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 <ti...@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-packag...@lists.alioth.debian.org> -Uploaders: Philipp Benner <phil...@debian.org> -Build-Depends: debhelper (>= 5), autotools-dev, quilt, zoem, tidy -Standards-Version: 3.8.4 +Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> +Uploaders: Philipp Benner <phil...@debian.org>, + Andreas Tille <ti...@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 <phil...@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) _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit