[med-svn] r2372 - trunk/packages/axparafit/trunk/debian

plessy at alioth.debian.org plessy at alioth.debian.org
Thu Jul 31 10:51:54 UTC 2008 

Author: plessy
Date: 2008-07-31 10:51:53 +0000 (Thu, 31 Jul 2008)
New Revision: 2372

Removed:
   trunk/packages/axparafit/trunk/debian/patches/
Modified:
   trunk/packages/axparafit/trunk/debian/axparafit.1
   trunk/packages/axparafit/trunk/debian/changelog
   trunk/packages/axparafit/trunk/debian/compat
   trunk/packages/axparafit/trunk/debian/control
   trunk/packages/axparafit/trunk/debian/copyright
   trunk/packages/axparafit/trunk/debian/rules
Log:
Updating for Lenny+1.

 - Added myself to the uploaders.
 - Removed the Makefile patch.
 - Modified debian/rules to call make with Debian-specific values.
   (This was done before by the Makefile patch.)
 - Refreshed manpage.
 - Updated build-dependancies to new names of Atlas packages.
 - Updated to Debhelper 7.
 - Started to update debian/copyright, found non-free headers and stopped work
   for the moment.


Modified: trunk/packages/axparafit/trunk/debian/axparafit.1
===================================================================
--- trunk/packages/axparafit/trunk/debian/axparafit.1	2008-07-31 10:21:43 UTC (rev 2371)
+++ trunk/packages/axparafit/trunk/debian/axparafit.1	2008-07-31 10:51:53 UTC (rev 2372)
@@ -11,7 +11,7 @@
 .\" disable justification (adjust text to left margin only)
 .ad l
 .SH "NAME"
-axparafit, axparafitblas, axparparafit, axparparafitblas, axparparafitblas_random - optimized statistical analysis of host-parasite coevolution
+axparafit, axparafitblas, axparparafit, axparparafitblas, axparparafitblas_random \- optimized statistical analysis of host-parasite coevolution
 .SH "SYNOPSIS"
 .HP 10
 \fBaxparafit\fR \fB\-p\ \fR\fB\fInumberOfPermutations\fR\fR \fB\-n1\ \fR\fB\fIN1\fR\fR \fB\-n2\ \fR\fB\fIN2\fR\fR \fB\-n3\ \fR\fB\fIN3\fR\fR \fB\-n4\ \fR\fB\fIN4\fR\fR \fB\-A\ \fR\fB\fIassociationMatrix\fR\fR
@@ -22,74 +22,74 @@
 .br
 \fB\-h\fR
 .HP 4
-(1) [\fB\-g\fR\ is\ \fInot\ available\fR\ in\ \fBaxparparafit\fR,\ \fBaxparparafitblas\fR\ and\ \fBaxparparafitblas_random\fR\.]
+(1) [\fB\-g\fR\ is\ \fInot\ available\fR\ in\ \fBaxparparafit\fR,\ \fBaxparparafitblas\fR\ and\ \fBaxparparafitblas_random\fR\&.]
 .sp -1n
 .HP 4
-(2) [\fB\-t\fR\ is\ \fIrequired\fR\ for\ \fBaxparparafit\fR,\ \fBaxparparafitblas\fR\ and\ \fBaxparparafitblas_random\fR\.]
+(2) [\fB\-t\fR\ is\ \fIrequired\fR\ for\ \fBaxparparafit\fR,\ \fBaxparparafitblas\fR\ and\ \fBaxparparafitblas_random\fR\&.]
 .sp -1n
 .HP 4
-(3) [\fB\-r\fR\ is\ \fIonly\fR\ available\ for\ \fBaxparparafitblas_random\fR\.]
+(3) [\fB\-r\fR\ is\ \fIonly\fR\ available\ for\ \fBaxparparafitblas_random\fR\&.]
 .SH "DESCRIPTION"
 .PP
-AxParafit is a highly optimized version of Pierre Legendre\'s Parafit program for statistical analysis of host\-parasite coevolution\. AxParafit has been parallelized with MPI (Message Passing Interface) for compute clusters and was used to carry out the largest co\-evolutionary analysis to date for the paper describing the software\.
+AxParafit is a highly optimized version of Pierre Legendre\'s Parafit program for statistical analysis of host\-parasite coevolution\&. AxParafit has been parallelized with MPI (Message Passing Interface) for compute clusters and was used to carry out the largest co\-evolutionary analysis to date for the paper describing the software\&.
 .PP
-AxParafit will start executing individual tests of cospeciation directly\. If you want to execute only global tests of cospeciation, please use the
+AxParafit will start executing individual tests of cospeciation directly\&. If you want to execute only global tests of cospeciation, please use the
 [\-g]
-option\.
+option\&.
 .SH "OPTIONS"
 .PP
 \fB\-p\fR
 .RS 4
-Specify the number of permutations you want to execute\.
+Specify the number of permutations you want to execute\&.
 .RE
 .PP
 \fB\-n1 \fR\fB\fIN1\fR\fR
 .RS 4
 Specify number of Rows in
-\fIassociationMatrix\fR\.
+\fIassociationMatrix\fR\&.
 .RE
 .PP
 \fB\-n2 \fR\fB\fIN2\fR\fR
 .RS 4
 Specify number of Columns in
-\fIassociationMatrix\fR\.
+\fIassociationMatrix\fR\&.
 .RE
 .PP
 \fB\-n3 \fR\fB\fIN3\fR\fR
 .RS 4
 Specify number of Rows in
-\fIhostMatrix\fR\.
+\fIhostMatrix\fR\&.
 .RE
 .PP
 \fB\-n4 \fR\fB\fIN4\fR\fR
 .RS 4
 Specify number of Columns in
-\fIparasiteMatrix\fR\.
+\fIparasiteMatrix\fR\&.
 .RE
 .PP
 \fB\-A \fR\fB\fIassociationMatrix\fR\fR
 .RS 4
-Specify file name of associaton matrix\.
+Specify file name of associaton matrix\&.
 .RE
 .PP
 \fB\-B \fR\fB\fIparasiteMatrix\fR\fR
 .RS 4
-Specify file name of parasite matrix\.
+Specify file name of parasite matrix\&.
 .RE
 .PP
 \fB\-C \fR\fB\fIhostMatrix\fR\fR
 .RS 4
-Specify file name of host matrix\.
+Specify file name of host matrix\&.
 .RE
 .PP
 \fB\-n \fR\fB\fIrunID\fR\fR
 .RS 4
-Specify a run Name/ID for this run which will be appended to the output files\.
+Specify a run Name/ID for this run which will be appended to the output files\&.
 .RE
 .PP
 [\fB\-g\fR]
 .RS 4
-Execute global test of cospeciation only\.
+Execute global test of cospeciation only\&.
 .sp
 This is
 \fInot available\fR
@@ -97,12 +97,12 @@
 \fBaxparparafit\fR,
 \fBaxparparafitblas\fR
 and
-\fBaxparparafitblas_random\fR\.
+\fBaxparparafitblas_random\fR\&.
 .RE
 .PP
 [\fB\-t \fR\fB\fItraceFileName\fR\fR]
 .RS 4
-Specify the name of a binary trace\-file written by a global cospeciation test with AxParafit\.
+Specify the name of a binary trace\-file written by a global cospeciation test with AxParafit\&.
 .sp
 This argument is
 \fIrequired\fR
@@ -110,20 +110,20 @@
 \fBaxparparafit\fR,
 \fBaxparparafitblas\fR
 and
-\fBaxparparafitblas_random\fR\.
+\fBaxparparafitblas_random\fR\&.
 .RE
 .PP
 [\fB\-r \fR\fB\fInumberOfRandomLinks\fR\fR]
 .RS 4
 Only for
-\fBaxparparafitblas_random\fR: specify the number of randomly selected individual cospeciation tests\. Defaults to the number of non\-zero entries in
+\fBaxparparafitblas_random\fR: specify the number of randomly selected individual cospeciation tests\&. Defaults to the number of non\-zero entries in
 \fIassociationMatrix\fR
-(equivalent to full analysis)\.
+(equivalent to full analysis)\&.
 .RE
 .PP
 \fB\-h\fR
 .RS 4
-Displays an help message\.
+Displays an help message\&.
 .RE
 .SH "SEE ALSO"
 .PP
@@ -131,21 +131,21 @@
 (1)
 .PP
 The programs are documented by
-Alexandros Stamatakis, Alexander Auch, Jan Meier\-Kolthoff, Markus G\(:oker: "AxPcoords & Parallel AxParafit: Statistical Co\-Phylogenetic Analyses on Thousands of Taxa", BMC Bioinformatics 8:405, 2007\.
+Alexandros Stamatakis, Alexander Auch, Jan Meier\-Kolthoff, Markus G\(:oker: "AxPcoords & Parallel AxParafit: Statistical Co\-Phylogenetic Analyses on Thousands of Taxa", BMC Bioinformatics 8:405, 2007\&.
 .PP
 Homepage:
-http://icwww\.epfl\.ch/~stamatak/AxParafit\.html
+http://icwww\&.epfl\&.ch/~stamatak/AxParafit\&.html
 .SH "AUTHOR"
 .PP
 This manual page was written by David Paleino
-<d\.paleino at gmail\.com>
+<d\&.paleino at gmail\&.com>
 for the
 Debian(TM)
-system (but may be used by others)\. Permission is granted to copy, distribute and/or modify this document under the terms of the
+system (but may be used by others)\&. Permission is granted to copy, distribute and/or modify this document under the terms of the
 GNU
-General Public License, Version 3 any later version published by the Free Software Foundation\.
+General Public License, Version 3 any later version published by the Free Software Foundation\&.
 .PP
-On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common\-licenses/GPL\.
+On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common\-licenses/GPL\&.
 .SH "COPYRIGHT"
 Copyright \(co 2007 Alexandros Stamatakis <Alexandros.Stamatakis at epfl.ch>, Alexander Auch, Jan Meier-Kolthoff, Markus G\(:oker
 .br

Modified: trunk/packages/axparafit/trunk/debian/changelog
===================================================================
--- trunk/packages/axparafit/trunk/debian/changelog	2008-07-31 10:21:43 UTC (rev 2371)
+++ trunk/packages/axparafit/trunk/debian/changelog	2008-07-31 10:51:53 UTC (rev 2372)
@@ -2,4 +2,4 @@
 
   * Initial release (Closes: #463219)
 
- -- David Paleino <d.paleino at gmail.com>  Wed, 30 Jan 2008 11:52:11 +0100
+ -- Charles Plessy <plessy at debian.org>  Thu, 31 Jul 2008 13:53:00 +0900

Modified: trunk/packages/axparafit/trunk/debian/compat
===================================================================
--- trunk/packages/axparafit/trunk/debian/compat	2008-07-31 10:21:43 UTC (rev 2371)
+++ trunk/packages/axparafit/trunk/debian/compat	2008-07-31 10:51:53 UTC (rev 2372)
@@ -1 +1 @@
-5
+7

Modified: trunk/packages/axparafit/trunk/debian/control
===================================================================
--- trunk/packages/axparafit/trunk/debian/control	2008-07-31 10:21:43 UTC (rev 2371)
+++ trunk/packages/axparafit/trunk/debian/control	2008-07-31 10:51:53 UTC (rev 2372)
@@ -2,10 +2,10 @@
 Section: science
 Priority: optional
 Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: David Paleino <d.paleino at gmail.com>
-Build-Depends: debhelper (>= 5.0.0), quilt,
- refblas3-dev, atlas3-base-dev, libmpich1.0-dev
-Standards-Version: 3.7.3
+Uploaders: David Paleino <d.paleino at gmail.com>, Charles Plessy <plessy at debian.org>
+Build-Depends: debhelper (>= 7), quilt,
+ libblas-dev, libmpich1.0-dev
+Standards-Version: 3.8.0
 Homepage: http://icwww.epfl.ch/~stamatak/AxParafit.html
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/axparafit/trunk/
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/axparafit/trunk/?rev=0&sc=0

Modified: trunk/packages/axparafit/trunk/debian/copyright
===================================================================
--- trunk/packages/axparafit/trunk/debian/copyright	2008-07-31 10:21:43 UTC (rev 2371)
+++ trunk/packages/axparafit/trunk/debian/copyright	2008-07-31 10:51:53 UTC (rev 2372)
@@ -1,23 +1,33 @@
-Source: http://icwww.epfl.ch/~stamatak/AxParafit.html
+Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=226
+Upstream-Name: AxParafit
+Upstream-Maintainer: Alexandros Stamatakis <Alexandros.Stamatakis at epfl.ch>
+                     Alexander Auch
+		     Jan Meier-Kolthoff
+		     Markus Göker
+Upstream-Source: http://icwww.epfl.ch/%7Estamatak/index-Dateien/countSourceAx.php
 
-Files: debian/*
-Copyright: © 2008, David Paleino <d.paleino at gmail.com>
-License: GPL-2+
- 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 3 of the License, or
- (at your option) any later version.
-
 Files: *
 Copyright: © 2007, Alexandros Stamatakis <Alexandros.Stamatakis at epfl.ch>
                    Alexander Auch
                    Jan Meier-Kolthoff
                    Markus Göker
+
+THE WEBSITE SAYS GPL BUT THE HEADERS SAY NON-COMMERCIAL. WE HAVE TO INVESTIGATE BEFORE UPLOADING.
+
 License: GPL-2+
  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
  (at your option) any later version.
 
-On Debian systems, the complete text of the licenses can be found in:
-GPL-2 - `/usr/share/common-licenses/GPL-2'
+X-Comment: On Debian systems, the complete text of the GNU GPL version 2 can be
+ found in: `/usr/share/common-licenses/GPL-2'
+
+Files: debian/*
+Copyright: © 2008, David Paleino <d.paleino at gmail.com>
+License: GPL-2+
+ 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 3 of the License, or
+ (at your option) any later version.
+

Modified: trunk/packages/axparafit/trunk/debian/rules
===================================================================
--- trunk/packages/axparafit/trunk/debian/rules	2008-07-31 10:21:43 UTC (rev 2371)
+++ trunk/packages/axparafit/trunk/debian/rules	2008-07-31 10:51:53 UTC (rev 2372)
@@ -6,20 +6,25 @@
 
 include /usr/share/quilt/quilt.make
 
+CFLAGS      = -Wall -g -fomit-frame-pointer -funroll-loops 
+LDFLAGS     =                      -Wl,-z,defs,--as-needed
+BLAS_CFLAGS =                       $(CFLAGS) -D_USE_ATLAS 
+BLAS        =                          -lm -lcblas -latlas
+
+
 DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
-CFLAGS = -Wall -g -fomit-frame-pointer -funroll-loops #-D_HAND_OPTIMIZED_MM
-LDFLAGS = -lm -lcblas -latlas -Wl,-z,defs,--as-needed
-
 ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
-	CFLAGS += -O0
+	CFLAGS      += -O0
+	BLAS_CFLAGS += -O0
 else
-	CFLAGS += -O2
+	CFLAGS      += -O2
+	BLAS_CFLAGS += -O2
 endif
 
 ifeq ($(DEB_BUILD_GNU_TYPE), x86-64-linux)
-	CFLAGS += -m64
+	ARCH=64
 else
-	CFLAGS += -m32
+	ARCH=32
 endif
 
 XP=xsltproc -o debian/ -nonet --param man.charmap.use.subset "0"
@@ -33,7 +38,11 @@
 build: build-stamp
 build-stamp: patch
 	dh_testdir
-	$(MAKE) CFLAGS="$(CFLAGS) -D_HAND_OPTIMIZED_MM" BLAS_CFLAGS="$(CFLAGS) -D_USE_ATLAS" LINKERFLAGS="$(LDFLAGS)"
+	$(MAKE)      CFLAGS="$(CFLAGS) -D_HAND_OPTIMIZED_MM" \
+		BLAS_CFLAGS="$(BLAS_CFLAGS)" \
+		       BLAS="$(BLAS)" \
+		LINKERFLAGS="$(LDFLAGS)" \
+		       ARCH="$(ARCH)"
 	touch $@
 
 clean: unpatch

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