[med-svn] r4650 - trunk/packages/phyml/trunk/debian

[Charles Plessy]

Author: plessy
Date: 2010-03-07 11:40:56 +0000 (Sun, 07 Mar 2010)
New Revision: 4650

Added:
   trunk/packages/phyml/trunk/debian/upstream-metadata.yaml
Removed:
   trunk/packages/phyml/trunk/debian/reference
Modified:
   trunk/packages/phyml/trunk/debian/changelog
   trunk/packages/phyml/trunk/debian/control
   trunk/packages/phyml/trunk/debian/rules
Log:
New upstream release, plus package updates.

  * Checked conformance with Policy 3.8.4 and incremented Standards-Version
    in debian/control to reflect this (no changes needed).
  * Moved the bibliographic reference from debian/reference to
    debian/upstream-metadata.yaml.
  * Adapted debian/rules to the new location of the auto(conf|make) files.


Modified: trunk/packages/phyml/trunk/debian/changelog
===================================================================
--- trunk/packages/phyml/trunk/debian/changelog	2010-03-07 05:51:23 UTC (rev 4649)
+++ trunk/packages/phyml/trunk/debian/changelog	2010-03-07 11:40:56 UTC (rev 4650)
@@ -1,14 +1,24 @@
-phyml (2:20090706-1) UNRELEASED; urgency=low
+phyml (2:20100123-1) unstable; urgency=low
 
+  * New upstream release.
+
+  [ Nelson A. de Oliveira ]
   * Fix watch file.
   * Increment the epoch number to fix a typo in the version number.
 
- -- Nelson A. de Oliveira <naoliv at debian.org>  Fri, 23 Oct 2009 17:19:09 -0200
+  [ Charles Plessy ]
+  * Checked conformance with Policy 3.8.4 and incremented Standards-Version
+    in debian/control to reflect this (no changes needed).
+  * Moved the bibliographic reference from debian/reference to
+    debian/upstream-metadata.yaml.
+  * Adapted debian/rules to the new location of the auto(conf|make) files.
 
+ -- Charles Plessy <plessy at debian.org>  Sun, 07 Mar 2010 19:55:08 +0900
+
 phyml (1:200900706-2) unstable; urgency=low
 
   * Disable parallel building, that was incorrectly supported and
-    induced build failures by race condidtion (Closes: #536967).
+    induced build failures by race condition (Closes: #536967).
 
  -- Charles Plessy <plessy at debian.org>  Wed, 15 Jul 2009 09:35:40 +0900
 

Modified: trunk/packages/phyml/trunk/debian/control
===================================================================
--- trunk/packages/phyml/trunk/debian/control	2010-03-07 05:51:23 UTC (rev 4649)
+++ trunk/packages/phyml/trunk/debian/control	2010-03-07 11:40:56 UTC (rev 4650)
@@ -5,7 +5,7 @@
 DM-Upload-Allowed: yes
 Uploaders: Charles Plessy <plessy at debian.org>
 Build-Depends: debhelper (>= 7), automake, autoconf
-Standards-Version: 3.8.2
+Standards-Version: 3.8.4
 Homepage: http://www.atgc-montpellier.fr/phyml
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/phyml/trunk/?rev=0&sc=0
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/phyml/trunk/

Deleted: trunk/packages/phyml/trunk/debian/reference
===================================================================
--- trunk/packages/phyml/trunk/debian/reference	2010-03-07 05:51:23 UTC (rev 4649)
+++ trunk/packages/phyml/trunk/debian/reference	2010-03-07 11:40:56 UTC (rev 4650)
@@ -1,12 +0,0 @@
- at article{StephaneGuindon10012003,
-author = {Guindon, Stephane and Gascuel, Olivier},
-title = {{A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood}},
-journal = {Syst Biol},
-volume = {52},
-number = {5},
-pages = {696-704},
-doi = {10.1080/10635150390235520},
-year = {2003},
-URL = {http://sysbio.oxfordjournals.org/cgi/content/abstract/52/5/696},
-eprint = {http://sysbio.oxfordjournals.org/cgi/reprint/52/5/696.pdf}
-}

Modified: trunk/packages/phyml/trunk/debian/rules
===================================================================
--- trunk/packages/phyml/trunk/debian/rules	2010-03-07 05:51:23 UTC (rev 4649)
+++ trunk/packages/phyml/trunk/debian/rules	2010-03-07 11:40:56 UTC (rev 4650)
@@ -20,12 +20,12 @@
 
 
 src/Makefile:
-	cd src ; aclocal ; autoconf -f ; automake -f ; ./configure
+	aclocal ; autoconf -f ; automake -f ; ./configure --prefix=/usr
 
 build: src/Makefile build-stamp
 build-stamp:
 	dh_testdir
-	$(MAKE) -C src CFLAGS="$(CFLAGS)"
+	$(MAKE) CFLAGS="$(CFLAGS)"
 	touch build-stamp
 
 clean:
@@ -36,7 +36,7 @@
 	dh_testroot
 	dh_prep
 	dh_installdirs
-	$(MAKE) -C src prefix=`pwd`/debian/`dh_listpackages`/usr install
+	$(MAKE) prefix=`pwd`/debian/`dh_listpackages`/usr install
 
 binary-indep: build install
 binary-arch: build install

Copied: trunk/packages/phyml/trunk/debian/upstream-metadata.yaml (from rev 4649, trunk/packages/phyml/trunk/debian/reference)
===================================================================
--- trunk/packages/phyml/trunk/debian/upstream-metadata.yaml	                        (rev 0)
+++ trunk/packages/phyml/trunk/debian/upstream-metadata.yaml	2010-03-07 11:40:56 UTC (rev 4650)
@@ -0,0 +1,23 @@
+Archive: Google code
+Contact: Stephane Guindon <guindon at stat.auckland.ac.nz>
+Name: PhyML
+Homepage: http://www.atgc-montpellier.fr/phyml
+Reference:
+ author: Guindon, Stephane and Gascuel, Olivier
+ title: A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
+ journal: Syst Biol
+ volume: 52
+ number: 5
+ pages: 696-704
+ doi: 10.1080/10635150390235520
+ year: 2003
+ URL: http://sysbio.oxfordjournals.org/cgi/content/abstract/52/5/696
+ eprint: http://sysbio.oxfordjournals.org/cgi/reprint/52/5/696.pdf
+ PMID: 14530136
+Repository: http://phyml.googlecode.com/svn/trunk/
+Repository-Browse: http://code.google.com/p/phyml/source/browse/
+Watch: |
+ version=3
+ http://code.google.com/p/phyml/downloads/list \
+     http://phyml[.]googlecode[.]com/files/phyml_(20.*)[.]tar[.]gz
+Webservice: http://www.atgc-montpellier.fr/phyml