[med-svn] r5695 - in trunk/packages/mcl/trunk/debian: . patches source

Mon Jan 24 15:31:11 UTC 2011

Author: tille
Date: 2011-01-24 15:31:09 +0000 (Mon, 24 Jan 2011)
New Revision: 5695

Added:
   trunk/packages/mcl/trunk/debian/source/
   trunk/packages/mcl/trunk/debian/source/format
Removed:
   trunk/packages/mcl/trunk/debian/patches/01-manpage-errors.patch
Modified:
   trunk/packages/mcl/trunk/debian/changelog
   trunk/packages/mcl/trunk/debian/control
   trunk/packages/mcl/trunk/debian/patches/02-wrong-interpreter-path.patch
   trunk/packages/mcl/trunk/debian/patches/series
   trunk/packages/mcl/trunk/debian/rules
Log:
Preparation for new upstream verison but not uploaded yet, do not use a patch for fixing the manpages but rather use sed to be safe for new upstream versions, general packaging updates


Modified: trunk/packages/mcl/trunk/debian/changelog
===================================================================

--- trunk/packages/mcl/trunk/debian/changelog	2011-01-24 14:42:35 UTC (rev 5694)
+++ trunk/packages/mcl/trunk/debian/changelog	2011-01-24 15:31:09 UTC (rev 5695)
@@ -1,3 +1,20 @@
+mcl (1:10-201-21) UNRELEASED; urgency=low
+
+  * New upstream version
+  * debian/control:
+    - Added myself to uploaders
+    - Fixed spelling of Debian Med
+    - Standards-Version: 3.9.1 (no changes needed)
+    - debhelper 7
+    - removed versioned conflicts for mcl-doc from quite old mcl version
+      which seems to be useless these days
+  * debian/source/format: 3.0 (quilt)
+  * debian/rules, debian/patches/01-manpage-errors.patch:
+    Use sed on installed packages to get the same effect as the patch but
+    there is no need to change the patch for new versions
+
+ -- Andreas Tille <tille at debian.org>  Mon, 24 Jan 2011 15:58:07 +0100
+
 mcl (1:10-148-1) unstable; urgency=low
 
   * New upstream release

Modified: trunk/packages/mcl/trunk/debian/control
===================================================================
--- trunk/packages/mcl/trunk/debian/control	2011-01-24 14:42:35 UTC (rev 5694)
+++ trunk/packages/mcl/trunk/debian/control	2011-01-24 15:31:09 UTC (rev 5695)
@@ -1,10 +1,11 @@
 Source: mcl
 Section: math
 Priority: optional
-Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Philipp Benner <philipp at debian.org>
-Build-Depends: debhelper (>= 5), autotools-dev, quilt, zoem, tidy
-Standards-Version: 3.8.4
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Philipp Benner <philipp at debian.org>,
+ Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 7), autotools-dev, quilt, zoem, tidy
+Standards-Version: 3.9.1
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mcl/
 Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mcl/
 Homepage: http://micans.org/mcl/
@@ -28,7 +29,6 @@
 Depends: ${misc:Depends}
 Section: doc
 Suggests: mcl
-Conflicts: mcl (<< 04-095-1)
 Description: documentation for mcl
  The MCL package is an implementation of the Markov Cluster algorithm,
  for manipulating sparse matricess and conducting cluster experiments.

Deleted: trunk/packages/mcl/trunk/debian/patches/01-manpage-errors.patch
===================================================================
--- trunk/packages/mcl/trunk/debian/patches/01-manpage-errors.patch	2011-01-24 14:42:35 UTC (rev 5694)
+++ trunk/packages/mcl/trunk/debian/patches/01-manpage-errors.patch	2011-01-24 15:31:09 UTC (rev 5695)
@@ -1,293 +0,0 @@
-Index: mcl-10-148/doc/clmclose.1
-===================================================================
---- mcl-10-148.orig/doc/clmclose.1	2009-06-28 14:18:27.000000000 +0000
-+++ mcl-10-148/doc/clmclose.1	2009-06-28 14:19:28.000000000 +0000
-@@ -1,5 +1,5 @@
- .\" Copyright (c) 2010 Stijn van Dongen
--.TH "clm close" 1 "28 May 2010" "clm close 1\&.008, 10-148" "USER COMMANDS "
-+.TH "clmclose" 1 "28 May 2010" "clm close 1\&.008, 10-148" "USER COMMANDS "
- .po 2m
- .de ZI
- .\" Zoem Indent/Itemize macro I.
-@@ -28,7 +28,7 @@
- .el .in 8m
- ..
- .SH NAME
--clm close \- Fetch connected components from graphs or subgraphs
-+clmclose \- Fetch connected components from graphs or subgraphs
- 
- clmclose is not in actual fact a program\&. This manual
- page documents the behaviour and options of the clm program when
-Index: mcl-10-148/doc/clmdist.1
-===================================================================
---- mcl-10-148.orig/doc/clmdist.1	2009-06-28 14:18:40.000000000 +0000
-+++ mcl-10-148/doc/clmdist.1	2009-06-28 14:19:45.000000000 +0000
-@@ -1,5 +1,5 @@
- .\" Copyright (c) 2010 Stijn van Dongen
--.TH "clm dist" 1 "28 May 2010" "clm dist 1\&.008, 10-148" "USER COMMANDS "
-+.TH "clmdist" 1 "28 May 2010" "clm dist 1\&.008, 10-148" "USER COMMANDS "
- .po 2m
- .de ZI
- .\" Zoem Indent/Itemize macro I.
-@@ -28,7 +28,7 @@
- .el .in 8m
- ..
- .SH NAME
--clm dist \- compute the distance between two or more partitions (clusterings)\&.
-+clmdist \- compute the distance between two or more partitions (clusterings)\&.
- 
- The distance that is computed can be any of
- \fIsplit/join distance\fP, \fIvariance of information\fP,
-Index: mcl-10-148/doc/clmformat.1
-===================================================================
---- mcl-10-148.orig/doc/clmformat.1	2009-06-28 14:18:48.000000000 +0000
-+++ mcl-10-148/doc/clmformat.1	2009-06-28 14:19:22.000000000 +0000
-@@ -28,7 +28,7 @@
- .el .in 8m
- ..
- .SH NAME
--clm format \- display cluster results in readable form
-+clmformat \- display cluster results in readable form
- 
- (optionally with labels and/or cohesion and stickiness measures
- attached)\&.
-Index: mcl-10-148/doc/clmimac.1
-===================================================================
---- mcl-10-148.orig/doc/clmimac.1	2009-06-28 14:19:53.000000000 +0000
-+++ mcl-10-148/doc/clmimac.1	2009-06-28 14:19:59.000000000 +0000
-@@ -1,5 +1,5 @@
- .\" Copyright (c) 2010 Stijn van Dongen
--.TH "clm imac" 1 "28 May 2010" "clm imac 1\&.008, 10-148" "USER COMMANDS "
-+.TH "clmimac" 1 "28 May 2010" "clm imac 1\&.008, 10-148" "USER COMMANDS "
- .po 2m
- .de ZI
- .\" Zoem Indent/Itemize macro I.
-@@ -28,7 +28,7 @@
- .el .in 8m
- ..
- .SH NAME
--clm imac \- Interpret Matrices (c\&.q\&. MCL iterands output by \fBmcl\fP) As Clusterings\&.
-+clmimac \- Interpret Matrices (c\&.q\&. MCL iterands output by \fBmcl\fP) As Clusterings\&.
- 
- clmimac is not in actual fact a program\&. This manual
- page documents the behaviour and options of the clm program when
-Index: mcl-10-148/doc/clminfo.1
-===================================================================
---- mcl-10-148.orig/doc/clminfo.1	2009-06-28 14:20:06.000000000 +0000
-+++ mcl-10-148/doc/clminfo.1	2009-06-28 14:20:11.000000000 +0000
-@@ -1,5 +1,5 @@
- .\" Copyright (c) 2010 Stijn van Dongen
--.TH "clm info" 1 "28 May 2010" "clm info 1\&.008, 10-148" "USER COMMANDS "
-+.TH "clminfo" 1 "28 May 2010" "clm info 1\&.008, 10-148" "USER COMMANDS "
- .po 2m
- .de ZI
- .\" Zoem Indent/Itemize macro I.
-@@ -28,7 +28,7 @@
- .el .in 8m
- ..
- .SH NAME
--clm info \- compute performance measures for graphs and clusterings\&.
-+clminfo \- compute performance measures for graphs and clusterings\&.
- 
- clminfo is not in actual fact a program\&. This manual
- page documents the behaviour and options of the clm program when
-Index: mcl-10-148/doc/clmmate.1
-===================================================================
---- mcl-10-148.orig/doc/clmmate.1	2009-06-28 14:20:17.000000000 +0000
-+++ mcl-10-148/doc/clmmate.1	2009-06-28 14:20:24.000000000 +0000
-@@ -1,5 +1,5 @@
- .\" Copyright (c) 2010 Stijn van Dongen
--.TH "clm mate" 1 "28 May 2010" "clm mate 1\&.008, 10-148" "USER COMMANDS "
-+.TH "clmmate" 1 "28 May 2010" "clm mate 1\&.008, 10-148" "USER COMMANDS "
- .po 2m
- .de ZI
- .\" Zoem Indent/Itemize macro I.
-@@ -28,7 +28,7 @@
- .el .in 8m
- ..
- .SH NAME
--clm mate \- compute best matches between two clusterings
-+clmmate \- compute best matches between two clusterings
- 
- clmmate is not in actual fact a program\&. This manual
- page documents the behaviour and options of the clm program when
-Index: mcl-10-148/doc/clmmeet.1
-===================================================================
---- mcl-10-148.orig/doc/clmmeet.1	2009-06-28 14:20:31.000000000 +0000
-+++ mcl-10-148/doc/clmmeet.1	2009-06-28 14:20:36.000000000 +0000
-@@ -1,5 +1,5 @@
- .\" Copyright (c) 2010 Stijn van Dongen
--.TH "clm meet" 1 "28 May 2010" "clm meet 1\&.008, 10-148" "USER COMMANDS "
-+.TH "clmmeet" 1 "28 May 2010" "clm meet 1\&.008, 10-148" "USER COMMANDS "
- .po 2m
- .de ZI
- .\" Zoem Indent/Itemize macro I.
-@@ -28,7 +28,7 @@
- .el .in 8m
- ..
- .SH NAME
--clm meet \- compute the intersection of a set of clusterings\&.
-+clmmeet \- compute the intersection of a set of clusterings\&.
- 
- clmmeet is not in actual fact a program\&. This manual
- page documents the behaviour and options of the clm program when
-Index: mcl-10-148/doc/clmorder.1
-===================================================================
---- mcl-10-148.orig/doc/clmorder.1	2009-06-28 14:20:41.000000000 +0000
-+++ mcl-10-148/doc/clmorder.1	2009-06-28 14:20:46.000000000 +0000
-@@ -1,5 +1,5 @@
- .\" Copyright (c) 2010 Stijn van Dongen
--.TH "clm order" 1 "28 May 2010" "clm order 1\&.008, 10-148" "USER COMMANDS "
-+.TH "clmorder" 1 "28 May 2010" "clm order 1\&.008, 10-148" "USER COMMANDS "
- .po 2m
- .de ZI
- .\" Zoem Indent/Itemize macro I.
-@@ -28,7 +28,7 @@
- .el .in 8m
- ..
- .SH NAME
--clm order \- reorder clusterings conformal to inclusion structure
-+clmorder \- reorder clusterings conformal to inclusion structure
- 
- clmorder is not in actual fact a program\&. This manual
- page documents the behaviour and options of the clm program when
-Index: mcl-10-148/doc/clmresidue.1
-===================================================================
---- mcl-10-148.orig/doc/clmresidue.1	2009-06-28 14:20:51.000000000 +0000
-+++ mcl-10-148/doc/clmresidue.1	2009-06-28 14:20:57.000000000 +0000
-@@ -1,5 +1,5 @@
- .\" Copyright (c) 2010 Stijn van Dongen
--.TH "clm residue" 1 "28 May 2010" "clm residue 1\&.008, 10-148" "USER COMMANDS "
-+.TH "clmresidue" 1 "28 May 2010" "clm residue 1\&.008, 10-148" "USER COMMANDS "
- .po 2m
- .de ZI
- .\" Zoem Indent/Itemize macro I.
-@@ -28,7 +28,7 @@
- .el .in 8m
- ..
- .SH NAME
--clm residue \- extend clustering of subgraph to clustering of graph\&.
-+clmresidue \- extend clustering of subgraph to clustering of graph\&.
- 
- clmresidue is not in actual fact a program\&. This manual
- page documents the behaviour and options of the clm program when
-Index: mcl-10-148/doc/clmvol.1
-===================================================================
---- mcl-10-148.orig/doc/clmvol.1	2009-06-28 14:21:02.000000000 +0000
-+++ mcl-10-148/doc/clmvol.1	2009-06-28 14:21:07.000000000 +0000
-@@ -1,5 +1,5 @@
- .\" Copyright (c) 2010 Stijn van Dongen
--.TH "clm vol" 1 "28 May 2010" "clm vol 1\&.008, 10-148" "USER COMMANDS "
-+.TH "clmvol" 1 "28 May 2010" "clm vol 1\&.008, 10-148" "USER COMMANDS "
- .po 2m
- .de ZI
- .\" Zoem Indent/Itemize macro I.
-@@ -28,7 +28,7 @@
- .el .in 8m
- ..
- .SH NAME
--clm vol \- compute volatile nodes from a set of clusterings
-+clmvol \- compute volatile nodes from a set of clusterings
- 
- clmvol is not in actual fact a program\&. This manual
- page documents the behaviour and options of the clm program when
-Index: mcl-10-148/doc/mcxclcf.1
-===================================================================
---- mcl-10-148.orig/doc/mcxclcf.1	2009-06-28 14:21:17.000000000 +0000
-+++ mcl-10-148/doc/mcxclcf.1	2009-06-28 14:21:22.000000000 +0000
-@@ -1,5 +1,5 @@
- .\" Copyright (c) 2010 Stijn van Dongen
--.TH "mcx clcf" 1 "28 May 2010" "mcx clcf 1\&.008, 10-148" "USER COMMANDS "
-+.TH "mcxclcf" 1 "28 May 2010" "mcx clcf 1\&.008, 10-148" "USER COMMANDS "
- .po 2m
- .de ZI
- .\" Zoem Indent/Itemize macro I.
-@@ -28,7 +28,7 @@
- .el .in 8m
- ..
- .SH NAME
--mcx clcf \- compute the clustering coefficient of a graph
-+mcxclcf \- compute the clustering coefficient of a graph
- .SH SYNOPSIS
- 
- \fBmcx clcf\fP [options] [matrix-file]
-Index: mcl-10-148/doc/mcxconvert.1
-===================================================================
---- mcl-10-148.orig/doc/mcxconvert.1	2009-06-28 14:21:30.000000000 +0000
-+++ mcl-10-148/doc/mcxconvert.1	2009-06-28 14:21:37.000000000 +0000
-@@ -1,5 +1,5 @@
- .\" Copyright (c) 2010 Stijn van Dongen
--.TH "mcx convert" 1 "28 May 2010" "mcx convert 1\&.008, 10-148" "USER COMMANDS "
-+.TH "mcxconvert" 1 "28 May 2010" "mcx convert 1\&.008, 10-148" "USER COMMANDS "
- .po 2m
- .de ZI
- .\" Zoem Indent/Itemize macro I.
-@@ -28,7 +28,7 @@
- .el .in 8m
- ..
- .SH NAME
--mcx convert \- convert between mcx storage types
-+mcxconvert \- convert between mcx storage types
- .SH SYNOPSIS
- 
- \fBmcx convert\fP <matrix-file-in> <matrix-file-out>
-Index: mcl-10-148/doc/mcxctty.1
-===================================================================
---- mcl-10-148.orig/doc/mcxctty.1	2009-06-28 14:21:49.000000000 +0000
-+++ mcl-10-148/doc/mcxctty.1	2009-06-28 14:21:53.000000000 +0000
-@@ -1,5 +1,5 @@
- .\" Copyright (c) 2010 Stijn van Dongen
--.TH "mcx ctty" 1 "28 May 2010" "mcx ctty 1\&.008, 10-148" "USER COMMANDS "
-+.TH "mcxctty" 1 "28 May 2010" "mcx ctty 1\&.008, 10-148" "USER COMMANDS "
- .po 2m
- .de ZI
- .\" Zoem Indent/Itemize macro I.
-@@ -28,7 +28,7 @@
- .el .in 8m
- ..
- .SH NAME
--mcx ctty \- compute betweenness centrality for network nodes
-+mcxctty \- compute betweenness centrality for network nodes
- .SH SYNOPSIS
- 
- \fBmcx ctty\fP [options] [matrix-file]
-Index: mcl-10-148/doc/mcxdiameter.1
-===================================================================
---- mcl-10-148.orig/doc/mcxdiameter.1	2009-06-28 14:21:59.000000000 +0000
-+++ mcl-10-148/doc/mcxdiameter.1	2009-06-28 14:22:04.000000000 +0000
-@@ -1,5 +1,5 @@
- .\" Copyright (c) 2010 Stijn van Dongen
--.TH "mcx diameter" 1 "28 May 2010" "mcx diameter 1\&.008, 10-148" "USER COMMANDS "
-+.TH "mcxdiameter" 1 "28 May 2010" "mcx diameter 1\&.008, 10-148" "USER COMMANDS "
- .po 2m
- .de ZI
- .\" Zoem Indent/Itemize macro I.
-@@ -28,7 +28,7 @@
- .el .in 8m
- ..
- .SH NAME
--mcx diameter \- compute the diameter of a graph
-+mcxdiameter \- compute the diameter of a graph
- .SH SYNOPSIS
- 
- \fBmcx diameter\fP [options]
-Index: mcl-10-148/doc/mcxerdos.1
-===================================================================
---- mcl-10-148.orig/doc/mcxerdos.1	2009-06-28 14:21:59.000000000 +0000
-+++ mcl-10-148/doc/mcxerdos.1	2009-06-28 14:22:04.000000000 +0000
-@@ -1,5 +1,5 @@
- .\" Copyright (c) 2010 Stijn van Dongen
--.TH "mcx erdos" 1 "28 May 2010" "mcx erdos 1\&.008, 10-148" "USER COMMANDS "
-+.TH "mcxerdos" 1 "28 May 2010" "mcx erdos 1\&.008, 10-148" "USER COMMANDS "
- .po 2m
- .de ZI
- .\" Zoem Indent/Itemize macro I.
-@@ -28,7 +28,7 @@
- .el .in 8m
- ..
- .SH NAME
--mcx erdos \- compute shortest paths in a graph
-+mcxerdos \- compute shortest paths in a graph
- .SH SYNOPSIS
- 
- \fBmcx erdos\fP [options]

Modified: trunk/packages/mcl/trunk/debian/patches/02-wrong-interpreter-path.patch
===================================================================
--- trunk/packages/mcl/trunk/debian/patches/02-wrong-interpreter-path.patch	2011-01-24 14:42:35 UTC (rev 5694)
+++ trunk/packages/mcl/trunk/debian/patches/02-wrong-interpreter-path.patch	2011-01-24 15:31:09 UTC (rev 5695)
@@ -1,7 +1,8 @@
-Index: mcl-09-149/src/alien/oxygen/src/mcxdeblast
-===================================================================
---- mcl-09-149.orig/src/alien/oxygen/src/mcxdeblast	2009-06-28 14:27:45.000000000 +0000
-+++ mcl-09-149/src/alien/oxygen/src/mcxdeblast	2009-06-28 14:27:48.000000000 +0000
+Author: Philipp Benner <philipp at debian.org>
+Purpose: Fix wrong path of perl interpreter
+
+--- mcl-10-201.orig/src/alien/oxygen/src/mcxdeblast
++++ mcl-10-201/src/alien/oxygen/src/mcxdeblast
 @@ -1,4 +1,4 @@
 -#!/usr/local/bin/perl -w
 +#!/usr/bin/perl -w

Modified: trunk/packages/mcl/trunk/debian/patches/series
===================================================================
--- trunk/packages/mcl/trunk/debian/patches/series	2011-01-24 14:42:35 UTC (rev 5694)
+++ trunk/packages/mcl/trunk/debian/patches/series	2011-01-24 15:31:09 UTC (rev 5695)
@@ -1,2 +1 @@
-01-manpage-errors.patch
 02-wrong-interpreter-path.patch

Modified: trunk/packages/mcl/trunk/debian/rules
===================================================================
--- trunk/packages/mcl/trunk/debian/rules	2011-01-24 14:42:35 UTC (rev 5694)
+++ trunk/packages/mcl/trunk/debian/rules	2011-01-24 15:31:09 UTC (rev 5695)
@@ -8,6 +8,8 @@
 
 include /usr/share/quilt/quilt.make
 
+pkg=mcl
+
 # allow bashism's in commandlines
 SHELL = /bin/bash
 
@@ -160,6 +162,10 @@
 
 binary-indep: build install
 	dh_installman
+	# Fix broken manpages instead
+	sed -i -e 's/^\(.TH "[cm][lc][mx]\) \+\(\w\)/\1\2/' \
+	       -e 's/^\([cm][lc][mx]\) \+\(\w\+ \\-\)/\1\2/' \
+	       $(CURDIR)/debian/$(pkg)/usr/share/man/man1/[cm]*.1
 	dh_installchangelogs ChangeLog
 	dh_compress
 	dh_fixperms

Added: trunk/packages/mcl/trunk/debian/source/format
===================================================================
--- trunk/packages/mcl/trunk/debian/source/format	                        (rev 0)
+++ trunk/packages/mcl/trunk/debian/source/format	2011-01-24 15:31:09 UTC (rev 5695)
@@ -0,0 +1 @@
+3.0 (quilt)


