[med-svn] r1293 - in trunk/packages/axpcoords/trunk: . debian debian/patches
hanska-guest at alioth.debian.org
hanska-guest at alioth.debian.org
Wed Feb 6 10:28:10 UTC 2008
Author: hanska-guest
Date: 2008-02-06 10:28:09 +0000 (Wed, 06 Feb 2008)
New Revision: 1293
Added:
trunk/packages/axpcoords/trunk/debian/
trunk/packages/axpcoords/trunk/debian/axpcoords.1
trunk/packages/axpcoords/trunk/debian/axpcoords.1.xml
trunk/packages/axpcoords/trunk/debian/changelog
trunk/packages/axpcoords/trunk/debian/compat
trunk/packages/axpcoords/trunk/debian/control
trunk/packages/axpcoords/trunk/debian/copyright
trunk/packages/axpcoords/trunk/debian/links
trunk/packages/axpcoords/trunk/debian/patches/
trunk/packages/axpcoords/trunk/debian/patches/00-fix_Makefile.patch
trunk/packages/axpcoords/trunk/debian/patches/01-fix_gcc_warnings.patch
trunk/packages/axpcoords/trunk/debian/patches/02-fix_help_screen.patch
trunk/packages/axpcoords/trunk/debian/patches/series
trunk/packages/axpcoords/trunk/debian/rules
Log:
[svn-inject] Applying Debian modifications to trunk
Property changes on: trunk/packages/axpcoords/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
+ 1
Added: trunk/packages/axpcoords/trunk/debian/axpcoords.1
===================================================================
--- trunk/packages/axpcoords/trunk/debian/axpcoords.1 (rev 0)
+++ trunk/packages/axpcoords/trunk/debian/axpcoords.1 2008-02-06 10:28:09 UTC (rev 1293)
@@ -0,0 +1,76 @@
+.\" Title: AXPCOORDS
+.\" Author: David Paleino <d.paleino at gmail.com>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 02/06/2008
+.\" Manual: AxPcoords User Manual
+.\" Source: axpcoords
+.\"
+.TH "AXPCOORDS" "1" "02/06/2008" "axpcoords" "AxPcoords User Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+axpcoords - highly optimized and parallelized porting of pcoords
+.SH "SYNOPSIS"
+.HP 10
+\fBaxpcoords\fR \fB\-f\ \fR\fB\fIinputMatrixName\fR\fR \fB\-n\ \fR\fB\fIrowNumber\fR\fR [\fB\-t\fR]
+.HP 10
+\fBaxpcoords\fR [\fB\-h\fR]
+.SH "DESCRIPTION"
+.PP
+This manual page documents briefly the
+\fBaxpcoords\fR
+command\.
+.PP
+This manual page was written for the Debian distribution because the original program does not have a manual page\.
+.PP
+AxPcoords is an highly optimized versions of Pierre Legendre\'s DistPCoA program for statistical analysis of host\-parasite coevolution\.
+.SH "OPTIONS"
+.PP
+\fB\-f \fR\fB\fIinputMatrixName\fR\fR
+.RS 4
+Specify filename of quadratic input matrix\.
+.RE
+.PP
+\fB\-n \fR\fB\fIrowNumber\fR\fR
+.RS 4
+Specify number of rows in quadratic input matrix\.
+.RE
+.PP
+\fB\-t\fR
+.RS 4
+Specify if the output matrix should be transposed (default: OFF)\.
+.RE
+.PP
+\fB\-h\fR
+.RS 4
+Show summary of options\.
+.RE
+.SH "BUGS"
+.PP
+The program is currently limited to only work with the
+libgsl0
+library\.
+.PP
+It could also be compiled for using AMD Core Math Library (ACML) and Intel Math Kernel Library (MKL) for improved performances, but these cannot be packaged/distributed in Debian\.
+.SH "SEE ALSO"
+.PP
+\fBaxparafit\fR(1)
+.SH "AUTHOR"
+.PP
+\fBDavid Paleino\fR <\&d\.paleino at gmail\.com\&>
+.sp -1n
+.IP "" 4
+Wrote this manpage for the Debian system\.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Alexandros Stamatakis <Alexandros.Stamatakis at epfl.ch>
+.br
+.PP
+This manual page was written for the Debian system (but may be used by others)\.
+.PP
+Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 3 or (at your option) 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
+\fI/usr/share/common\-licenses/GPL\fR\.
+.sp
Added: trunk/packages/axpcoords/trunk/debian/axpcoords.1.xml
===================================================================
--- trunk/packages/axpcoords/trunk/debian/axpcoords.1.xml (rev 0)
+++ trunk/packages/axpcoords/trunk/debian/axpcoords.1.xml 2008-02-06 10:28:09 UTC (rev 1293)
@@ -0,0 +1,178 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<?xml-stylesheet type="text/xsl"
+ href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.5//EN"
+"http://www.oasis-open.org/docbook/xml/4.5/docbookx.dtd" [
+
+<!--
+
+`xsltproc -''-nonet \
+ -''-param man.charmap.use.subset "0" \
+ -''-param make.year.ranges "1" \
+ -''-param make.single.year.ranges "1" \
+ /usr/share/xml/docbook/stylesheet/nwalsh/manpages/docbook.xsl \
+ manpage.xml'
+
+A manual page <package>.<section> will be generated. You may view the
+manual page with: nroff -man <package>.<section> | less'. A typical entry
+in a Makefile or Makefile.am is:
+
+DB2MAN = /usr/share/sgml/docbook/stylesheet/xsl/nwalsh/manpages/docbook.xsl
+XP = xsltproc -''-nonet -''-param man.charmap.use.subset "0"
+
+manpage.1: manpage.xml
+ $(XP) $(DB2MAN) $<
+
+The xsltproc binary is found in the xsltproc package. The XSL files are in
+docbook-xsl. A description of the parameters you can use can be found in the
+docbook-xsl-doc-* packages. Please remember that if you create the nroff
+version in one of the debian/rules file targets (such as build), you will need
+to include xsltproc and docbook-xsl in your Build-Depends control field.
+Alternatively use the xmlto command/package. That will also automatically
+pull in xsltproc and docbook-xsl.
+
+Notes for using docbook2x: docbook2x-man does not automatically create the
+AUTHOR(S) and COPYRIGHT sections. In this case, please add them manually as
+<refsect1> ... </refsect1>.
+
+To disable the automatic creation of the AUTHOR(S) and COPYRIGHT sections
+read /usr/share/doc/docbook-xsl/doc/manpages/authors.html. This file can be
+found in the docbook-xsl-doc-html package.
+
+Validation can be done using: `xmllint -''-noout -''-valid manpage.xml`
+
+General documentation about man-pages and man-page-formatting:
+man(1), man(7), http://www.tldp.org/HOWTO/Man-Page/
+
+-->
+
+ <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+ <!ENTITY dhfirstname "David">
+ <!ENTITY dhsurname "Paleino">
+ <!-- dhusername could also be set to "&firstname; &surname;". -->
+ <!ENTITY dhusername "Alexandros Stamatakis">
+ <!ENTITY dhemail "d.paleino at gmail.com">
+ <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+ allowed: see man(7), man(1) and
+ http://www.tldp.org/HOWTO/Man-Page/q2.html. -->
+ <!ENTITY dhsection "1">
+ <!-- TITLE should be something like "User commands" or similar (see
+ http://www.tldp.org/HOWTO/Man-Page/q2.html). -->
+ <!ENTITY dhtitle "AxPcoords User Manual">
+ <!ENTITY dhucpackage "AXPCOORDS">
+ <!ENTITY dhpackage "axpcoords">
+]>
+
+<refentry>
+ <refentryinfo>
+ <title>&dhtitle;</title>
+ <productname>&dhpackage;</productname>
+ <authorgroup>
+ <author>
+ <firstname>&dhfirstname;</firstname>
+ <surname>&dhsurname;</surname>
+ <contrib>Wrote this manpage for the Debian system.</contrib>
+ <address>
+ <email>&dhemail;</email>
+ </address>
+ </author>
+ </authorgroup>
+ <copyright>
+ <year>2007</year>
+ <holder>Alexandros Stamatakis <Alexandros.Stamatakis at epfl.ch></holder>
+ </copyright>
+ <legalnotice>
+ <para>This manual page was written for the Debian system
+ (but may be used by others).</para>
+ <para>Permission is granted to copy, distribute and/or modify this
+ document under the terms of the GNU General Public License,
+ Version 3 or (at your option) any later version published by
+ the Free Software Foundation.</para>
+ <para>On Debian systems, the complete text of the GNU General Public
+ License can be found in
+ <filename>/usr/share/common-licenses/GPL</filename>.</para>
+ </legalnotice>
+ </refentryinfo>
+ <refmeta>
+ <refentrytitle>&dhucpackage;</refentrytitle>
+ <manvolnum>&dhsection;</manvolnum>
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+ <refpurpose>highly optimized and parallelized porting of pcoords</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <!-- These are several examples, how syntaxes could look -->
+ <arg choice="plain"><option>-f <replaceable>inputMatrixName</replaceable></option></arg>
+ <arg choice="plain"><option>-n <replaceable>rowNumber</replaceable></option></arg>
+ <arg choice="opt"><option>-t</option></arg>
+ </cmdsynopsis>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <group choice="opt">
+ <arg choice="plain"><option>-h</option></arg>
+ </group>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1 id="description">
+ <title>DESCRIPTION</title>
+ <para>This manual page documents briefly the
+ <command>&dhpackage;</command> command.</para>
+ <para>This manual page was written for the Debian distribution
+ because the original program does not have a manual page.</para>
+ <para>AxPcoords is an highly optimized versions of Pierre Legendre's DistPCoA
+ program for statistical analysis of host-parasite coevolution.</para>
+ </refsect1>
+ <refsect1 id="options">
+ <title>OPTIONS</title>
+ <variablelist>
+ <!-- Use the variablelist.term.separator and the
+ variablelist.term.break.after parameters to
+ control the term elements. -->
+ <varlistentry>
+ <term><option>-f <replaceable>inputMatrixName</replaceable></option></term>
+ <listitem>
+ <para>Specify filename of quadratic input matrix.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-n <replaceable>rowNumber</replaceable></option></term>
+ <listitem>
+ <para>Specify number of rows in quadratic input matrix.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-t</option></term>
+ <listitem>
+ <para>Specify if the output matrix should be transposed (default: OFF).</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-h</option></term>
+ <listitem>
+ <para>Show summary of options.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+ <refsect1 id="bugs">
+ <!-- Or use this section to tell about upstream BTS. -->
+ <title>BUGS</title>
+ <para>The program is currently limited to only work
+ with the <package>libgsl0</package> library.</para>
+ <para>It could also be compiled for using AMD Core Math Library
+ (ACML) and Intel Math Kernel Library (MKL) for improved
+ performances, but these cannot be packaged/distributed
+ in Debian.</para>
+ </refsect1>
+ <refsect1 id="see_also">
+ <title>SEE ALSO</title>
+ <!-- In alpabetical order. -->
+ <para><citerefentry>
+ <refentrytitle>axparafit</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry></para>
+ </refsect1>
+</refentry>
Added: trunk/packages/axpcoords/trunk/debian/changelog
===================================================================
--- trunk/packages/axpcoords/trunk/debian/changelog (rev 0)
+++ trunk/packages/axpcoords/trunk/debian/changelog 2008-02-06 10:28:09 UTC (rev 1293)
@@ -0,0 +1,6 @@
+axpcoords (1.0-1) unstable; urgency=low
+
+ * Initial release (Closes: #464323)
+
+ -- David Paleino <d.paleino at gmail.com> Wed, 06 Feb 2008 09:29:46 +0100
+
Added: trunk/packages/axpcoords/trunk/debian/compat
===================================================================
--- trunk/packages/axpcoords/trunk/debian/compat (rev 0)
+++ trunk/packages/axpcoords/trunk/debian/compat 2008-02-06 10:28:09 UTC (rev 1293)
@@ -0,0 +1 @@
+5
Added: trunk/packages/axpcoords/trunk/debian/control
===================================================================
--- trunk/packages/axpcoords/trunk/debian/control (rev 0)
+++ trunk/packages/axpcoords/trunk/debian/control 2008-02-06 10:28:09 UTC (rev 1293)
@@ -0,0 +1,17 @@
+Source: axpcoords
+Section: science
+Priority: optional
+Maintainer: David Paleino <d.paleino at gmail.com>
+Build-Depends: debhelper (>= 5.0.0), quilt,
+ libgsl0-dev
+Standards-Version: 3.7.3
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/axpcoords/trunk
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/axpcoords/trunk/?rev=0&sc=0
+Homepage: http://icwww.epfl.ch/~stamatak/AxParafit.html
+
+Package: axpcoords
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: highly optimized and parallelized porting of pcoords
+ AxPcoords is an highly optimized versions of Pierre Legendre's DistPCoA
+ program for statistical analysis of host-parasite coevolution.
Added: trunk/packages/axpcoords/trunk/debian/copyright
===================================================================
--- trunk/packages/axpcoords/trunk/debian/copyright (rev 0)
+++ trunk/packages/axpcoords/trunk/debian/copyright 2008-02-06 10:28:09 UTC (rev 1293)
@@ -0,0 +1,88 @@
+Source: http://icwww.epfl.ch/~stamatak/AxParafit.html
+
+Files: debian/*
+Copyright: © 2008, David Paleino <d.paleino at gmail.com>
+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 3 of the License, or
+ (at your option) any later version.
+
+Files: *
+Copyright: ©, Alexandros Stamatakis <Alexandros.Stamatakis at epfl.ch>
+ <stamatakis at bio.ifi.lmu.de>
+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.
+
+ ---NOTE---
+ I (David Paleino, current maintainer of axpcoords) have contacted
+ the upstream author to clarify the license (as there was no information
+ in the source code). I've asked debian-legal for help, and someone
+ replied [1] that quoting the relevant parts of the emails was sufficient.
+ The thread is available at [2], but here's the relevant part (re-arranging
+ as he top-quoted my reply):
+
+ ---BEGIN---
+ From: Alexandros Stamatakis <Alexandros.Stamatakis at epfl.ch>
+ To: David Paleino <d.paleino at gmail.com>
+ Cc: Debian-Med <debian-med at lists.debian.org>
+ Subject: Re: Packaging AxPcoords for Debian
+ Date: Wed, 30 Jan 2008 12:49:07 +0200
+ User-Agent: Thunderbird 1.5.0.13 (X11/20070824)
+ Newsgroups: gmane.linux.debian.devel.medical
+
+ David Paleino wrote:
+ > Hi,
+ > I'm a member of the Debian-Med Group, which aim is to provide medical,
+ > biological and scientific software into the Debian distribution.
+ >
+ > I was going to package AxPcoords, but the copyright statement in the source
+ > file says:
+ >
+ > ---8<---
+ > /* This code may be used and modified for non-commercial purposes */
+ > /* but redistribution in any form requires written permission. */
+ > --->8---
+ >
+ > This means that your software, according to the Debian Free Software Guidelines
+ > (DFSG) [1], is non-free.
+ >
+ > Moreover, with that statement, Debian can't even distribute this software in
+ > the non-free "branch".
+ >
+ > Would you please consider relicensing it under a free (i.e. DFSG-free) license,
+ > such as the GNU General Public License (possibly v3+), BSD or Artistic?
+ >
+ > Thank you.
+ >
+ > Kind regards,
+ > David Paleino
+ > Debian-Med Group
+ >
+ > [1] http://www.debian.org/social_contract#guidelines
+ >
+
+ Hi David,
+
+ I intended to put it under GPL soon, that's what is actually stated on the Axparafit web page:
+
+ "Manual, Source Code (under GPL), and Binaries" what is quoted in the source file must be left over
+ from some other project, so please go ahead with the packaging.
+
+ I will change that asap, the only thing is that I am just setting up my new lab at Munich and am very
+ busy with other things right now.
+
+ Cheers,
+
+ Alexis
+ ---END---
+
+ [1] http://permalink.gmane.org/gmane.linux.debian.devel.medical/3081
+ [2] http://lists.debian.org/debian-med/2008/01/msg00213.html
+
+On Debian systems, the complete text of the licenses can be found in:
+GPL-3 - `/usr/share/common-licenses/GPL'
+GPL-2 - `/usr/share/common-licenses/GPL-2'
Added: trunk/packages/axpcoords/trunk/debian/links
===================================================================
--- trunk/packages/axpcoords/trunk/debian/links (rev 0)
+++ trunk/packages/axpcoords/trunk/debian/links 2008-02-06 10:28:09 UTC (rev 1293)
@@ -0,0 +1,2 @@
+usr/bin/AxPcoordsGSL usr/bin/axpcoords
+usr/share/man/man1/axpcoords.1 usr/share/man/man1/AxPcoordsGSL.1
Added: trunk/packages/axpcoords/trunk/debian/patches/00-fix_Makefile.patch
===================================================================
--- trunk/packages/axpcoords/trunk/debian/patches/00-fix_Makefile.patch (rev 0)
+++ trunk/packages/axpcoords/trunk/debian/patches/00-fix_Makefile.patch 2008-02-06 10:28:09 UTC (rev 1293)
@@ -0,0 +1,11 @@
+--- AxPcoords.dist.orig/Makefile
++++ AxPcoords.dist/Makefile
+@@ -9,7 +9,7 @@
+ # on some systems
+
+ GSL = -lm -lgsl -lgslcblas
+-GSL_CFLAGS = -O3 -fomit-frame-pointer -funroll-loops -D_USE_GSL
++GSL_CFLAGS = $(CFLAGS) -fomit-frame-pointer -funroll-loops -D_USE_GSL
+
+ ######################################################################################################
+ # AMD ACML-specific FLAGS
Added: trunk/packages/axpcoords/trunk/debian/patches/01-fix_gcc_warnings.patch
===================================================================
--- trunk/packages/axpcoords/trunk/debian/patches/01-fix_gcc_warnings.patch (rev 0)
+++ trunk/packages/axpcoords/trunk/debian/patches/01-fix_gcc_warnings.patch 2008-02-06 10:28:09 UTC (rev 1293)
@@ -0,0 +1,10 @@
+--- AxPcoords.dist.orig/AxPcoords.c
++++ AxPcoords.dist/AxPcoords.c
+@@ -36,6 +36,7 @@
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <math.h>
++#include <string.h>
+
+ #ifdef _USE_GSL
+ #include <gsl/gsl_math.h>
Added: trunk/packages/axpcoords/trunk/debian/patches/02-fix_help_screen.patch
===================================================================
--- trunk/packages/axpcoords/trunk/debian/patches/02-fix_help_screen.patch (rev 0)
+++ trunk/packages/axpcoords/trunk/debian/patches/02-fix_help_screen.patch 2008-02-06 10:28:09 UTC (rev 1293)
@@ -0,0 +1,11 @@
+--- AxPcoords.dist.orig/AxPcoords.c
++++ AxPcoords.dist/AxPcoords.c
+@@ -113,7 +113,7 @@
+ printf("Please also consult the Manual\n");
+ printf("To report bugs send an email to Alexandros.Stamatakis at epfl.ch\n\n\n");
+
+- printf("AxPcoords[GSL|ACML|MKL] -f inputMatrixName -n rowNumber [-h] [-t]\n");
++ printf("AxPcoordsGSL -f inputMatrixName -n rowNumber [-h] [-t]\n");
+ printf("\n");
+ printf(" -f Specify file Name of quadratic input matrix\n");
+ printf("\n");
Added: trunk/packages/axpcoords/trunk/debian/patches/series
===================================================================
--- trunk/packages/axpcoords/trunk/debian/patches/series (rev 0)
+++ trunk/packages/axpcoords/trunk/debian/patches/series 2008-02-06 10:28:09 UTC (rev 1293)
@@ -0,0 +1,3 @@
+00-fix_Makefile.patch
+01-fix_gcc_warnings.patch
+02-fix_help_screen.patch
Added: trunk/packages/axpcoords/trunk/debian/rules
===================================================================
--- trunk/packages/axpcoords/trunk/debian/rules (rev 0)
+++ trunk/packages/axpcoords/trunk/debian/rules 2008-02-06 10:28:09 UTC (rev 1293)
@@ -0,0 +1,54 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+include /usr/share/quilt/quilt.make
+
+XP=xsltproc -o debian/ --nonet \
+ --param man.charmap.use.subset "0" \
+ --param make.year.ranges "1" \
+ --param make.single.year.ranges "1"
+manpages: axpcoords.1
+axpcoords.1: debian/axpcoords.1.xml
+ $(XP) $<
+
+build: build-stamp
+build-stamp: patch
+ dh_testdir
+ $(MAKE) AxPcoordsGSL
+ touch $@
+
+clean: unpatch
+ dh_testdir
+ dh_testroot
+ dh_clean build-stamp
+ $(MAKE) clean
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs usr/bin
+ dh_install AxPcoordsGSL usr/bin
+
+binary-indep: build install
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs
+ dh_installman debian/axpcoords.1
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install
Property changes on: trunk/packages/axpcoords/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
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