[med-svn] r7813 - in trunk/packages/eigensoft/trunk/debian: . patches

Steffen Möller moeller at alioth.debian.org
Thu Sep 15 12:34:42 UTC 2011 

Author: moeller
Date: 2011-09-15 12:34:41 +0000 (Thu, 15 Sep 2011)
New Revision: 7813

Modified:
   trunk/packages/eigensoft/trunk/debian/changelog
   trunk/packages/eigensoft/trunk/debian/control
   trunk/packages/eigensoft/trunk/debian/copyright
   trunk/packages/eigensoft/trunk/debian/patches/series
   trunk/packages/eigensoft/trunk/debian/rules
   trunk/packages/eigensoft/trunk/debian/watch
Log:
New upstream version.


Modified: trunk/packages/eigensoft/trunk/debian/changelog
===================================================================
--- trunk/packages/eigensoft/trunk/debian/changelog	2011-09-15 09:31:48 UTC (rev 7812)
+++ trunk/packages/eigensoft/trunk/debian/changelog	2011-09-15 12:34:41 UTC (rev 7813)
@@ -1,3 +1,9 @@
+eigensoft (4.2-1) UNRELEASED; urgency=low
+
+  * New upstream release.
+
+ -- Steffen Moeller <moeller at debian.org>  Thu, 15 Sep 2011 14:20:03 +0200
+
 eigensoft (3.0-1) UNRELEASED; urgency=low
 
   * Initial release (Closes: #nnnn).

Modified: trunk/packages/eigensoft/trunk/debian/control
===================================================================
--- trunk/packages/eigensoft/trunk/debian/control	2011-09-15 09:31:48 UTC (rev 7812)
+++ trunk/packages/eigensoft/trunk/debian/control	2011-09-15 12:34:41 UTC (rev 7813)
@@ -1,5 +1,5 @@
 Source: eigensoft
-Section: science
+Section: non-free/science
 Priority: extra
 Maintainer: Steffen Moeller <moeller at debian.org>
 Build-Depends: debhelper (>= 8.0.0),
@@ -7,9 +7,9 @@
  libblas-dev,
  liblapack-dev
 Standards-Version: 3.9.2
-Homepage: http://genepath.med.harvard.edu/~reich/Software.htm
-#Vcs-Git: git://git.debian.org/collab-maint/eigenstrat.git
-#Vcs-Browser: http://git.debian.org/?p=collab-maint/eigenstrat.git;a=summary
+Homepage: http://www.hsph.harvard.edu/faculty/alkes-price/software/
+Vcs-Svn: svn+ssh://svn.debian.org/svn/debian-med/trunk/packages/eigensoft/trunk
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/eigensoft/trunk/
 
 Package: eigensoft
 Architecture: any

Modified: trunk/packages/eigensoft/trunk/debian/copyright
===================================================================
--- trunk/packages/eigensoft/trunk/debian/copyright	2011-09-15 09:31:48 UTC (rev 7812)
+++ trunk/packages/eigensoft/trunk/debian/copyright	2011-09-15 12:34:41 UTC (rev 7813)
@@ -1,24 +1,26 @@
 Format: http://dep.debian.net/deps/dep5
 Upstream-Name: eigenstrat
-Source: <url://example.com>
+Source: http://www.hsph.harvard.edu/faculty/alkes-price/software/
 
 Files: *
-Copyright: <years> <put author's name and email here>
-           <years> <likewise for another author>
-License: <special license>
- <Put the license of the package here indented by 1 space>
- <This follows the format of Description: lines in control file>
- .
- <Including paragraphs>
+Copyright: 2010 Harvard University and The Broad Institute
+	   Samuela Pollack <spollack at hsph.harvard.edu>
 
-# If you want to use GPL v2 or later for the /debian/* files use 
-# the following clauses, or change it to suit. Delete these two lines
+License: 
+ SOFTWARE COPYRIGHT NOTICE AGREEMENT
+ This software and its documentation are copyright (2010) by Harvard University 
+ and The Broad Institute. All rights are reserved. This software is supplied 
+ without any warranty or guaranteed support whatsoever. Neither Harvard 
+ University nor The Broad Institute can be responsible for its use, misuse, or 
+ functionality. The software may be freely copied for non-commercial purposes, 
+ provided this copyright notice is retained.
+
 Files: debian/*
 Copyright: 2011 Steffen Moeller <moeller at debian.org>
-License: GPL-2+
+License: GPL-3+
  This package is free software; you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
+ the Free Software Foundation; either version 3 of the License, or
  (at your option) any later version.
  .
  This package is distributed in the hope that it will be useful,
@@ -30,7 +32,4 @@
  along with this program. If not, see <http://www.gnu.org/licenses/>
  .
  On Debian systems, the complete text of the GNU General
- Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
-
-# Please also look if there are files or directories which have a
-# different copyright/license attached and list them here.
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".

Modified: trunk/packages/eigensoft/trunk/debian/patches/series
===================================================================
--- trunk/packages/eigensoft/trunk/debian/patches/series	2011-09-15 09:31:48 UTC (rev 7812)
+++ trunk/packages/eigensoft/trunk/debian/patches/series	2011-09-15 12:34:41 UTC (rev 7813)
@@ -1,3 +1,3 @@
-g772gfortran.patch
-atlasLinkNotNeeded.patch
-optimizingBlasDependencies.patch
+#g772gfortran.patch
+#atlasLinkNotNeeded.patch
+#optimizingBlasDependencies.patch

Modified: trunk/packages/eigensoft/trunk/debian/rules
===================================================================
--- trunk/packages/eigensoft/trunk/debian/rules	2011-09-15 09:31:48 UTC (rev 7812)
+++ trunk/packages/eigensoft/trunk/debian/rules	2011-09-15 12:34:41 UTC (rev 7813)
@@ -18,21 +18,21 @@
 
 override_dh_clean:
 	dh_clean
-	$(MAKE) -C src clean
-	rm -fr smartinclude smartlib smarttables
+	$(MAKE) -C src clobber
 
 override_dh_strip:
 	dh_strip --dbg-package=eigensoft-dbg
 
-VERSION=3.0
+VERSION=4.2
 get-orig-source:
-	[ ! -r ../EIG$(VERSION) ] || wget http://www.hsph.harvard.edu/faculty/alkes-price/files/EIG$(VERSION).tar.gz -O ../EIG$(VERSION).tar.gz
-	rm -rf ../eigensoft-$(VERSION)
-	mkdir ../eigensoft-$(VERSION)
-	cd ../eigensoft-$(VERSION) && tar xzf ../EIG$(VERSION).tar.gz
+	[ -r ../eig$(VERSION).tar.gz ] || wget http://www.hsph.harvard.edu/faculty/alkes-price/files/eig$(VERSION).tar.gz -O ../eig$(VERSION).tar.gz
+	rm -rf ../EIG$(VERSION)
+	cd .. && tar xzf eig$(VERSION).tar.gz
+	cd .. && mv EIG$(VERSION) eigensoft-$(VERSION)
 	find ../eigensoft-$(VERSION)/bin -type f | grep -v '.perl$$' | xargs -r rm
 	find ../eigensoft-$(VERSION)/POPGEN -type f | grep -v '.perl$$' | xargs -r chmod -x
 	find ../eigensoft-$(VERSION)/CONVERTF -type f | grep -v '.perl$$' | xargs -r chmod -x
 	find ../eigensoft-$(VERSION)/EIGENSTRAT -type f | grep -v '.perl$$' | xargs -r chmod -x
+	#find ../eigensoft-$(VERSION) -name "*.o" -delete
 	make -C ../eigensoft-$(VERSION)/src clean
 	cd .. && tar cjf eigensoft_$(VERSION).orig.tar.bz2 eigensoft-$(VERSION)

Modified: trunk/packages/eigensoft/trunk/debian/watch
===================================================================
--- trunk/packages/eigensoft/trunk/debian/watch	2011-09-15 09:31:48 UTC (rev 7812)
+++ trunk/packages/eigensoft/trunk/debian/watch	2011-09-15 12:34:41 UTC (rev 7813)
@@ -5,4 +5,4 @@
 
 # Compulsory line, this is a version 3 file
 version=3
-http://www.hsph.harvard.edu/faculty/alkes-price/files/EIG([0-9.]+)\.tar\.gz
+http://www.hsph.harvard.edu/faculty/alkes-price/files/eig([0-9.]+).tar.gz

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