[med-svn] r6151 - in trunk/packages: . dotur dotur/trunk dotur/trunk/debian dotur/trunk/debian/patches dotur/trunk/debian/source
Steffen Möller
moeller at alioth.debian.org
Wed Mar 2 23:13:51 UTC 2011
Author: moeller
Date: 2011-03-02 23:13:49 +0000 (Wed, 02 Mar 2011)
New Revision: 6151
Added:
trunk/packages/dotur/
trunk/packages/dotur/trunk/
trunk/packages/dotur/trunk/debian/
trunk/packages/dotur/trunk/debian/README.Debian
trunk/packages/dotur/trunk/debian/README.source
trunk/packages/dotur/trunk/debian/changelog
trunk/packages/dotur/trunk/debian/compat
trunk/packages/dotur/trunk/debian/control
trunk/packages/dotur/trunk/debian/copyright
trunk/packages/dotur/trunk/debian/docs
trunk/packages/dotur/trunk/debian/patches/
trunk/packages/dotur/trunk/debian/patches/Makefile.patch
trunk/packages/dotur/trunk/debian/patches/compilation.patch
trunk/packages/dotur/trunk/debian/patches/series
trunk/packages/dotur/trunk/debian/rules
trunk/packages/dotur/trunk/debian/source/
trunk/packages/dotur/trunk/debian/source/format
trunk/packages/dotur/trunk/debian/watch
Log:
First short at the package dotor - one of those
that help qiime.
Property changes on: trunk/packages/dotur/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/dotur/trunk/debian/README.Debian
===================================================================
--- trunk/packages/dotur/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/dotur/trunk/debian/README.Debian 2011-03-02 23:13:49 UTC (rev 6151)
@@ -0,0 +1,7 @@
+dotur for Debian
+----------------
+
+The package was only prepared for internal purposes. Please feel invited
+to complete it.
+
+ -- Steffen Moeller <steffen_moeller at gmx.de> Wed, 02 Mar 2011 23:48:37 +0100
Added: trunk/packages/dotur/trunk/debian/README.source
===================================================================
--- trunk/packages/dotur/trunk/debian/README.source (rev 0)
+++ trunk/packages/dotur/trunk/debian/README.source 2011-03-02 23:13:49 UTC (rev 6151)
@@ -0,0 +1,7 @@
+dotur for Debian
+----------------
+
+The patches provide a Makefile and fix some build errors with gcc > 4.3.
+
+
+
Added: trunk/packages/dotur/trunk/debian/changelog
===================================================================
--- trunk/packages/dotur/trunk/debian/changelog (rev 0)
+++ trunk/packages/dotur/trunk/debian/changelog 2011-03-02 23:13:49 UTC (rev 6151)
@@ -0,0 +1,5 @@
+dotur (1.53-1) UNRELEAED; urgency=low
+
+ * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+
+ -- Steffen Moeller <moeller at debian.org> Wed, 02 Mar 2011 23:48:37 +0100
Added: trunk/packages/dotur/trunk/debian/compat
===================================================================
--- trunk/packages/dotur/trunk/debian/compat (rev 0)
+++ trunk/packages/dotur/trunk/debian/compat 2011-03-02 23:13:49 UTC (rev 6151)
@@ -0,0 +1 @@
+7
Added: trunk/packages/dotur/trunk/debian/control
===================================================================
--- trunk/packages/dotur/trunk/debian/control (rev 0)
+++ trunk/packages/dotur/trunk/debian/control 2011-03-02 23:13:49 UTC (rev 6151)
@@ -0,0 +1,21 @@
+Source: dotur
+Section: science
+Priority: extra
+Maintainer: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 7.0.50~)
+Standards-Version: 3.9.1
+Homepage: http://www.plantpath.wisc.edu/fac/joh/DOTUR/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/dotur/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/dotur/trunk/
+
+Package: dotur
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: distance based OTU and richness estimation
+ DOTUR is a computer program that takes a distance matrix describing
+ the genetic distance between DNA sequence data and assigns sequences to
+ operational taxonomic units (OTUs) using either the furthest, average,
+ or nearest neighbor algorithms for all possible distances that can be
+ described using the distance matrix. Using the OTU composition data,
+ DOTUR constructs collector's and rarefaction curves for sampling
+ intensity, richness estimators, and diversity indices.
Added: trunk/packages/dotur/trunk/debian/copyright
===================================================================
--- trunk/packages/dotur/trunk/debian/copyright (rev 0)
+++ trunk/packages/dotur/trunk/debian/copyright 2011-03-02 23:13:49 UTC (rev 6151)
@@ -0,0 +1,32 @@
+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: dotur
+Source: <url://example.com>
+
+Files: *
+Copyright: <years> <put author's name and email here>
+ <years> <likewise for another author>
+License: GPL-2.0+
+
+Files: debian/*
+Copyright: 2011 Steffen Moeller <steffen_moeller at gmx.de>
+License: GPL-2.0+
+
+License: GPL-2.0+
+ 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.
+ .
+ This package 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, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+# Please also look if there are files or directories which have a
+# different copyright/license attached and list them here.
Added: trunk/packages/dotur/trunk/debian/docs
===================================================================
--- trunk/packages/dotur/trunk/debian/docs (rev 0)
+++ trunk/packages/dotur/trunk/debian/docs 2011-03-02 23:13:49 UTC (rev 6151)
@@ -0,0 +1 @@
+README
Added: trunk/packages/dotur/trunk/debian/patches/Makefile.patch
===================================================================
--- trunk/packages/dotur/trunk/debian/patches/Makefile.patch (rev 0)
+++ trunk/packages/dotur/trunk/debian/patches/Makefile.patch 2011-03-02 23:13:49 UTC (rev 6151)
@@ -0,0 +1,11 @@
+Index: dotur-1.53/Makefile
+===================================================================
+--- /dev/null 1970-01-01 00:00:00.000000000 +0000
++++ dotur-1.53/Makefile 2011-03-03 00:05:18.000000000 +0100
+@@ -0,0 +1,6 @@
++
++dotur: dotur.C
++ $(CXX) $(CFLAGS) -o $@ $<
++
++clean:
++ rm -f dotur
Added: trunk/packages/dotur/trunk/debian/patches/compilation.patch
===================================================================
--- trunk/packages/dotur/trunk/debian/patches/compilation.patch (rev 0)
+++ trunk/packages/dotur/trunk/debian/patches/compilation.patch 2011-03-02 23:13:49 UTC (rev 6151)
@@ -0,0 +1,36 @@
+Index: dotur-1.53/dotur.C
+===================================================================
+--- dotur-1.53.orig/dotur.C 2011-03-03 00:04:37.000000000 +0100
++++ dotur-1.53/dotur.C 2011-03-03 00:05:36.000000000 +0100
+@@ -3,13 +3,15 @@
+
+ using namespace std;
+
++#include <cstdlib>
++#include <algorithm>
+ #include "otu.h"
+ #include "richness.h"
+ #include <iostream>
+ #include <fstream>
+ #include <iomanip>
+ #include <vector>
+-#include <string>
++#include <cstring>
+ #include <sstream>
+ #include <list>
+ #include <ctime>
+Index: dotur-1.53/otu.h
+===================================================================
+--- dotur-1.53.orig/otu.h 2011-03-03 00:04:37.000000000 +0100
++++ dotur-1.53/otu.h 2011-03-03 00:05:36.000000000 +0100
+@@ -1,8 +1,9 @@
++#include <cstdlib>
+ #include <iostream>
+ #include <fstream>
+ #include <iomanip>
+ #include <vector>
+-#include <string>
++#include <cstring>
+ #include <sstream>
+ #include <list>
+ #include <cmath>
Added: trunk/packages/dotur/trunk/debian/patches/series
===================================================================
--- trunk/packages/dotur/trunk/debian/patches/series (rev 0)
+++ trunk/packages/dotur/trunk/debian/patches/series 2011-03-02 23:13:49 UTC (rev 6151)
@@ -0,0 +1,2 @@
+Makefile.patch
+compilation.patch
Added: trunk/packages/dotur/trunk/debian/rules
===================================================================
--- trunk/packages/dotur/trunk/debian/rules (rev 0)
+++ trunk/packages/dotur/trunk/debian/rules 2011-03-02 23:13:49 UTC (rev 6151)
@@ -0,0 +1,13 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ dh $@
Property changes on: trunk/packages/dotur/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/dotur/trunk/debian/source/format
===================================================================
--- trunk/packages/dotur/trunk/debian/source/format (rev 0)
+++ trunk/packages/dotur/trunk/debian/source/format 2011-03-02 23:13:49 UTC (rev 6151)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/dotur/trunk/debian/watch
===================================================================
--- trunk/packages/dotur/trunk/debian/watch (rev 0)
+++ trunk/packages/dotur/trunk/debian/watch 2011-03-02 23:13:49 UTC (rev 6151)
@@ -0,0 +1,2 @@
+version=3
+http://www.plantpath.wisc.edu/fac/joh/DOTUR/dotur-([\d.]+).tgz
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