[med-svn] r5410 - in trunk/packages/mrbayes/trunk/debian: . patches
Dominique Belhachemi
domibel at alioth.debian.org
Thu Nov 4 14:24:44 UTC 2010
Author: domibel
Date: 2010-11-04 14:24:40 +0000 (Thu, 04 Nov 2010)
New Revision: 5410
Added:
trunk/packages/mrbayes/trunk/debian/patches/debian-changes-3.1.2-1
Removed:
trunk/packages/mrbayes/trunk/debian/patches/misc/
Modified:
trunk/packages/mrbayes/trunk/debian/changelog
trunk/packages/mrbayes/trunk/debian/control
trunk/packages/mrbayes/trunk/debian/patches/series
trunk/packages/mrbayes/trunk/debian/rules
Log:
Using debhelper, added mrbayes-mpi
Modified: trunk/packages/mrbayes/trunk/debian/changelog
===================================================================
--- trunk/packages/mrbayes/trunk/debian/changelog 2010-11-02 22:14:26 UTC (rev 5409)
+++ trunk/packages/mrbayes/trunk/debian/changelog 2010-11-04 14:24:40 UTC (rev 5410)
@@ -3,7 +3,9 @@
* 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.
-- Steffen Moeller <moeller at debian.org> Mon, 01 Nov 2010 01:32:14 +0100
Modified: trunk/packages/mrbayes/trunk/debian/control
===================================================================
--- trunk/packages/mrbayes/trunk/debian/control 2010-11-02 22:14:26 UTC (rev 5409)
+++ trunk/packages/mrbayes/trunk/debian/control 2010-11-04 14:24:40 UTC (rev 5410)
@@ -4,7 +4,7 @@
Maintainer: Fernando Ribeiro <fernando at staff.nerdgroup.org>
Uploaders: Steffen Moeller <moeller at debian.org>, Dominique Belhachemi <domibel at debian.org>, Pjotr Prins <pjotr.debian at thebird.nl>
Standards-Version: 3.9.1
-Build-Depends: libncurses-dev, libreadline-dev, mpi-default-dev, quilt
+Build-Depends: debhelper (>= 7), libncurses-dev, libreadline-dev, mpi-default-dev, quilt
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/
@@ -12,8 +12,7 @@
Package: mrbayes
Architecture: any
-Depends: ${shlibs:Depends}, bash (>=3.1)
-Suggests: mpi-default
+Depends: ${shlibs:Depends}, bash (>=3.1), ${misc:Depends}
Description: A program for the Bayesian estimation 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
@@ -22,6 +21,18 @@
impossible to calculate analytically; instead, MrBayes uses a simulation
technique called Markov chain Monte Carlo (or MCMC) to approximate the
posterior probabilities of trees.
+
+Package: mrbayes-mpi
+Architecture: any
+Depends: ${shlibs:Depends}, bash (>=3.1), ${misc:Depends}
+Suggests: mpi-default
+Description: A program for the Bayesian estimation 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
+ Bayes's theorem. The posterior probability distribution of trees is
+ impossible to calculate analytically; instead, MrBayes uses a simulation
+ technique called Markov chain Monte Carlo (or MCMC) to approximate the
+ posterior probabilities of trees.
.
- The package offers both a regular compilation and such for parallel
- computation with MPI.
+ This package offers a binary compiled for parallel computation with MPI.
Added: trunk/packages/mrbayes/trunk/debian/patches/debian-changes-3.1.2-1
===================================================================
--- trunk/packages/mrbayes/trunk/debian/patches/debian-changes-3.1.2-1 (rev 0)
+++ trunk/packages/mrbayes/trunk/debian/patches/debian-changes-3.1.2-1 2010-11-04 14:24:40 UTC (rev 5410)
@@ -0,0 +1,54 @@
+Description: Upstream changes introduced in version 3.1.2-1
+ This patch has been created by dpkg-source during the package build.
+ Here's the last changelog entry, hopefully it gives details on why
+ those changes were made:
+ .
+ mrbayes (3.1.2-1) unstable; urgency=low
+ .
+ * 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.
+ .
+ The person named in the Author field signed this changelog entry.
+Author: Steffen Moeller <moeller at debian.org>
+
+---
+The information above should follow the Patch Tagging Guidelines, please
+checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
+are templates for supplementary fields that you might want to add:
+
+Origin: <vendor|upstream|other>, <url of original patch>
+Bug: <url in upstream bugtracker>
+Bug-Debian: http://bugs.debian.org/<bugnumber>
+Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber>
+Forwarded: <no|not-needed|url proving that it has been forwarded>
+Reviewed-By: <name and email of someone who approved the patch>
+Last-Update: <YYYY-MM-DD>
+
+--- mrbayes-3.1.2.orig/Makefile
++++ mrbayes-3.1.2/Makefile
+@@ -88,6 +88,7 @@ all: $(PROGS)
+
+ clean:
+ rm -f *.o
++ rm -f $(PROGS)
+
+ showdep:
+ @$(CC) -MM bayes.c command.c mbmath.c mcmc.c model.c plot.c sump.c sumt.c
+--- /dev/null
++++ mrbayes-3.1.2/doc/man/man1/mb.1
+@@ -0,0 +1,10 @@
++.TH mrbayes "1" "Nov 2006" "mrbayes 3.1.2" "User Commands"
++.SH NAME
++mb \- A program for the Bayesian estimation
++.SH SYNOPSIS
++.B mb [OPTION]... [FILE]...
++.SH DESCRIPTION
++A program for the Bayesian estimation of phylogeny Bayesian inference of phylogeny
++.SH OPTIONS
++.B \-i
++interactive mode
Modified: trunk/packages/mrbayes/trunk/debian/patches/series
===================================================================
--- trunk/packages/mrbayes/trunk/debian/patches/series 2010-11-02 22:14:26 UTC (rev 5409)
+++ trunk/packages/mrbayes/trunk/debian/patches/series 2010-11-04 14:24:40 UTC (rev 5410)
@@ -1,2 +1 @@
-misc/makefile_clean_binary.diff -p0
-misc/man1.diff -p1
+debian-changes-3.1.2-1
Modified: trunk/packages/mrbayes/trunk/debian/rules
===================================================================
--- trunk/packages/mrbayes/trunk/debian/rules 2010-11-02 22:14:26 UTC (rev 5409)
+++ trunk/packages/mrbayes/trunk/debian/rules 2010-11-04 14:24:40 UTC (rev 5410)
@@ -1,56 +1,77 @@
#!/usr/bin/make -f
package = mrbayes
+
+include /usr/share/quilt/quilt.make
+
docdir = debian/tmp/usr/share/doc/$(package)
mandir = debian/tmp/usr/share/man
+export DH_VERBOSE=1
+
build:
- $(checkdir)
+ dh_testdir
quilt push -a || test $$? = 2
+
+ # build mb-mpi
MPI=yes $(MAKE)
mv mb mb-mpi
+
+ # build mb
$(MAKE) clean
MPI=no $(MAKE)
touch build
clean:
- $(checkdir)
- -$(MAKE) -i clean
+ dh_testdir
+ dh_testroot
+ [ ! -f Makefile ] || $(MAKE) clean
ln -sf debian/patches
quilt pop -a || test $$? = 2
+ rm -f mb-mpi
rm -f build
rm -rf *~ .pc debian/tmp debian/*~ debian/files* debian/substvars patches
+ dh_clean
-binary-indep: checkroot build
- $(checkdir)
+install-arch: build
+ dh_testdir
+ dh_testroot
+ dh_prep
-binary-arch: checkroot build
- $(checkdir)
- rm -rf debian/tmp
install -d debian/tmp/DEBIAN $(docdir) $(mandir) debian/tmp/usr/bin
- install -s -m 755 mb debian/tmp/usr/bin
+ install -s -m 755 mb debian/tmp/usr/bin
install -s -m 755 mb-mpi debian/tmp/usr/bin
- cp -a debian/copyright $(docdir)
- cp -a debian/changelog $(docdir)/changelog.Debian
cp -a doc/man/man1 $(mandir)
- cd $(docdir) && gzip -9 changelog.Debian
- dpkg-shlibdeps debian/tmp/usr/bin/mb
- dpkg-shlibdeps debian/tmp/usr/bin/mb-mpi
- dpkg-gencontrol -isp
- gzip -r9 debian/tmp/usr/share/man
- chown -R root:root debian/tmp
- chmod -R u+w,go=rX debian/tmp
- chmod u=rwx,go=rx debian/tmp/usr/bin/mb
- dpkg --build debian/tmp ..
-define checkdir
- test -f mb.c -a -f debian/rules
-endef
+ dh_install -pmrbayes usr/bin/mb usr/bin
+ dh_install -pmrbayes-mpi usr/bin/mb-mpi usr/bin
+
+# Build architecture-independent files here.
+binary-indep: build install
+# We have nothing to do by default.
+
+# Build architecture-dependent files here.
+binary-arch: build install-arch
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs
+ dh_lintian
+ dh_installexamples
+ dh_installman
+# dh_install --sourcedir=$(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
-checkroot:
- $(checkdir)
- test $$(id -u) = 0
-
-.PHONY: clean binary binary-arch binary-indep checkroot
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