes-mpi.install
===================================================================
--- trunk/packages/mrbayes/trunk/debian/mrbayes-mpi.install (rev 0)
+++ trunk/packages/mrbayes/trunk/debian/mrbayes-mpi.install 2011-02-03 22:05:22 UTC (rev 5879)
@@ -0,0 +1 @@
+mb-mpi usr/bin
Added: trunk/packages/mrbayes/trunk/debian/mrbayes-mpi.manpages
===================================================================
--- trunk/packages/mrbayes/trunk/debian/mrbayes-mpi.manpages (rev 0)
+++ trunk/packages/mrbayes/trunk/debian/mrbayes-mpi.manpages 2011-02-03 22:05:22 UTC (rev 5879)
@@ -0,0 +1 @@
+debian/mb-mpi.1
Added: trunk/packages/mrbayes/trunk/debian/mrbayes.README.Debian
===================================================================
--- trunk/packages/mrbayes/trunk/debian/mrbayes.README.Debian (rev 0)
+++ trunk/packages/mrbayes/trunk/debian/mrbayes.README.Debian 2011-02-03 22:05:22 UTC (rev 5879)
@@ -0,0 +1,10 @@
+MrBayes for Debian
+------------------
+
+You can download the Manual for MrBayes as PDF from
+ http://mrbayes.sourceforge.net/mb3.1_manual.pdf
+
+The command reference can be downloaded here
+ http://mrbayes.sourceforge.net/commref_mb3.1.pdf
+
+ -- Andreas Tille <tille at debian.org> Thu, 03 Feb 2011 22:23:31 +0100
Added: trunk/packages/mrbayes/trunk/debian/mrbayes.install
===================================================================
--- trunk/packages/mrbayes/trunk/debian/mrbayes.install (rev 0)
+++ trunk/packages/mrbayes/trunk/debian/mrbayes.install 2011-02-03 22:05:22 UTC (rev 5879)
@@ -0,0 +1 @@
+mb usr/bin
Added: trunk/packages/mrbayes/trunk/debian/mrbayes.manpages
===================================================================
--- trunk/packages/mrbayes/trunk/debian/mrbayes.manpages (rev 0)
+++ trunk/packages/mrbayes/trunk/debian/mrbayes.manpages 2011-02-03 22:05:22 UTC (rev 5879)
@@ -0,0 +1 @@
+debian/mb.1
Added: trunk/packages/mrbayes/trunk/debian/patches/no_ncurses.patch
===================================================================
--- trunk/packages/mrbayes/trunk/debian/patches/no_ncurses.patch (rev 0)
+++ trunk/packages/mrbayes/trunk/debian/patches/no_ncurses.patch 2011-02-03 22:05:22 UTC (rev 5879)
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Date: Thu, 03 Feb 2011 16:39:19 +0100
+Description: There is no need to link against ncurses
+
+--- mrbayes-3.1.2.orig/Makefile
++++ mrbayes-3.1.2/Makefile
+@@ -49,7 +49,7 @@
+
+ ifeq ($(strip $(USEREADLINE)),yes)
+ CFLAGS += -DUSE_READLINE
+- LIBS += -lncurses -lreadline
++ LIBS += -lreadline
+ endif
+
+ ifeq ($(strip $(MPI)),yes)
Added: trunk/packages/mrbayes/trunk/debian/patches/series
===================================================================
--- trunk/packages/mrbayes/trunk/debian/patches/series (rev 0)
+++ trunk/packages/mrbayes/trunk/debian/patches/series 2011-02-03 22:05:22 UTC (rev 5879)
@@ -0,0 +1 @@
+no_ncurses.patch
Modified: trunk/packages/mrbayes/trunk/debian/rules
===================================================================
--- trunk/packages/mrbayes/trunk/debian/rules 2011-02-03 16:03:01 UTC (rev 5878)
+++ trunk/packages/mrbayes/trunk/debian/rules 2011-02-03 22:05:22 UTC (rev 5879)
@@ -1,77 +1,27 @@
#!/usr/bin/make -f
+# debian/rules for mrbayes
+# Andreas Tille <tille at debian.org>
+# GPL
-package = mrbayes
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
-include /usr/share/quilt/quilt.make
+mpipkg=mrbayes-mpi
+mpibin=mb-mpi
-docdir = debian/$(package)/usr/share/doc/$(package)
-mandir = debian/$(package)/usr/share/man
+%:
+ dh $@
-export DH_VERBOSE=1
+override_dh_auto_clean:
+ $(MAKE) clean
+ rm -f mb mb-mpi
-build:
- dh_testdir
- quilt push -a || test $$? = 2
-
- # build mb-mpi
+override_dh_auto_build:
+ # build mb-mpi
MPI=yes $(MAKE)
mv mb mb-mpi
# build mb
- $(MAKE) clean
+ # $(MAKE) clean # <-- seems to delete mb-mpi somehow
+ rm -f *.o
MPI=no $(MAKE)
- touch build
-
-clean:
- dh_testdir
- dh_testroot
- [ ! -f Makefile ] || $(MAKE) clean
- ln -sf debian/patches
- quilt pop -a || test $$? = 2
- rm -f mb-mpi
- rm -f build
- rm -rf *~ .pc debian/$(package) debian/*~ debian/files* debian/substvars patches
- dh_clean
-
-install-arch:
- dh_testdir
- dh_testroot
- dh_prep
-
- install -d debian/$(package)/DEBIAN $(docdir) $(mandir) debian/$(package)/usr/bin
- install -s -m 755 mb debian/$(package)/usr/bin
- install -s -m 755 mb-mpi debian/$(package)/usr/bin
- cp -a doc/man/man1 $(mandir)
-
- dh_install -pmrbayes usr/bin/mb usr/bin
- dh_install -pmrbayes-mpi usr/bin/mb-mpi usr/bin
-
-
-# Build architecture-independent files here.
-binary-indep:
-# We have nothing to do by default.
-
-# Build architecture-dependent files here.
-binary-arch: install-arch
- dh_testdir
- dh_testroot
- dh_installchangelogs
- dh_installdocs
- dh_lintian
- dh_installexamples
- dh_installman
-# dh_install --sourcedir=$(CURDIR)/debian/tmp --list-missing
- dh_link
- dh_strip
- dh_compress
- dh_fixperms
- dh_makeshlibs
- dh_installdeb
- dh_shlibdeps
- dh_gencontrol
- dh_md5sums
- dh_builddeb
-
-binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install configure
-
More information about the debian-med-commit
mailing list