Author: alteholz
Date: 2012-07-18 17:47:04 +0000 (Wed, 18 Jul 2012)
New Revision: 11828
Added:
trunk/packages/cluster3/trunk/debian/cluster3.doc-base
trunk/packages/cluster3/trunk/debian/patches/
trunk/packages/cluster3/trunk/debian/patches/compile-warnings.patch
trunk/packages/cluster3/trunk/debian/patches/series
trunk/packages/cluster3/trunk/debian/source/
trunk/packages/cluster3/trunk/debian/source/format
trunk/packages/cluster3/trunk/debian/upstream
Modified:
trunk/packages/cluster3/trunk/debian/changelog
trunk/packages/cluster3/trunk/debian/cluster3-doc.docs
trunk/packages/cluster3/trunk/debian/cluster3.docs
trunk/packages/cluster3/trunk/debian/compat
trunk/packages/cluster3/trunk/debian/control
trunk/packages/cluster3/trunk/debian/copyright
trunk/packages/cluster3/trunk/debian/menu
trunk/packages/cluster3/trunk/debian/rules
Log:
cluster3 almost finished now
Modified: trunk/packages/cluster3/trunk/debian/changelog
===================================================================
--- trunk/packages/cluster3/trunk/debian/changelog 2012-07-18 09:31:37 UTC
(rev 11827)
+++ trunk/packages/cluster3/trunk/debian/changelog 2012-07-18 17:47:04 UTC
(rev 11828)
@@ -1,7 +1,5 @@
-cluster3 (1.50-1) UNRELEASED; urgency=low
+cluster3 (1.50-1) unstable; urgency=low
- * XXX TODO: before uploading the ITP needs to be reopened
-
[ Thorsten Alteholz ]
* New upstream release (1.50).
* debian/rules: target get-orig-source added
@@ -14,17 +12,17 @@
[ Charles Plessy ]
* Initial release.
* Manpage built before source package generation, removed docbook-to-man
- build dependancy.
+ build dependency.
- -- DMPT <debian-med-packag...@lists.alioth.debian.org> Fri, 01 Aug 2008
13:29:25 +0900
+ -- Thorsten Alteholz <deb...@alteholz.de> Wed, 18 Jul 2012 18:00:00 +0200
-cluster3 (1.25-0.2) unstable; urgency=low
+cluster3 (1.25-0.2) UNRELEASED; urgency=low
* Provides both the motif gui and command line interface.
-- Steffen Moeller <moel...@pzr.uni-rostock.de> Tue, 7 Apr 2004 18:31:37
+0200
-cluster3 (1.25-0.1) unstable; urgency=low
+cluster3 (1.25-0.1) UNRELEASED; urgency=low
* Initial Release.
Modified: trunk/packages/cluster3/trunk/debian/cluster3-doc.docs
===================================================================
--- trunk/packages/cluster3/trunk/debian/cluster3-doc.docs 2012-07-18
09:31:37 UTC (rev 11827)
+++ trunk/packages/cluster3/trunk/debian/cluster3-doc.docs 2012-07-18
17:47:04 UTC (rev 11828)
@@ -3,3 +3,5 @@
docs/cluster3.pdf
docs/cluster3.texinfo
docs/structure.eps
+html/*.html
+html/images/*
Added: trunk/packages/cluster3/trunk/debian/cluster3.doc-base
===================================================================
--- trunk/packages/cluster3/trunk/debian/cluster3.doc-base
(rev 0)
+++ trunk/packages/cluster3/trunk/debian/cluster3.doc-base 2012-07-18
17:47:04 UTC (rev 11828)
@@ -0,0 +1,24 @@
+Document: cluster3
+Title: Cluster 3.0 for Windows, Mac OS X, Linux, Unix
+Author: Michael Eisen; updated by Michiel de Hoon
+Abstract: This is the manual for Cluster 3.0.
+ Cluster was originally written by Michael Eisen while at Stanford
+ University. We have modified the clustering algorithm in Cluster,
+ and extended the algorithm for Self-Organizing Maps to include
+ two-dimensional rectangular grids. The Euclidean distance and the
+ city-block distance were added as new distance measures between gene
+ expression data. The proprietary Numerical Recipes routines, which
+ were used in the original version of Cluster/TreeView, have been
+ replaced by open source software.
+ .
+ Cluster 3.0 is available for Windows, Mac OS X, Linux, and Unix.
+Section: Science/Biology
+
+Format: PDF
+Files: /usr/share/doc/cluster3/cluster.pdf.gz
+ /usr/share/doc/cluster3/cluster3.pdf.gz
+
+Format: html
+Index: /usr/share/doc/cluster3/html/index.html
+Files: /usr/share/doc/cluster3/html/*.html
+
Modified: trunk/packages/cluster3/trunk/debian/cluster3.docs
===================================================================
--- trunk/packages/cluster3/trunk/debian/cluster3.docs 2012-07-18 09:31:37 UTC
(rev 11827)
+++ trunk/packages/cluster3/trunk/debian/cluster3.docs 2012-07-18 17:47:04 UTC
(rev 11828)
@@ -1,2 +1,3 @@
NEWS
README
+html/
Modified: trunk/packages/cluster3/trunk/debian/compat
===================================================================
--- trunk/packages/cluster3/trunk/debian/compat 2012-07-18 09:31:37 UTC (rev
11827)
+++ trunk/packages/cluster3/trunk/debian/compat 2012-07-18 17:47:04 UTC (rev
11828)
@@ -1 +1 @@
-4
+9
Modified: trunk/packages/cluster3/trunk/debian/control
===================================================================
--- trunk/packages/cluster3/trunk/debian/control 2012-07-18 09:31:37 UTC
(rev 11827)
+++ trunk/packages/cluster3/trunk/debian/control 2012-07-18 17:47:04 UTC
(rev 11828)
@@ -2,9 +2,11 @@
Section: non-free/science
Priority: optional
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
-Uploaders: Steffen Moeller <moel...@debian.org>, Charles Plessy
<ple...@debian.org>
-Build-Depends: debhelper (>= 7), libmotif-dev, autotools-dev, perl
-Standards-Version: 3.6.1.1
+Uploaders: Steffen Moeller <moel...@debian.org>,
+ Charles Plessy <ple...@debian.org>,
+ Thorsten Alteholz <deb...@alteholz.de>
+Build-Depends: debhelper (>= 9), libmotif-dev, autotools-dev, perl
+Standards-Version: 3.9.3
Homepage: http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/
Package: cluster3
Modified: trunk/packages/cluster3/trunk/debian/copyright
===================================================================
--- trunk/packages/cluster3/trunk/debian/copyright 2012-07-18 09:31:37 UTC
(rev 11827)
+++ trunk/packages/cluster3/trunk/debian/copyright 2012-07-18 17:47:04 UTC
(rev 11828)
@@ -1,32 +1,47 @@
-This package was debianized by Steffen Moeller <moel...@pzr.uni-rostock.de> on
-Tue, 6 Apr 2004 18:31:37 +0200.
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: cluster
+Upstream-Contact: M. J. L. de Hoon <mdeh...@ims.u-tokyo.ac.jp>
+Source: http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm
-It was downloaded from
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm
+Files: *
+Copyright: M. J. L. de Hoon <mdeh...@ims.u-tokyo.ac.jp>, S. Imoto, J. Nolan,
and S. Miyano, Michael Eisen
+License: different
+ The Open Source Clustering Software consists of several packages, which have
+ different licenses.
+ .
+ * Cluster 3.0 is a GUI-based program for Windows, Mac OS X, Linux, and Unix.
+ It is based on Michael Eisen's Cluster/TreeView code. Cluster 3.0 is covered
+ by Michael Eisen's original license, available at
+ http://rana.lbl.gov/EisenSoftwareSource.htm. The command-line version of
+ Cluster 3.0 is also covered by this license.
+ * Pycluster is an extension module to the scripting language Python. It is
+ covered by the Python License (same license as Python itself).
+ * Algorithm::Cluster, the interface to the scripting language Perl. It was
+ released under the Artistic License (same license as Perl itself).
+ * The routines in the C Clustering Library can also be used directly by
calling
+ them from other C programs. In that case, the Python License applies.
+ .
+ In all cases, copyright notices must be retained in their original form.
+ .
+ The Artistic License is usually distributed in
+ /usr/share/common-licenses/Artistic
-Upstream Authors: M. J. L. de Hoon <mdeh...@ims.u-tokyo.ac.jp>, S. Imoto, J.
Nolan, and S. Miyano
-
-Copyright:
-
-
-License Information
-===================
-
-The Open Source Clustering Software consists of several packages, which have
-different licenses.
-
-* Cluster 3.0 is a GUI-based program for Windows, Mac OS X, Linux, and Unix.
- It is based on Michael Eisen's Cluster/TreeView code. Cluster 3.0 is covered
- by Michael Eisen's original license, available at
- http://rana.lbl.gov/EisenSoftwareSource.htm. The command-line version of
- Cluster 3.0 is also covered by this license.
-* Pycluster is an extension module to the scripting language Python. It is
- covered by the Python License (same license as Python itself).
-* Algorithm::Cluster, the interface to the scripting language Perl. It was
- released under the Artistic License (same license as Perl itself).
-* The routines in the C Clustering Library can also be used directly by calling
- them from other C programs. In that case, the Python License applies.
-
-In all cases, copyright notices must be retained in their original form.
-
-The Artistic License is usually distributed in
/usr/share/common-licenses/Artistic
-and the GPL is /usr/share/common-licenses/GLP on Debian systems.
+Files: debian/*
+Copyright: 2004 Steffen Moeller <moel...@debian.org>
+ 2012 Thorsten Alteholz <deb...@alteholz.de>
+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 version 3 as published
+ by the Free Software Foundation.
+ .
+ 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 package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License can be found in `/usr/share/common-licenses/GPL-3'.
Modified: trunk/packages/cluster3/trunk/debian/menu
===================================================================
--- trunk/packages/cluster3/trunk/debian/menu 2012-07-18 09:31:37 UTC (rev
11827)
+++ trunk/packages/cluster3/trunk/debian/menu 2012-07-18 17:47:04 UTC (rev
11828)
@@ -1,2 +1,2 @@
-?package(cluster3):needs="X11" section="Apps/Science" \
+?package(cluster3):needs="X11" section="Applications/Science/Biology" \
title="cluster3" command="/usr/bin/xcluster3"
Added: trunk/packages/cluster3/trunk/debian/patches/compile-warnings.patch
===================================================================
--- trunk/packages/cluster3/trunk/debian/patches/compile-warnings.patch
(rev 0)
+++ trunk/packages/cluster3/trunk/debian/patches/compile-warnings.patch
2012-07-18 17:47:04 UTC (rev 11828)
@@ -0,0 +1,23 @@
+Description: remove compiler warning
+Index: cluster-1.50/src/command.c
+===================================================================
+--- cluster-1.50.orig/src/command.c 2010-03-28 04:02:14.000000000 +0200
++++ cluster-1.50/src/command.c 2012-07-11 14:37:03.000000000 +0200
+@@ -382,7 +382,7 @@
+ fclose(coordinatefile);
+ fclose(pcfile);
+ if (error)
+- { printf(error);
++ { printf("%s",error);
+ free(filename);
+ return;
+ }
+@@ -403,7 +403,7 @@
+ fclose(coordinatefile);
+ fclose(pcfile);
+ if (error)
+- { printf(error);
++ { printf("%s",error);
+ free(filename);
+ return;
+ }
Added: trunk/packages/cluster3/trunk/debian/patches/series
===================================================================
--- trunk/packages/cluster3/trunk/debian/patches/series
(rev 0)
+++ trunk/packages/cluster3/trunk/debian/patches/series 2012-07-18 17:47:04 UTC
(rev 11828)
@@ -0,0 +1 @@
+compile-warnings.patch
Modified: trunk/packages/cluster3/trunk/debian/rules
===================================================================
--- trunk/packages/cluster3/trunk/debian/rules 2012-07-18 09:31:37 UTC (rev
11827)
+++ trunk/packages/cluster3/trunk/debian/rules 2012-07-18 17:47:04 UTC (rev
11828)
@@ -17,8 +17,12 @@
DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE)
DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
+CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
+CFLAGS:=$(shell dpkg-buildflags --get CFLAGS)
+CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS)
+LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
-CFLAGS = -Wall -g
+CFLAGS += -Wall -g -fPIC
ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
CFLAGS += -O0
@@ -37,18 +41,24 @@
cp -f /usr/share/misc/config.guess config.guess
touch configure-stamp
-build-arch: build-arch-stamp-nox build-arch-stamp-x cluster3.1 xcluster3.1
+build-arch: build-arch-stamp-nox build-arch-clean build-arch-stamp-x
cluster3.1 xcluster3.1
build-arch-stamp-nox: configure
# Add here commands to compile the arch part of the package.
CFLAGS="$(CFLAGS)" ./configure -C --host=$(DEB_HOST_GNU_TYPE)
--build=$(DEB_BUILD_GNU_TYPE) --prefix=/usr --mandir=\$${prefix}/share/man
--infodir=\$${prefix}/share/info --without-x
- $(MAKE) CFLAGS="$(CFLAGS)"
+ $(MAKE) CFLAGS="$(CFLAGS)" CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)"
+ cp src/cluster cluster.nox
touch build-arch-stamp-nox
build-arch-stamp-x: configure
CFLAGS="$(CFLAGS)" ./configure -C --host=$(DEB_HOST_GNU_TYPE)
--build=$(DEB_BUILD_GNU_TYPE) --prefix=/usr --mandir=\$${prefix}/share/man
--infodir=\$${prefix}/share/info --with-x
- $(MAKE) CFLAGS="$(CFLAGS)"
+ $(MAKE) CFLAGS="$(CFLAGS)" CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)"
+ cp src/cluster cluster.x
touch build-arch-stamp-x
+# in order to build build-arch-stamp-x after build-arch-stamp-nox
+# any object file needs to be cleaned
+build-arch-clean: configure
+ $(MAKE) clean
install-arch-perl: install-arch-perl-stamp
install-arch-perl-stamp:
@@ -75,7 +85,7 @@
rm -f build-arch-stamp* build-indep-stamp #CONFIGURE-STAMP#
# Add here commands to clean up after the build process.
- -$(MAKE) clean
+ [ ! -f Makefile ] || $(MAKE) clean
-find . -name .deps -a -type d | xargs rm -rf
@@ -85,7 +95,7 @@
install-indep:
dh_testdir -i
dh_testroot -i
- dh_clean -k -i
+ dh_prep -i
dh_installdirs -i
# Add here commands to install the indep part of the package into
@@ -97,13 +107,13 @@
install-arch: build-arch install-arch-perl
dh_testdir -a
dh_testroot -a
- dh_clean -k -a
+ dh_prep -a
dh_installdirs -a
# Add here commands to install the arch part of the package into
# debian/tmp.
- cp X11/cluster $(CURDIR)/debian/cluster3/usr/bin/xcluster3
- cp src/cluster $(CURDIR)/debian/cluster3/usr/bin/cluster3
+ cp cluster.x $(CURDIR)/debian/cluster3/usr/bin/xcluster3
+ cp cluster.nox $(CURDIR)/debian/cluster3/usr/bin/cluster3
cp doc/* $(CURDIR)/debian/cluster3/usr/share/doc/cluster3
cp -r example $(CURDIR)/debian/cluster3/usr/share/cluster3
dh_install -s
Added: trunk/packages/cluster3/trunk/debian/source/format
===================================================================
--- trunk/packages/cluster3/trunk/debian/source/format
(rev 0)
+++ trunk/packages/cluster3/trunk/debian/source/format 2012-07-18 17:47:04 UTC
(rev 11828)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/cluster3/trunk/debian/upstream
===================================================================
--- trunk/packages/cluster3/trunk/debian/upstream
(rev 0)
+++ trunk/packages/cluster3/trunk/debian/upstream 2012-07-18 17:47:04 UTC
(rev 11828)
@@ -0,0 +1,17 @@
+Contact: M. J. L. de Hoon <mdeh...@ims.u-tokyo.ac.jp>
+Homepage: http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/
+Name: cluster3
+Reference:
+ debian-package: cluster3
+ author: M. J. L. de Hoon AND S. Imoto AND J. Nolan AND S. Miyano
+ journal: Bioinformatics
+ title: Open Source Clustering Software
+ year: 2004
+ month: 06
+ volume: 20
+ pages: 1453-4
+ number: 9
+ DOI: 10.1093/bioinformatics/bth078
+ PMID: 14871861
+ url: http://bioinformatics.oxfordjournals.org/content/20/9/1453.long
+Watch: http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm
cluster-(.*)\.tar.gz
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