[med-svn] r1597 - in trunk/packages: . biococoa biococoa/trunk biococoa/trunk/debian biococoa/trunk/debian/patches
tille at alioth.debian.org
tille at alioth.debian.org
Sat Mar 15 07:05:22 UTC 2008
Author: tille
Date: 2008-03-15 07:05:21 +0000 (Sat, 15 Mar 2008)
New Revision: 1597
Added:
trunk/packages/biococoa/
trunk/packages/biococoa/trunk/
trunk/packages/biococoa/trunk/debian/
trunk/packages/biococoa/trunk/debian/BioCocoa.1
trunk/packages/biococoa/trunk/debian/BioCocoa.desktop
trunk/packages/biococoa/trunk/debian/changelog
trunk/packages/biococoa/trunk/debian/compat
trunk/packages/biococoa/trunk/debian/control
trunk/packages/biococoa/trunk/debian/copyright
trunk/packages/biococoa/trunk/debian/dirs
trunk/packages/biococoa/trunk/debian/lintian-override
trunk/packages/biococoa/trunk/debian/manpages
trunk/packages/biococoa/trunk/debian/menu
trunk/packages/biococoa/trunk/debian/patches/
trunk/packages/biococoa/trunk/debian/patches/01_plist.patch
trunk/packages/biococoa/trunk/debian/patches/02_Controller.patch
trunk/packages/biococoa/trunk/debian/patches/03_GNUmakefile.patch
trunk/packages/biococoa/trunk/debian/patches/04_Interface.patch
trunk/packages/biococoa/trunk/debian/patches/05_main.patch
trunk/packages/biococoa/trunk/debian/patches/series
trunk/packages/biococoa/trunk/debian/rules
Log:
Initial check in of biococoa with quiltified patches
Added: trunk/packages/biococoa/trunk/debian/BioCocoa.1
===================================================================
--- trunk/packages/biococoa/trunk/debian/BioCocoa.1 (rev 0)
+++ trunk/packages/biococoa/trunk/debian/BioCocoa.1 2008-03-15 07:05:21 UTC (rev 1597)
@@ -0,0 +1,27 @@
+.TH BIOCOCOA 1 "December 21, 2004"
+.SH NAME
+BioCocoa \- Sequence file format conversion
+.SH SYNOPSIS
+.B BioCocoa
+.SH DESCRIPTION
+This manual page documents briefly the
+.B BioCocoa
+command.
+This manual page was written for the Debian distribution
+because the original program does not have a manual page.
+.PP
+\fBBioCocoa\fP provides developers with the opportunity to add
+support for reading and writing BEAST, Clustal, EMBL, Fasta, GCG-MSF, GDE,
+Hennig86, NCBI, NEXUS, NONA, PDB, Phylip, PIR, Plain/Raw, Swiss-Prot and
+TNT files by writing only three lines of code. The framework is written in
+Cocoa (Objective-C).
+.SH OPTIONS
+These programs follow the usual GNU command line syntax, with long
+options starting with two dashes (`-').
+A summary of options is included below.
+.SH SEE ALSO
+.BR GNUstep (7).
+.br
+.SH AUTHOR
+This manual page was written by G\[:u]rkan Seng\[:u]n <gurkan at linuks.mine.nu>,
+for the Debian project (but may be used by others).
Added: trunk/packages/biococoa/trunk/debian/BioCocoa.desktop
===================================================================
--- trunk/packages/biococoa/trunk/debian/BioCocoa.desktop (rev 0)
+++ trunk/packages/biococoa/trunk/debian/BioCocoa.desktop 2008-03-15 07:05:21 UTC (rev 1597)
@@ -0,0 +1,8 @@
+[Desktop Entry]
+Type=Application
+Version=0.94
+Categories=Education;Science;Biology;
+Name=BioCocoa
+Comment=GNUstep BioCocoa
+Icon=/usr/lib/GNUstep/Applications/BioCocoa.app/Resources/biococoa.tiff
+Exec=BioCocoa
Added: trunk/packages/biococoa/trunk/debian/changelog
===================================================================
--- trunk/packages/biococoa/trunk/debian/changelog (rev 0)
+++ trunk/packages/biococoa/trunk/debian/changelog 2008-03-15 07:05:21 UTC (rev 1597)
@@ -0,0 +1,48 @@
+biococoa.app (1.6.0-6) unstable; urgency=low
+
+ * Put biococoa.app under group maintenance of Debian Med packaging
+ team
+
+ -- Andreas Tille <tille at debian.org> Mon, 10 Mar 2008 22:48:09 +0100
+
+biococoa.app (1.6.0-5) unstable; urgency=low
+
+ * Orphaning package, setting maintainer to the Debian QA Group.
+
+ -- Ana Beatriz Guerrero Lopez <ana at debian.org> Fri, 07 Dec 2007 02:05:38 +0100
+
+biococoa.app (1.6.0-4) unstable; urgency=low
+
+ * GNUstep transition.
+ + Updated debian/rules.
+ + Updated debian/dirs.
+ * Menu transition: Moved from Apps/Tools to Applications/Science/Biology.
+ * Added a desktop file.
+
+ -- Gürkan Sengün <gurkan at linuks.mine.nu> Sat, 06 Oct 2007 16:02:26 +0200
+
+biococoa.app (1.6.0-3) unstable; urgency=low
+
+ * Rebuild against latest libgnustep-gui-dev.
+ * Bump standards version.
+
+ -- Gürkan Sengün <gurkan at linuks.mine.nu> Mon, 18 Sep 2006 23:02:34 +0200
+
+biococoa.app (1.6.0-2) unstable; urgency=low
+
+ * Rebuild against latest libgnustep-gui.
+ * Update manual page.
+ * Bump standards version.
+
+ -- Gürkan Sengün <gurkan at linuks.mine.nu> Fri, 20 Jan 2006 10:48:05 +0100
+
+biococoa.app (1.6.0-1) unstable; urgency=low
+
+ * Initial Release. (closes: #287312)
+ * Incorporated small changes sent in by upstream developer Peter Schols.
+ * Slightly modified source to let the application be consistent
+ with other GNUstep applications:
+ + default background color
+ + main menu enabled
+
+ -- Gürkan Sengün <gurkan at linuks.mine.nu> Tue, 21 Dec 2004 00:30:09 +0100
Added: trunk/packages/biococoa/trunk/debian/compat
===================================================================
--- trunk/packages/biococoa/trunk/debian/compat (rev 0)
+++ trunk/packages/biococoa/trunk/debian/compat 2008-03-15 07:05:21 UTC (rev 1597)
@@ -0,0 +1 @@
+4
Added: trunk/packages/biococoa/trunk/debian/control
===================================================================
--- trunk/packages/biococoa/trunk/debian/control (rev 0)
+++ trunk/packages/biococoa/trunk/debian/control 2008-03-15 07:05:21 UTC (rev 1597)
@@ -0,0 +1,18 @@
+Source: biococoa.app
+Section: science
+Priority: optional
+Maintainer: Debian QA Group <packages at qa.debian.org>
+Build-Depends: debhelper (>= 4.0.0), gnustep-make, libgnustep-gui-dev (>= 0.12.0)
+Standards-Version: 3.7.2
+
+Package: biococoa.app
+Architecture: any
+Depends: ${shlibs:Depends}
+Description: Sequence file format conversion for GNUstep
+ The BioCocoa framework provides developers with the opportunity to add
+ support for reading and writing BEAST, Clustal, EMBL, Fasta, GCG-MSF, GDE,
+ Hennig86, NCBI, NEXUS, NONA, PDB, Phylip, PIR, Plain/Raw, Swiss-Prot and
+ TNT files by writing only three lines of code. The framework is written in
+ Cocoa (Objective-C).
+ .
+ Homepage: http://bioinformatics.org/biococoa/
Added: trunk/packages/biococoa/trunk/debian/copyright
===================================================================
--- trunk/packages/biococoa/trunk/debian/copyright (rev 0)
+++ trunk/packages/biococoa/trunk/debian/copyright 2008-03-15 07:05:21 UTC (rev 1597)
@@ -0,0 +1,27 @@
+This package was debianized by Gürkan Sengün <gurkan at linuks.mine.nu> on
+Tue, 21 Dec 2004 00:30:09 +0100.
+
+It was downloaded from http://bioinformatics.org/biococoa/
+
+Upstream Author: Peter Schols <peter.schols at bio.kuleuven.ac.be>
+
+Copyright:
+
+ Copyright (C) 2004 The BioCocoa team
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Library General Public
+ License as published by the Free Software Foundation; either
+ version 2 of the License, or (at your option) any later version.
+
+ This library 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
+ Library General Public License for more details.
+
+ You should have received a copy of the GNU Library General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston MA 02110-1301 USA
+
+Released under the GNU Lesser General Public Library 2.0
+Please see /usr/share/common-licenses/LGPL-2 for the full license.
Added: trunk/packages/biococoa/trunk/debian/dirs
===================================================================
--- trunk/packages/biococoa/trunk/debian/dirs (rev 0)
+++ trunk/packages/biococoa/trunk/debian/dirs 2008-03-15 07:05:21 UTC (rev 1597)
@@ -0,0 +1,2 @@
+usr/bin
+usr/share/lintian/overrides
Added: trunk/packages/biococoa/trunk/debian/lintian-override
===================================================================
--- trunk/packages/biococoa/trunk/debian/lintian-override (rev 0)
+++ trunk/packages/biococoa/trunk/debian/lintian-override 2008-03-15 07:05:21 UTC (rev 1597)
@@ -0,0 +1 @@
+biococoa.app: image-file-in-usr-lib
Added: trunk/packages/biococoa/trunk/debian/manpages
===================================================================
--- trunk/packages/biococoa/trunk/debian/manpages (rev 0)
+++ trunk/packages/biococoa/trunk/debian/manpages 2008-03-15 07:05:21 UTC (rev 1597)
@@ -0,0 +1 @@
+debian/BioCocoa.1
Added: trunk/packages/biococoa/trunk/debian/menu
===================================================================
--- trunk/packages/biococoa/trunk/debian/menu (rev 0)
+++ trunk/packages/biococoa/trunk/debian/menu 2008-03-15 07:05:21 UTC (rev 1597)
@@ -0,0 +1,2 @@
+?package(biococoa.app):needs="X11" section="Applications/Science/Biology"\
+ title="BioCocoa" command="/usr/bin/BioCocoa"
Added: trunk/packages/biococoa/trunk/debian/patches/01_plist.patch
===================================================================
--- trunk/packages/biococoa/trunk/debian/patches/01_plist.patch (rev 0)
+++ trunk/packages/biococoa/trunk/debian/patches/01_plist.patch 2008-03-15 07:05:21 UTC (rev 1597)
@@ -0,0 +1,13 @@
+--- biococoa.orig/BioCocoaInfo.plist
++++ biococoa/BioCocoaInfo.plist
+@@ -1,7 +1,7 @@
+ {
+- ApplicationName = BioCocoa
+- ApplicationDescription = "GNUstep BioCocoaDemo";
+- ApplicationRelease = BioCocoa 1.6";
++ ApplicationName = "BioCocoa";
++ ApplicationDescription = "GNUstep BioCocoa";
++ ApplicationRelease = "BioCocoa 1.6";
+ FullVersionID = "1.6.0 Nov 2004";
+ Authors = ("Peter Schols <peter.schols at bio.kuleuven.ac.be>");
+ Copyright = "Copyright (C) 2004 The BioCocoa team.";
Added: trunk/packages/biococoa/trunk/debian/patches/02_Controller.patch
===================================================================
--- trunk/packages/biococoa/trunk/debian/patches/02_Controller.patch (rev 0)
+++ trunk/packages/biococoa/trunk/debian/patches/02_Controller.patch 2008-03-15 07:05:21 UTC (rev 1597)
@@ -0,0 +1,13 @@
+--- biococoa.orig/Controller.m
++++ biococoa/Controller.m
+@@ -49,9 +49,7 @@
+ [panel setCanChooseDirectories:NO];
+ [panel setPrompt:@"Choose File"];
+ [panel runModalForDirectory:nil file:nil types:nil];
+- if ([panel filename]) {
+- [self readSequenceFile:[panel filename]];
+- }
++ [self readSequenceFile:[panel filename]];
+ }
+
+
Added: trunk/packages/biococoa/trunk/debian/patches/03_GNUmakefile.patch
===================================================================
--- trunk/packages/biococoa/trunk/debian/patches/03_GNUmakefile.patch (rev 0)
+++ trunk/packages/biococoa/trunk/debian/patches/03_GNUmakefile.patch 2008-03-15 07:05:21 UTC (rev 1597)
@@ -0,0 +1,27 @@
+--- biococoa.orig/GNUmakefile
++++ biococoa/GNUmakefile
+@@ -1,12 +1,14 @@
+ # GNUmakefile: makefile for Biococoa
+ #
++# Copyright (C) 1999 Free Software Foundation, Inc.
++#
+ # Author: Peter Schols
+ # Date: 2004
+ #
+ # This file is part of GNUstep.
+ #
+ # This program is free software; you can redistribute it and/or modify
+-# it under the terms of the GNU Lesser General Public License as published by
++# 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.
+ #
+@@ -25,7 +27,7 @@
+ BioCocoa_HEADERS = Controller.h Interface.h BCReader.h BCCreator.h StringAdditions.h
+ BioCocoa_OBJC_FILES = main.m Controller.m Interface.m BCReader.m BCCreator.m StringAdditions.m
+ BioCocoa_APPLICATION_ICON = biococoa.tiff
+-BioCocoa_RESOURCE_FILES = biococoa.tiff
++BioCocoa_RESOURCE_FILES = biococoa.tiff BioCocoaInfo.plist
+
+ include $(GNUSTEP_MAKEFILES)/application.make
+
Added: trunk/packages/biococoa/trunk/debian/patches/04_Interface.patch
===================================================================
--- trunk/packages/biococoa/trunk/debian/patches/04_Interface.patch (rev 0)
+++ trunk/packages/biococoa/trunk/debian/patches/04_Interface.patch 2008-03-15 07:05:21 UTC (rev 1597)
@@ -0,0 +1,11 @@
+--- biococoa.orig/Interface.m
++++ biococoa/Interface.m
+@@ -101,7 +101,7 @@
+ backing: NSBackingStoreBuffered
+ defer: NO];
+
+- [self setBackgroundColor:[NSColor colorWithCalibratedRed:0.9254 green:0.91372 blue:0.8470 alpha:1.0]];
++/* [self setBackgroundColor:[NSColor colorWithCalibratedRed:0.9254 green:0.91372 blue:0.8470 alpha:1.0]]; */
+
+ [self setInitialFirstResponder: openButton];
+
Added: trunk/packages/biococoa/trunk/debian/patches/05_main.patch
===================================================================
--- trunk/packages/biococoa/trunk/debian/patches/05_main.patch (rev 0)
+++ trunk/packages/biococoa/trunk/debian/patches/05_main.patch 2008-03-15 07:05:21 UTC (rev 1597)
@@ -0,0 +1,18 @@
+--- biococoa.orig/main.m
++++ biococoa/main.m
+@@ -17,7 +17,6 @@
+ app = [NSApplication sharedApplication];
+ [app setApplicationIconImage: [NSImage imageNamed: @"Calculator.app.tiff"]];
+
+- /*
+ mainMenu = [[NSMenu new]autorelease];
+ // Info
+ [mainMenu addItemWithTitle: @"Info..."
+@@ -44,7 +43,6 @@
+ keyEquivalent: @"q"];
+
+ [app setMainMenu: mainMenu];
+- */
+
+ brain = [Controller new];
+ face = [Interface new];
Added: trunk/packages/biococoa/trunk/debian/patches/series
===================================================================
--- trunk/packages/biococoa/trunk/debian/patches/series (rev 0)
+++ trunk/packages/biococoa/trunk/debian/patches/series 2008-03-15 07:05:21 UTC (rev 1597)
@@ -0,0 +1,5 @@
+01_plist.patch
+02_Controller.patch
+03_GNUmakefile.patch
+04_Interface.patch
+05_main.patch
Added: trunk/packages/biococoa/trunk/debian/rules
===================================================================
--- trunk/packages/biococoa/trunk/debian/rules (rev 0)
+++ trunk/packages/biococoa/trunk/debian/rules 2008-03-15 07:05:21 UTC (rev 1597)
@@ -0,0 +1,55 @@
+#!/usr/bin/make -f
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+include /usr/share/GNUstep/debian/config.mk
+GNUSTEP_MAKEFILES=$(GS_MAKE_DIR)
+
+build: build-stamp
+
+build-stamp:
+ dh_testdir
+ gs_make
+ touch build-stamp
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp
+ gs_make distclean clean
+ dh_clean
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+ gs_make install DESTDIR=$(CURDIR)/debian/biococoa.app GNUSTEP_INSTALLATION_DOMAIN=SYSTEM
+ find `pwd`/debian/biococoa.app -name "*.plist" -exec chmod -x {} \;
+ dh_install debian/*.desktop usr/share/applications/
+ rm $(CURDIR)/debian/*.app/usr/lib/GNUstep/Applications/*.app/Resources/*.desktop
+
+# Build architecture-independent files here.
+binary-indep: build install
+# We have nothing to do by default.
+
+# Build architecture-dependent files here.
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ install -m 644 debian/lintian-override $(CURDIR)/debian/biococoa.app/usr/share/lintian/overrides/biococoa.app
+ dh_installdocs
+ dh_installmenu
+ dh_installman
+ 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/biococoa/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
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