[med-svn] r1507 - in trunk/packages/amap-align/trunk/debian: . patches
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Tue Mar 4 09:59:40 UTC 2008
Author: charles-guest
Date: 2008-03-04 09:59:39 +0000 (Tue, 04 Mar 2008)
New Revision: 1507
Added:
trunk/packages/amap-align/trunk/debian/examples
trunk/packages/amap-align/trunk/debian/patches/fix-gcc-4.3.diff
trunk/packages/amap-align/trunk/debian/patches/rename-amap.diff
trunk/packages/amap-align/trunk/debian/patches/series
Removed:
trunk/packages/amap-align/trunk/debian/patches/00list
trunk/packages/amap-align/trunk/debian/patches/10_rename-amap
trunk/packages/amap-align/trunk/debian/patches/20_fix-gcc-4.3-build
Modified:
trunk/packages/amap-align/trunk/debian/amap.1
trunk/packages/amap-align/trunk/debian/amap.1.xml
trunk/packages/amap-align/trunk/debian/changelog
trunk/packages/amap-align/trunk/debian/control
trunk/packages/amap-align/trunk/debian/copyright
trunk/packages/amap-align/trunk/debian/docs
trunk/packages/amap-align/trunk/debian/rules
Log:
New upstream version, switched to quilt
Modified: trunk/packages/amap-align/trunk/debian/amap.1
===================================================================
--- trunk/packages/amap-align/trunk/debian/amap.1 2008-03-04 06:52:15 UTC (rev 1506)
+++ trunk/packages/amap-align/trunk/debian/amap.1 2008-03-04 09:59:39 UTC (rev 1507)
@@ -1,11 +1,11 @@
.\" Title: AMAP
.\" Author: Ariel Schwartz <sariel at cs.berkeley.edu>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: March 10, 2007
+.\" Date: 03/04/2008
.\" Manual: User Manual
-.\" Source: amap-align 2.0
+.\" Source: amap-align 2.2
.\"
-.TH "AMAP" "1" "March 10, 2007" "amap-align 2.0" "User Manual"
+.TH "AMAP" "1" "03/04/2008" "amap-align 2.2" "User Manual"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
@@ -129,6 +129,15 @@
.RS 4
only print the posterior probability matrices (default: off)
.RE
+.PP
+\fB\-gui\fR \fISTART\fR \fISTEP\fR
+.RS 4
+print output for the AMAP Display Java based GUI (default: ) starting at weight
+\fISTART\fR
+(default: infinity) with step size
+\fISTEP\fR
+(default: )
+.RE
.SH "NOTE"
.PP
In older versions ( <\ 2\.0\-1) of the package for
Modified: trunk/packages/amap-align/trunk/debian/amap.1.xml
===================================================================
--- trunk/packages/amap-align/trunk/debian/amap.1.xml 2008-03-04 06:52:15 UTC (rev 1506)
+++ trunk/packages/amap-align/trunk/debian/amap.1.xml 2008-03-04 09:59:39 UTC (rev 1507)
@@ -6,13 +6,12 @@
<!ENTITY dhfirstname "Charles">
<!ENTITY dhsurname "Plessy>">
- <!ENTITY dhdate "March 10, 2007">
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
<!ENTITY dhemail "charles-debian-nospam at plessy.org">
<!ENTITY dhusername "&dhfirstname; &dhsurname;">
<!ENTITY dhucpackage "<refentrytitle>AMAP</refentrytitle>">
<!ENTITY dhpackage "amap-align">
- <!ENTITY dhrelease "2.0">
+ <!ENTITY dhrelease "2.2">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
@@ -26,7 +25,6 @@
<title>&dhtitle;</title>
<productname>&dhpackage;</productname>
<releaseinfo role="version">&dhrelease;</releaseinfo>
- <date>&dhdate;</date>
<authorgroup>
<author>
<firstname>Ariel</firstname>
@@ -251,6 +249,17 @@
<para>only print the posterior probability matrices (default: off)</para>
</listitem>
</varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-gui</option>
+ <varname>START</varname>
+ <varname>STEP</varname>
+ </term>
+ <listitem>
+ <para> print output for the AMAP Display Java based GUI (default: ) starting at weight <varname>START</varname> (default: infinity) with step size <varname>STEP</varname> (default: )</para>
+ </listitem>
+ </varlistentry>
</variablelist>
</refsect1>
Modified: trunk/packages/amap-align/trunk/debian/changelog
===================================================================
--- trunk/packages/amap-align/trunk/debian/changelog 2008-03-04 06:52:15 UTC (rev 1506)
+++ trunk/packages/amap-align/trunk/debian/changelog 2008-03-04 09:59:39 UTC (rev 1507)
@@ -1,7 +1,13 @@
-amap-align (2.0-3) unstable; urgency=low
+amap-align (2.2-1) unstable; urgency=low
[ Charles Plessy ]
+ * New upstream release:
+ - Corrected DNA alignment parameters file. Improved debug output. (2.01)
+ - Includes new output for the AMAP Display Java based GUI. (2.1)
* Moved the Homepage: field out from the package's description.
+ * debian/amap.1: updated the manpage.
+ * debian/watch: changed URI to monitor.
+ * debian/patches, debian/rules, debian/control: switched to quilt.
[ David Paleino ]
* debian/amap.1 - the manpage is now generated offline: this saves
@@ -13,6 +19,10 @@
- Using DM-Upload-Allowed instead of the XS- version
* debian/rules - minor changes
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Mon, 18 Feb 2008 22:34:20 +0900
+
+amap-align (2.0-3) unstable; urgency=low
+
[ Andreas Tille ]
* Added myself as uploader
* Reformatted debian/NEWS according to Developers Reference,
Modified: trunk/packages/amap-align/trunk/debian/control
===================================================================
--- trunk/packages/amap-align/trunk/debian/control 2008-03-04 06:52:15 UTC (rev 1506)
+++ trunk/packages/amap-align/trunk/debian/control 2008-03-04 09:59:39 UTC (rev 1507)
@@ -7,7 +7,7 @@
Uploaders: Charles Plessy <charles-debian-nospam at plessy.org>,
David Paleino <d.paleino at gmail.com>,
Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 5), dpatch
+Build-Depends: debhelper (>= 5), quilt
Standards-Version: 3.7.3
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/amap-align/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/amap-align/trunk/
Modified: trunk/packages/amap-align/trunk/debian/copyright
===================================================================
--- trunk/packages/amap-align/trunk/debian/copyright 2008-03-04 06:52:15 UTC (rev 1506)
+++ trunk/packages/amap-align/trunk/debian/copyright 2008-03-04 09:59:39 UTC (rev 1507)
@@ -1,30 +1,51 @@
-This package was debianized by Charles Plessy <charles-debian-nospam at plessy.org>
-on Sun, 9 Jul 2006 12:53:25 +0900. The packaging and the manpages work are in
-the public domain unless stated otherwise.
+X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
+X-Debianized-By: Charles Plessy <charles-debian-nospam at plessy.org>
+X-Debinized-Date: Sun, 9 Jul 2006 12:53:25 +0900.
+X-Source-Downloaded-From: http://bio.math.berkeley.edu/amap/download
+X-Upstream-Author: 2005—2007 Ariel Schwartz <sariel at cs.berkeley.edu>
+Files: debian/*
+Copyright: © 2007 David Paleino <d.paleino at gmail.com>
+ © 2006—2008 Charles Plessy <chalres-debian-nospam at plessy.org>
+License: Same as AMAP itelf
-AMAP was downloaded from http://bio.math.berkeley.edu/amap/download
+Files: display/*
+Copyright: © 2007 Michael E. Smoot
+License: GPL-2+
+ This program 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.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+X-Comment: On Debian systems, the complete text of the GNU General Public
+ License can be found in `/usr/share/common-licenses/GPL'.
-AMAP is copyright (C) 2005-2006 Ariel Schwartz <sariel at cs.berkeley.edu>
-
-The current version of AMAP uses the PROBCONS 1.09 code base for some of the
-input/output procedures, and for the calculation of posterior probabilities
-(see PROBCONS.README).
-
-AMAP has been made freely available as PUBLIC DOMAIN software and hence is
-not subject to copyright in the United States. This system and/or any portion
-of the source code may be used, modified, or redistributed without
-restrictions. AMAP is distributed WITHOUT WARRANTY, express or implied. The
-authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for loss due to reliance on
-the program.
-
-
-PROBCONS is copyright (C) 2004 Chuong Do <chuongdo at cs.stanford.edu>
-
-PROBCONS has been made freely available as PUBLIC DOMAIN software and
-hence is not subject to copyright in the United States. This system and/or
-any portion of the source code may be used, modified, or redistributed
-without restrictions. PROBCONS is distributed WITHOUT WARRANTY, express or
-implied. The authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for loss
-due to reliance on the program.
-
+Files: *
+License: PD
+ The current version of AMAP uses the PROBCONS 1.09 code base for some of the
+ input/output procedures, and for the calculation of posterior probabilities
+ (see PROBCONS.README).
+ .
+ AMAP has been made freely available as PUBLIC DOMAIN software and hence is
+ not subject to copyright in the United States. This system and/or any portion
+ of the source code may be used, modified, or redistributed without
+ restrictions. AMAP is distributed WITHOUT WARRANTY, express or implied. The
+ authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for loss due to reliance on
+ the program.
+ .
+ PROBCONS is copyright (C) 2004 Chuong Do <chuongdo at cs.stanford.edu>
+ .
+ PROBCONS has been made freely available as PUBLIC DOMAIN software and
+ hence is not subject to copyright in the United States. This system and/or
+ any portion of the source code may be used, modified, or redistributed
+ without restrictions. PROBCONS is distributed WITHOUT WARRANTY, express or
+ implied. The authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for loss
+ due to reliance on the program.
Modified: trunk/packages/amap-align/trunk/debian/docs
===================================================================
--- trunk/packages/amap-align/trunk/debian/docs 2008-03-04 06:52:15 UTC (rev 1506)
+++ trunk/packages/amap-align/trunk/debian/docs 2008-03-04 09:59:39 UTC (rev 1507)
@@ -1,2 +1,2 @@
-PROBCONS.README
+align/PROBCONS.README
README
Added: trunk/packages/amap-align/trunk/debian/examples
===================================================================
--- trunk/packages/amap-align/trunk/debian/examples (rev 0)
+++ trunk/packages/amap-align/trunk/debian/examples 2008-03-04 09:59:39 UTC (rev 1507)
@@ -0,0 +1 @@
+examples/*
Deleted: trunk/packages/amap-align/trunk/debian/patches/00list
===================================================================
--- trunk/packages/amap-align/trunk/debian/patches/00list 2008-03-04 06:52:15 UTC (rev 1506)
+++ trunk/packages/amap-align/trunk/debian/patches/00list 2008-03-04 09:59:39 UTC (rev 1507)
@@ -1 +0,0 @@
-20_fix-gcc-4.3-build
Deleted: trunk/packages/amap-align/trunk/debian/patches/10_rename-amap
===================================================================
--- trunk/packages/amap-align/trunk/debian/patches/10_rename-amap 2008-03-04 06:52:15 UTC (rev 1506)
+++ trunk/packages/amap-align/trunk/debian/patches/10_rename-amap 2008-03-04 09:59:39 UTC (rev 1507)
@@ -1,28 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 10_rename-amap.dpatch by Charles Plessy <charles-debian-nospam at plessy.org>
-## This patch is hereby released in the public domain.
-##
-## All lines beginning with `## DP:' are a description of the patch.
-## DP: Rename amap to amap-align
-## DP: Since version 2.0-2, this patch is not applied anymore, because the old
-## DP: amap package related to networking has been removed from Debian.
-
-
- at DPATCH@
-
---- amap-2.0/Amap.cc 2006-04-07 06:41:21.000000000 +0900
-+++ amap-align-2.0/Amap.cc 2006-07-09 14:43:13.000000000 +0900
-@@ -625,7 +625,12 @@
- << "files README and README.PROBCONS for details." << endl
- << endl
- << "Usage:" << endl
-- << " amap [OPTION]... [MFAFILE]..." << endl
-+ << " amap-align [OPTION]... [MFAFILE]..." << endl
-+ << endl
-+ << "Note:" << endl
-+ << "On Debian systems, amap is renamed amap-align because there is already" << endl
-+ << "an amap program in our archives. On other systems, it is possible that " << endl
-+ << "you will find this program under its original amap name." << endl
- << endl
- << "Description:" << endl
- << " Align sequences in MFAFILE(s) and print result to standard output" << endl
Deleted: trunk/packages/amap-align/trunk/debian/patches/20_fix-gcc-4.3-build
===================================================================
--- trunk/packages/amap-align/trunk/debian/patches/20_fix-gcc-4.3-build 2008-03-04 06:52:15 UTC (rev 1506)
+++ trunk/packages/amap-align/trunk/debian/patches/20_fix-gcc-4.3-build 2008-03-04 09:59:39 UTC (rev 1507)
@@ -1,18 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 20_fix-gcc-4.3-build.dpatch by Charles Plessy <charles-debian-nospam at plessy.org>
-##
-## DP: Allows building with gcc-4.3.
-## DP: Many thanks to Martin Michlmayr (http://bugs.debian.org/413477)
-
- at DPATCH@
-
---- ./Amap.cc~ 2007-03-05 11:29:54.000000000 +0000
-+++ ./Amap.cc 2007-03-05 11:30:58.000000000 +0000
-@@ -12,6 +12,7 @@
- #include "ProbabilisticModel.h"
- #include "EvolutionaryTree.h"
- #include "SparseMatrix.h"
-+#include <climits>
- #include <string>
- #include <sstream>
- #include <iomanip>
Added: trunk/packages/amap-align/trunk/debian/patches/fix-gcc-4.3.diff
===================================================================
--- trunk/packages/amap-align/trunk/debian/patches/fix-gcc-4.3.diff (rev 0)
+++ trunk/packages/amap-align/trunk/debian/patches/fix-gcc-4.3.diff 2008-03-04 09:59:39 UTC (rev 1507)
@@ -0,0 +1,10 @@
+--- a/align/Amap.cc
++++ b/align/Amap.cc
+@@ -12,6 +12,7 @@
+ #include "ProbabilisticModel.h"
+ #include "EvolutionaryTree.h"
+ #include "SparseMatrix.h"
++#include <climits>
+ #include <string>
+ #include <sstream>
+ #include <iomanip>
Added: trunk/packages/amap-align/trunk/debian/patches/rename-amap.diff
===================================================================
--- trunk/packages/amap-align/trunk/debian/patches/rename-amap.diff (rev 0)
+++ trunk/packages/amap-align/trunk/debian/patches/rename-amap.diff 2008-03-04 09:59:39 UTC (rev 1507)
@@ -0,0 +1,16 @@
+--- a/align/Amap.cc
++++ b/align/Amap.cc
+@@ -660,7 +660,12 @@
+ << "files README and README.PROBCONS for details." << endl
+ << endl
+ << "Usage:" << endl
+- << " amap [OPTION]... [MFAFILE]..." << endl
++ << " amap-align [OPTION]... [MFAFILE]..." << endl
++ << endl
++ << "Note:" << endl
++ << "On Debian systems, amap is renamed amap-align because there is already" << endl
++ << "an amap program in our archives. On other systems, it is possible that " << endl
++ << "you will find this program under its original amap name." << endl
+ << endl
+ << "Description:" << endl
+ << " Align sequences in MFAFILE(s) and print result to standard output" << endl
Added: trunk/packages/amap-align/trunk/debian/patches/series
===================================================================
--- trunk/packages/amap-align/trunk/debian/patches/series (rev 0)
+++ trunk/packages/amap-align/trunk/debian/patches/series 2008-03-04 09:59:39 UTC (rev 1507)
@@ -0,0 +1,2 @@
+rename-amap.diff
+fix-gcc-4.3.diff
Modified: trunk/packages/amap-align/trunk/debian/rules
===================================================================
--- trunk/packages/amap-align/trunk/debian/rules 2008-03-04 06:52:15 UTC (rev 1506)
+++ trunk/packages/amap-align/trunk/debian/rules 2008-03-04 09:59:39 UTC (rev 1507)
@@ -25,12 +25,12 @@
CFLAGS += -O2
endif
-include /usr/share/dpatch/dpatch.make
+include /usr/share/quilt/quilt.make
build: build-stamp
build-stamp: patch
dh_testdir
- $(MAKE)
+ $(MAKE) -C align
touch $@
amap.1: debian/amap.1.xml
@@ -40,7 +40,7 @@
dh_testdir
dh_testroot
rm -f build-stamp
- [ ! -f Makefile ] || $(MAKE) clean
+ [ ! -f align/Makefile ] || $(MAKE) -C align clean
dh_clean
install: build
@@ -56,7 +56,7 @@
dh_installchangelogs
dh_installdocs
dh_installexamples
- dh_install amap debian/wrapper/amap-align usr/bin/
+ dh_install align/amap debian/wrapper/amap-align usr/bin/
dh_installman debian/amap.1
dh_link usr/share/man/man1/amap.1 usr/share/man/man1/amap-align.1
dh_strip
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