adun.app (0.81-4) debian-dir only changes

Summary

 debian/AdunCore.1                         |   85 +++++++++++++++
 debian/AdunServer.1                       |   35 ++++++
 debian/README.Debian                      |   41 +++++++
 debian/README.source                      |    8 +
 debian/UL.1                               |   25 ++++
 debian/UL.desktop                         |    8 +
 debian/changelog                          |  164 ++++++++++++++++++++++++++++++
 debian/compat                             |    1 
 debian/control                            |   28 +++++
 debian/copyright                          |   42 +++++++
 debian/manpages                           |    3 
 debian/menu                               |    5 
 debian/patches/00list                     |    3 
 debian/patches/05_no-plugin-script.dpatch |   18 +++
 debian/patches/15_link-properly.dpatch    |  116 +++++++++++++++++++++
 debian/patches/20_paths.dpatch            |   41 +++++++
 debian/rules                              |  123 ++++++++++++++++++++++
 debian/source/format                      |    1 
 debian/upstream-metadata.yaml             |   23 ++++
 debian/watch                              |    7 +
 20 files changed, 777 insertions(+)

    
download this patch

Patch contents

--- adun.app-0.81.orig/debian/watch
+++ adun.app-0.81/debian/watch
@@ -0,0 +1,7 @@
+version=3
+# Upstream used a broken versioning scheme where a major release is
+# 0.7 and point releases are 0.71, 0.72, etc.  Hopefully this is no
+# longer a concern, but if it turns out it is, uncommenting and
+# amending the line below should "fix" the watchfile accordingly.
+#opts=uversionmangle=s/^0\.([78])(\d)/0.$1.$2/, \
+ http://download.gna.org/adun/Adun-([\d.]+)\.tar\.gz
--- adun.app-0.81.orig/debian/copyright
+++ adun.app-0.81/debian/copyright
@@ -0,0 +1,42 @@
+This package was debianized by Gürkan Sengün <gurkan@linuks.mine.nu> on
+Sun,  3 Sep 2006 18:34:19 +0200.
+
+It was downloaded from http://diana.imim.es/Adun
+
+Upstream Authors:
+
+    Michael A. Johnston,
+    I. F. Galvn,
+    Jordi Vill-Freixa,
+    Alexander V. Diemand (MolTalk)
+
+Copyright: © 2003-2007 Alexander V. Diemand (MolTalk)
+           © 2005-2009 Michael A. Johnston
+           © 2005-2009 Jordi Vill-Freixa
+
+License:
+    Adun 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
+
+Note that because Adun dynamically links against a version of GSL that
+is under GPLv3+, Debian distributes the adun.app package under GPLv3+.
+
+On Debian systems, the complete text of the GNU General Public License
+can be found in /usr/share/common-licenses/GPL file.
+
+The Debian packaging is
+   © 2006, Gürkan Sengün <gurkan@linuks.mine.nu> and
+   © 2009, Yavor Doganov <yavor@gnu.org>
+is licensed under the GPL, see `/usr/share/common-licenses/GPL'.
--- adun.app-0.81.orig/debian/manpages
+++ adun.app-0.81/debian/manpages
@@ -0,0 +1,3 @@
+debian/UL.1
+debian/AdunCore.1
+debian/AdunServer.1
--- adun.app-0.81.orig/debian/UL.desktop
+++ adun.app-0.81/debian/UL.desktop
@@ -0,0 +1,8 @@
+[Desktop Entry]
+Type=Application
+Name=Adun
+Comment=Biomoleculal Simulator
+Version=1.0
+Icon=/usr/lib/GNUstep/Applications/UL.app/Resources/icon.tiff
+Categories=Education;Science;Biology;
+Exec=UL
--- adun.app-0.81.orig/debian/changelog
+++ adun.app-0.81/debian/changelog
@@ -0,0 +1,164 @@
+adun.app (0.81-4) unstable; urgency=low
+
+  * debian/rules (mipsen-flags): New variable, conditionally define only
+    when building on mips/mipsel as a workaround for gcc-4.4 bug #519006.
+    (build-stamp): Use it.
+  * debian/control (Build-Depends): Remove obsolete version requirement
+    for libgnustep-gui-dev.
+    (Standards-Version): Compliant with 3.9.1 (no changes required).
+
+ -- Yavor Doganov <yavor@gnu.org>  Mon, 09 Aug 2010 16:16:34 +0300
+
+adun.app (0.81-3) unstable; urgency=low
+
+  [ Charles Plessy ]
+  * Documented informations in ‘debian/upstream-metadata.yaml’.
+
+  [ Yavor Doganov ]
+  * debian/rules: Export GNUSTEP_MAKEFILES and avoid gs_make.  All uses
+    updated.  Add verbose comments about GNUstep-specific stuff for the
+    benefit of other debian-med contributors.
+    (OPTFLAG): Remove and simplify noopt handling to be compatible with
+    gnustep-make/2.4.x (Closes: #581886).
+  * debian/control (Depends): Add ${misc:Depends}.
+    (Standards-Version): Compliant with 3.8.4 (no changes needed).
+  * debian/source/format: New file.
+
+ -- Yavor Doganov <yavor@gnu.org>  Thu, 20 May 2010 17:06:31 +0300
+
+adun.app (0.81-2) unstable; urgency=high
+
+  * debian/rules (build-stamp): Pass GNUSTEP_MAKE_PARALLEL_BUILDING=no;
+    fixes FTBFS with gnustep-make/2.2.0.  (Closes: #560514)
+
+ -- Yavor Doganov <yavor@gnu.org>  Fri, 11 Dec 2009 10:55:02 +0200
+
+adun.app (0.81-1) unstable; urgency=low
+
+  [ Andreas Tille ]
+  * Fixed watch file (Thanks to Daniel Leidert <daniel.leidert@wgdd.de>)
+    Closes: #520917
+  * Standards-Version: 3.8.1 (no changes needed)
+
+  [ David Paleino ]
+  * Using DM-Upload-Allowed instead of the XS- version.
+  * Fixing Vcs-* fields.
+
+  [ Yavor Doganov ]
+  * New upstream release.
+  * debian/compat: Set to 7.
+  * debian/control (Uploaders): Reluctantly add myself.
+    (Section): Change to gnustep to match the override.
+    (Build-Depends): Bump debhelper to >= 7.  Add imagemagick for the icon
+    conversion.
+    (Standards-Version): Claim compliance with 3.8.3.
+    (Depends): Add ${gnustep:Depends}.
+  * debian/patches/10_gcc-4.3-inline.dpatch:
+  * debian/patches/25_mipsel-ftbfs.dpatch: Remove; fixed upstream.
+  * debian/patches/15_link-properly.dpatch: Update and remove the
+    workaround for the GSL linking issue; fixed in binutils
+    (http://sourceware.org/ml/binutils/2009-01/msg00413.html).
+  * debian/patches/20_paths.dpatch: Refresh.
+  * debian/patches/00list: Update.
+  * debian/rules (external): New variable.
+    (build-stamp): Convert the icon in XPM format.
+    (install): Use dh_prep instead of dh_clean -k.  Install the XPM icon.
+    (clean-patched): Don't make the `clean' target, `distclean' is
+    sufficient.  Delete the generated icon.
+  * debian/UL.desktop: Set Version to 1.0, add Icon field.
+  * debian/menu: Add icon.
+  * debian/watch: Comment out the uversionmangle option, does harm with
+    the current state of affairs.
+  * debian/copyright: Update copyright years.  Mention that the package is
+    distributed under GPLv3+.
+  * debian/README.source: New file.
+
+  [ Andreas Tille ]
+  * debian/copyright: Use © as copyright symbol because (C) is not
+    considered as a valid way to express the copyright ownership any more
+  * debian/control: More verbose long description
+
+ -- Yavor Doganov <yavor@gnu.org>  Thu, 08 Oct 2009 08:47:14 +0300
+
+adun.app (0.8.2-1) unstable; urgency=low
+
+  * QA upload.
+
+  [ Gürkan Sengün ]
+  * New upstream version.
+  * GNUstep transition.
+    + Updated debian/rules.
+  * Added a desktop file.
+  * Applied patch to fix FTBFS with GCC 4.3, thanks to Martin Michlmayr.
+    (Closes: #416859)
+
+  [ Yavor Doganov ]
+  * debian/control (Maintainer): Package is orphaned, set to the Debian QA
+    Group.
+    (Standards-Version): Claim compliance with 3.7.3; no changes needed.
+    (Build-Depends): Add dpatch; list all build-deps one per line.  Bump
+    debhelper to >= 6.
+    (Recommends): Add gnuplot.
+  * debian/compat: Set to level 6.
+  * debian/dirs: Delete.
+  * debian/rules: Include /usr/share/dpatch/dpatch.make and adjust all
+    rules to use it.  Do not source GNUstep.sh (Closes: #450469).
+    (LDFLAGS, d_app): Define.
+    (OPTFLAG): New conditionally defined variable (support for `noopt').
+    (build-stamp): Prepend MAKELEVEL=0 before make so that conditionals in
+    some of the makefiles relying on this internal variable actually work.
+    (install): Install the private libraries in /usr/lib/adun.app.  Remove
+    the executable bit of some files and delete the empty directories.
+    (binary-arch): Invoke dh_link to make all symlinks policy-compliant.
+    Run `gsdh_gnustep' and move conditionally the Resources to /usr/share.
+  * debian/lintian-override: Delete.
+  * debian/UL.desktop: Add Comment field.
+  * debian/menu (section): Prepend `Biology'.
+    (longtitle): Add.
+  * debian/README.Debian: Add; instructions how to build and install the
+    plugins and the ResultsConverter tool.
+  * debian/AdunCore.1: New manpage.
+  * debian/AdunServer.1: Likewise.
+  * debian/UL.1: Link to AdunCore and AdunServer.
+  * debian/manpages: Add AdunCore.1 and AdunServer.1.
+  * debian/patches/05_no-plugin-script.dpatch: New patch, do not install
+    InstallPlugin.py.
+  * debian/patches/10_gcc-4.3-inline.dpatch: Actually add this patch;
+    modified since tbm's patch was for an old Adun version.
+  * debian/patches/15_link-properly.dpatch: New, link all objects with the
+    necessary libs and workaround #456898.
+  * debian/patches/20_paths.dpatch: New, fix some paths and settings.
+  * debian/patches/25_mipsel-ftbfs.dpatch: New, fixes FTBFS on mipsel
+    where $HOME is not readable; thanks Steve Langasek (Closes: #457723).
+  * debian/patches/00list: Create and populate.
+
+  [ Andreas Tille ]
+  * Maintainer: Debian-Med Packaging Team
+    <debian-med-packaging@lists.alioth.debian.org>
+    Closes: #454459
+  * Added watch file
+  * Added Vcs-Browser, Vcs-Svn, XS-DM-Upload-Allowed
+  * Uploaders: Andreas Tille <tille@debian.org>
+  * debian/rules: ifdef GS_MAKE_DIR condition to avoid problems on
+    systems that do not have gnustep-make installed
+
+ -- Andreas Tille <tille@debian.org>  Mon, 21 Jan 2008 19:01:19 +0100
+
+adun.app (0.6-3) unstable; urgency=low
+
+  * Fix the FTBFS for non-i386 properly.
+
+ -- Gürkan Sengün <gurkan@linuks.mine.nu>  Mon, 23 Oct 2006 19:40:24 +0200
+
+adun.app (0.6-2) unstable; urgency=low
+
+  * Added Defs for the archs that failed to build.
+
+ -- Gürkan Sengün <gurkan@linuks.mine.nu>  Mon, 23 Oct 2006 17:07:59 +0200
+
+adun.app (0.6-1) unstable; urgency=low
+
+  * Initial release. (Closes: #385340)
+  * Added Defs/GNU/kFreeBSD_i586.def to build on GNU/kFreeBSD.
+
+ -- Gürkan Sengün <gurkan@linuks.mine.nu>  Sun,  3 Sep 2006 18:34:19 +0200
--- adun.app-0.81.orig/debian/README.Debian
+++ adun.app-0.81/debian/README.Debian
@@ -0,0 +1,41 @@
+Adun for Debian
+---------------
+
+The Debian package adun.app is capable of running simulations, but to
+perform analysis on the results you need to build and install various
+plugins.  Upstream's build system and the operation of Adun are
+designed in a way that assumes plugins to be installed under
+$HOME/adun.  Although not trivial, it is possible to modify the
+Debian package so that the plugins are installed by default.  However,
+this would require that every user modifies the extra available
+plugins at http://download.gna.org/adun/ in order to build and use
+them.
+
+Here are some basic instructions to build and install the plugins that
+come with the adun.app package:
+
+1) Start the application (UL) once so that the directories are
+   created.
+2) Obtain the source.
+
+   $ apt-get source adun.app && cd adun.app-*
+
+3) Install the build dependencies.
+
+   # aptitude install build-essential
+   # apt-get build-dep adun.app
+
+4) Build and install the Plugins.
+
+   $ PATH=`pwd`/Tools:"${PATH}" gs_make -C Plugins
+
+5) Optionally, build and install the ResultsConverter tool.
+
+   $ gs_make install -C Tools LDFLAGS=-Wl,-rpath,/usr/lib/adun.app \
+       ADDITIONAL_LIB_DIRS=-L/usr/lib/adun.app
+
+   The tool will be installed by default in $HOME/GNUstep/Tools so you
+   might want to add this directory to your PATH or move/symlink the
+   binary.
+
+ -- Yavor Doganov <yavor@gnu.org>, Sat, 19 Jan 2008 14:19:24 +0200
--- adun.app-0.81.orig/debian/README.source
+++ adun.app-0.81/debian/README.source
@@ -0,0 +1,8 @@
+This package uses dpatch (in a fairly standard/straightforward way) to
+manage all modifications to the upstream source.  Please see
+
+  /usr/share/doc/dpatch/README.source.gz
+
+for further instructions.
+
+ -- Yavor Doganov <yavor@gnu.org>, Thu,  8 Oct 2009 00:59:53 +0300
--- adun.app-0.81.orig/debian/compat
+++ adun.app-0.81/debian/compat
@@ -0,0 +1 @@
+7
--- adun.app-0.81.orig/debian/menu
+++ adun.app-0.81/debian/menu
@@ -0,0 +1,5 @@
+?package(adun.app):needs="X11" \
+  section="Applications/Science/Biology" \
+  title="Adun" command="/usr/bin/UL" \
+  longtitle="Biomolecular Simulator" \
+  icon="/usr/share/pixmaps/adun.xpm"
--- adun.app-0.81.orig/debian/rules
+++ adun.app-0.81/debian/rules
@@ -0,0 +1,123 @@
+#!/usr/bin/make -f
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+include /usr/share/dpatch/dpatch.make
+-include /usr/share/GNUstep/debian/config.mk
+
+export GNUSTEP_MAKEFILES := $(GS_MAKE_DIR)
+
+d_app := $(CURDIR)/debian/adun.app
+LDFLAGS := -Wl,-z,defs -Wl,--as-needed -Wl,-rpath,/usr/lib/adun.app
+
+# Avoid building the bundled StepTalk framework.
+export external := no
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+optim := debug=yes
+endif
+
+# Workaround for gcc-4.4 bug 519006.
+ifneq (,$(findstring mips,$(DEB_BUILD_ARCH)))
+mipsen-flags := ADDITIONAL_OBJCFLAGS=-g0 ADDITIONAL_CFLAGS=-g0
+endif
+
+build: patch build-stamp
+
+build-stamp:
+	dh_testdir
+# Upstream's makefiles have conditionals based on $(MAKELEVEL) so that
+# building separate components and the whole package from toplevel
+# works.  They all evaluate to false when building the Debian package,
+# because debian/rules is itself a makefile -- resetting MAKELEVEL
+# does the trick.
+# GNUstep Make 2.2.0 gained support for parallel (-jN) building, which
+# is implemented by delegating the actual compilation to sub-makes
+# which run in parallel (i.e. the build system invokes
+# $(MAKE) -f GNUmakefile ...).  This is the default mode of operation,
+# even if no -j option is used.  GNUSTEP_MAKE_PARALLEL_BUILDING=no
+# prevents messing the MAKELEVEL again.
+	MAKELEVEL=0 $(MAKE) GNUSTEP_MAKE_PARALLEL_BUILDING=no $(optim) \
+	  messages=yes LDFLAGS="$(LDFLAGS)" $(mipsen-flags)
+	convert UL/Resources/icon.tiff -resize 32x32 adun.xpm
+	touch $@
+
+clean: clean-patched unpatch
+
+clean-patched:
+	dh_testdir
+	dh_testroot
+ifdef GS_MAKE_DIR
+# This conditional and the ignored config.mk include at the top is to
+# make life easier for the usual debian-med contributors who do not
+# have gnustep-make installed.  Otherwise, the package will fail to
+# build before pbuilder/etc. even manage to install the build-deps
+# because the clean rule is doomed to fail.
+	$(MAKE) distclean
+endif
+	dh_clean build-stamp adun.xpm
+
+install: build
+	dh_testdir
+	dh_testroot
+	dh_prep
+# Install private libraries in /usr/lib/adun.app; fixes a Policy
+# `SHOULD' violation (10.2).
+	dh_installdirs usr/lib/adun.app
+	$(MAKE) install messages=yes DESTDIR=$(d_app) \
+	  GNUSTEP_SYSTEM_LIBRARIES=/usr/lib/adun.app \
+	  GNUSTEP_INSTALLATION_DOMAIN=SYSTEM
+
+	find  $(d_app)/usr/lib/GNUstep/Applications/UL.app/Resources \
+	  -type f -exec chmod -x '{}' \;
+	chmod -x $(d_app)/usr/lib/GNUstep/Frameworks/ULFramework.framework/Versions/0/Resources/ForceFields/Enzymix/*.ffml
+# Delete empty directories (fixes a lintian warning).
+	rm -r $(d_app)/usr/include/GNUstep/Framework \
+	      $(d_app)/usr/lib/GNUstep/Tools
+# Delete the invalid .desktop file and install ours.
+	rm $(d_app)/usr/lib/GNUstep/Applications/*.app/Resources/*.desktop
+	install -D -m 644 debian/*.desktop \
+	  $(d_app)/usr/share/applications/UL.desktop
+	dh_install adun.xpm usr/share/pixmaps/
+
+# Build architecture-independent files here.
+binary-indep: build install
+# We have nothing to do by default.
+
+# Build architecture-dependent files here.
+binary-arch: build install
+	dh_testdir
+	dh_testroot
+	dh_installchangelogs 
+	dh_installdocs
+	dh_installmenu
+	dh_installman
+	dh_link
+	gsdh_gnustep
+ifeq ($(GS_USE_FHS),yes)
+# On (official) Debian systems, this conditional is always true --
+# arch-independent Resources are moved to /usr/share, and the
+# Resources dir in the app bundle is a symlink (this approach was
+# explicitly approved by the Debian Release Team back in 2005).
+# The GNUstep LiveCD is based on Debian and its maintainer (who as a
+# coincident :-) is also a member of the Debian GNUstep team) doesn't
+# like FHS very much.  Setting GS_USE_FHS=no allows to rebuild the
+# package(s) with more relaxed (and not Debian Policy-compliant)
+# layout.
+	dh_installdirs usr/share/GNUstep
+	mv $(d_app)$(GNUSTEP_SYSTEM_APPS)/UL.app/Resources \
+	   $(d_app)/usr/share/GNUstep/UL.app
+	dh_link usr/share/GNUstep/UL.app \
+	  $(GNUSTEP_SYSTEM_APPS)/UL.app/Resources
+endif
+	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
--- adun.app-0.81.orig/debian/UL.1
+++ adun.app-0.81/debian/UL.1
@@ -0,0 +1,25 @@
+.TH UL 1 "September  3, 2006"
+.SH NAME
+UL \- Molecular Simulator
+.SH SYNOPSIS
+.B UL
+.SH DESCRIPTION
+This manual page documents briefly the
+.B UL
+command.
+.PP
+\fBUL\fP is a new extendible molecular simulation program that also
+includes data management and analysis capabilities.
+.SH SEE ALSO
+.BR AdunCore (1),
+.BR AdunServer (1),
+.BR GNUstep (7),
+.BR defaults (1),
+.BR BioCocoa (1).
+.br
+.SH AUTHOR
+UL was written by Michael A. Johnston, I. F. Galvn, Jordi Vill-Freixa,
+Alexander V. Diemand.
+.PP
+This manual page was written by G\[:u]rkan Seng\[:u]n <gurkan@linuks.mine.nu>,
+for the Debian project (but may be used by others).
--- adun.app-0.81.orig/debian/AdunCore.1
+++ adun.app-0.81/debian/AdunCore.1
@@ -0,0 +1,85 @@
+.TH ADUNCORE 1 "January 19, 2008"
+.SH NAME
+AdunCore \- core module of the Adun molecular simulator
+.SH SYNOPSIS
+.B AdunCore
+[\fIOPTIONS\fR]
+.SH DESCRIPTION
+This manual page documents briefly the
+.B AdunCore
+command.
+.PP
+.B AdunCore
+is the core module of the
+.IR Adun
+molecular simulator.  It is launched automatically from the
+.IR UL
+GUI but can be used from the GNU/Linux console as well.  Options to
+.B AdunCore
+must be specified as value pairs in the form `\-Option Value'.  The
+following options are available:
+.TP
+.BR \-Template
+A valid Adun template.  This is the only option that is mandatory.
+.TP
+.BR \-ExternalObjects
+A dictionary in plist format.  Its contents extend the externalObjects
+section of the template.  If there are duplicate keys this dictionary
+takes precedence.
+.TP
+.BR \-SimulationOutputDir
+Directory where simulation data directory will be stored.  (Default value:
+SimulationOutput)
+.TP
+.BR \-ControllerOutputDir
+Directory where controller data will be stored.  (Default value:
+ControllerOutput)
+.TP
+.BR \-CreateLogFiles
+If
+.IR YES
+log files are created.  If 
+.IR NO
+they are not.  (Default value: YES)
+.TP
+.BR \-LogFile
+File where the program output will be written.  (Default value:
+AdunCore.log)
+.TP
+.BR \-ErrorFile
+File where program errors and warnings will be written.  (Default
+value: AdunCore.errors)
+.TP
+.BR \-RedirectOutput
+If
+.IR YES
+the log files will be moved to the simulation output
+directory. (Default value: YES)
+.TP
+.BR \-RunInteractive
+If
+.IR YES
+the simulation loop is spawned as a separate thread.  The main thread
+then enters a run loop and can serve external requests.  If
+.IR NO
+then interaction is not possible with the simulation.  (Default value:
+NO)
+.TP
+.BR \-ConnectToAdServer
+If
+.IR YES
+the simulation registers its existance with a local AdServer daemon.
+This allows the simulation to be viewed and controlled from the Adun
+GUI.  (Default value: NO)
+.PP
+.SH SEE ALSO
+.BR UL (1),
+.BR AdunServer (1),
+.BR GNUstep (7).
+.br
+.SH AUTHOR
+AdunServer was written by Michael A. Johnston, I. F. Galvn, Jordi
+Vill-Freixa, Alexander V. Diemand.
+.PP
+This manual page was written by Yavor Doganov <yavor@gnu.org> for the
+Debian project (but may be used by others).
--- adun.app-0.81.orig/debian/upstream-metadata.yaml
+++ adun.app-0.81/debian/upstream-metadata.yaml
@@ -0,0 +1,23 @@
+Archive: Gna
+DOI: 10.1002/jcc.20312
+Homepage: http://diana.imim.es/Adun
+Name: Adun
+PMID: 16175583
+Reference:
+ Author: Michael A. Johnston, Ignacio Fdez. Galván and Jordi Villà-Freixa
+ Title: Framework-based design of a new all-purpose molecular simulation application: The Adun simulator
+ Journal: J. Comp. Chem.
+ Volume: 26
+ Number: 15
+ Pages: 1647-1659
+ Year: 2005
+ URL: http://www3.interscience.wiley.com/journal/112094040/abstract
+Screenshots: http://cbbl.imim.es:8080/Adun/screenshots
+Watch: |
+ version=3
+ # Upstream used a broken versioning scheme where a major release is
+ # 0.7 and point releases are 0.71, 0.72, etc.  Hopefully this is no
+ # longer a concern, but if it turns out it is, uncommenting and
+ # amending the line below should "fix" the watchfile accordingly.
+ #opts=uversionmangle=s/^0\.([78])(\d)/0.$1.$2/, \
+  http://download.gna.org/adun/Adun-([\d.]+)\.tar\.gz
--- adun.app-0.81.orig/debian/control
+++ adun.app-0.81/debian/control
@@ -0,0 +1,28 @@
+Source: adun.app
+Section: gnustep
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille@debian.org>,
+	   Yavor Doganov <yavor@gnu.org>
+Build-Depends: debhelper (>= 7),
+	       dpatch,
+	       libgnustep-gui-dev,
+	       libgsl0-dev,
+	       imagemagick
+Standards-Version: 3.9.1
+Homepage: http://diana.imim.es/Adun
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/adun.app/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/adun.app/trunk/
+
+Package: adun.app
+Architecture: any
+Depends: ${shlibs:Depends},
+	 ${misc:Depends},
+	 ${gnustep:Depends}
+Recommends: gnuplot
+Description: Molecular Simulator for GNUstep
+ Adun is a biomolecular simulator that also includes data management and
+ analysis capabilities.  It was developed at the Computational Biophysics
+ and Biochemistry Laboratory, a part of the Research Unit on Biomedical
+ Informatics of the UPF.
--- adun.app-0.81.orig/debian/AdunServer.1
+++ adun.app-0.81/debian/AdunServer.1
@@ -0,0 +1,35 @@
+.TH ADUNSERVER 1 "January 19, 2008"
+.SH NAME
+AdunServer \- server for the Adun molecular simulator
+.SH SYNOPSIS
+.B AdunServer
+.SH DESCRIPTION
+This manual page documents briefly the
+.B AdunServer
+command.
+.PP
+.B AdunServer
+is a
+.IR GNUstep
+program that runs as a daemon, serving connections and controlling the
+interaction between the Adun GUI
+.IR UL
+and
+.IR AdunCore .
+.PP
+.IR UL
+will detect that 
+.B AdunServer 
+is not running and will ask the user to launch it.
+.PP
+.SH SEE ALSO
+.BR UL (1),
+.BR AdunCore (1),
+.BR GNUstep (7).
+.br
+.SH AUTHOR
+AdunServer was written by Michael A. Johnston, I. F. Galvn, Jordi
+Vill-Freixa, Alexander V. Diemand.
+.PP
+This manual page was written by Yavor Doganov <yavor@gnu.org> for the
+Debian project (but may be used by others).
--- adun.app-0.81.orig/debian/source/format
+++ adun.app-0.81/debian/source/format
@@ -0,0 +1 @@
+1.0
--- adun.app-0.81.orig/debian/patches/20_paths.dpatch
+++ adun.app-0.81/debian/patches/20_paths.dpatch
@@ -0,0 +1,41 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 20_paths.dpatch by Yavor Doganov <yavor@gnu.org>
+## Forwarded: no
+##  This patch contains `x-terminal-emulator', which is specific to Debian.
+## DP: Adjust some essential paths.
+
+@DPATCH@
+diff -urNad adun.app-0.8.2~/UL/AdunServer/main.m adun.app-0.8.2/UL/AdunServer/main.m
+--- adun.app-0.8.2~/UL/AdunServer/main.m	2007-07-31 16:28:35.000000000 +0300
++++ adun.app-0.8.2/UL/AdunServer/main.m	2008-01-14 00:35:16.000000000 +0200
+@@ -39,7 +39,7 @@
+ 	[defaults setObject: [NSHomeDirectory() stringByAppendingPathComponent: @".adun/AdunServer.log"]
+ 		     forKey: @"LogFile"];
+ #else
+-	adunCorePath = [NSHomeDirectory() stringByAppendingPathComponent: @"GNUstep/Tools"];
++	adunCorePath = @"/usr/bin";
+ 	[defaults setObject: adunCorePath forKey: @"AdunCorePath"];
+ 	[defaults setObject: [NSHomeDirectory() stringByAppendingPathComponent: @"adun/AdunServer.log"]
+ 		forKey: @"LogFile"];
+diff -urNad adun.app-0.8.2~/UL/AdunServer/ViewController.m adun.app-0.8.2/UL/AdunServer/ViewController.m
+--- adun.app-0.8.2~/UL/ViewController.m	2008-01-14 00:31:57.000000000 +0200
++++ adun.app-0.8.2/UL/ViewController.m	2008-01-14 00:32:09.000000000 +0200
+@@ -84,7 +84,7 @@
+ #ifdef GNUSTEP 
+ 	[defaults setObject: [NSHomeDirectory() stringByAppendingPathComponent: @"adun/UL.log"]
+ 		forKey: @"LogFile"];
+-	[defaults setObject: @"gedit" forKey: @"Editor"];
++	[defaults setObject: @"x-terminal-emulator -e editor" forKey: @"Editor"];
+ #else	
+ 	[defaults setObject: [NSHomeDirectory() stringByAppendingPathComponent: @".adun/UL.log"]
+ 		     forKey: @"LogFile"];
+@@ -434,8 +433,7 @@
+ 				stringForKey: @"AdunServerPath"];
+ 		launchPath = [launchPath stringByAppendingPathComponent: @"AdunServer"];		
+ #else				
+-		launchPath = [NSHomeDirectory() 
+-				stringByAppendingPathComponent: @"GNUstep/Tools/AdunServer"];
++		launchPath = @"/usr/bin/AdunServer";
+ #endif		
+ 		NS_DURING
+ 		{
--- adun.app-0.81.orig/debian/patches/15_link-properly.dpatch
+++ adun.app-0.81/debian/patches/15_link-properly.dpatch
@@ -0,0 +1,116 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 15_build.dpatch by Yavor Doganov <yavor@gnu.org>
+## Forwarded: not yet
+## DP: Link all objects with the libs they use symbols from.
+
+@DPATCH@
+diff -urNad adun.app-0.8.2~/Kernel/AdunKernel/GNUmakefile adun.app-0.8.2/Kernel/AdunKernel/GNUmakefile
+--- adun.app-0.8.2~/Kernel/AdunKernel/GNUmakefile	2008-01-17 12:37:12.000000000 +0200
++++ adun.app-0.8.2/Kernel/AdunKernel/GNUmakefile	2008-01-17 12:38:28.000000000 +0200
+@@ -9,7 +9,7 @@
+ VERSION = 0.13
+ FRAMEWORK_NAME =AdunKernel 
+ AdunKernel_LIB_DIRS = -L../Base/$(GNUSTEP_OBJ_DIR) -L$(GSL_LIB_DIR) 
+-AdunKernel_LIBRARIES_DEPEND_UPON = -ladun_base -lgnustep-base -lgsl -lgslcblas
++AdunKernel_LIBRARIES_DEPEND_UPON = -ladun_base -lgsl -lgslcblas -lm $(FND_LIBS) $(OBJC_LIBS)
+ endif
+ 
+ export KERNEL_COMPILER ?= gcc
+diff -urNad adun.app-0.8.2~/Kernel/GNUmakefile adun.app-0.8.2/Kernel/GNUmakefile
+--- adun.app-0.8.2~/Kernel/GNUmakefile	2008-01-17 12:37:12.000000000 +0200
++++ adun.app-0.8.2/Kernel/GNUmakefile	2008-01-17 12:38:28.000000000 +0200
+@@ -10,7 +10,7 @@
+ ifeq ($(ADUN_LIBRARY_COMPILER), icc)
+ 	AdunCore_TOOL_LIBS =   -lAdunKernel -ladun_base -lgsl -lgslcblas -lfl -limf -lsvml -lm -ladun_base 
+ else
+-	AdunCore_TOOL_LIBS = -lAdunKernel -ladun_base  -lgsl -lgslcblas 
++	AdunCore_TOOL_LIBS = -lAdunKernel -ladun_base
+ endif
+ 
+ GNUSTEP_INSTALLATION_DOMAIN=USER
+diff -urNad adun.app-0.8.2~/MolTalk/GNUmakefile.preamble adun.app-0.8.2/MolTalk/GNUmakefile.preamble
+--- adun.app-0.8.2~/MolTalk/GNUmakefile.preamble	2008-01-17 12:37:12.000000000 +0200
++++ adun.app-0.8.2/MolTalk/GNUmakefile.preamble	2008-01-17 12:38:28.000000000 +0200
+@@ -63,7 +63,7 @@
+ ifeq ($(GNUSTEP_TARGET_OS),mingw32)
+ LIBRARIES_DEPEND_UPON += -lgnustep-base -lobjc
+ endif
+-LIBRARIES_DEPEND_UPON +=
++LIBRARIES_DEPEND_UPON += -lm $(FND_LIBS) $(OBJC_LIBS)
+ 
+ #
+ # Flags dealing with installing and uninstalling
+diff -urNad adun.app-0.8.2~/UL/AdunServer/GNUmakefile adun.app-0.8.2/UL/AdunServer/GNUmakefile
+--- adun.app-0.8.2~/UL/AdunServer/GNUmakefile	2007-05-30 20:36:59.000000000 +0300
++++ adun.app-0.8.2/UL/AdunServer/GNUmakefile	2008-01-17 12:39:12.000000000 +0200
+@@ -18,7 +18,7 @@
+ #
+ 
+ AdunServer_LIB_DIRS +=  -L../ULFramework/ULFramework.framework/Versions/Current -L../XMLLib/obj  
+-AdunServer_TOOL_LIBS +=  -lXMLLib -lULFramework
++AdunServer_TOOL_LIBS +=  -lXMLLib -lULFramework -ladun_base -lAdunKernel -lMolTalk
+ 
+ #
+ # Resource files
+diff -urNad adun.app-0.8.2~/UL/AdunServer/GNUmakefile.preamble adun.app-0.8.2/UL/AdunServer/GNUmakefile.preamble
+--- adun.app-0.8.2~/UL/AdunServer/GNUmakefile.preamble	2008-01-17 12:37:12.000000000 +0200
++++ adun.app-0.8.2/UL/AdunServer/GNUmakefile.preamble	2008-01-17 12:38:28.000000000 +0200
+@@ -15,9 +15,7 @@
+ ADDITIONAL_CFLAGS += 
+ 
+ # Additional flags to pass to the linker
+-ifeq ($(MAKELEVEL), 3)
+-ADDITIONAL_LDFLAGS += -ladun_base -lAdunKernel -lMolTalk 
+-endif
++ADDITIONAL_LDFLAGS +=  
+ 
+ # Additional include directories the compiler should search
+ ifeq ($(MAKELEVEL),3)
+diff -urNad adun.app-0.8.2~/UL/GNUmakefile adun.app-0.8.2/UL/GNUmakefile
+--- adun.app-0.8.2~/UL/GNUmakefile	2008-01-17 12:37:12.000000000 +0200
++++ adun.app-0.8.2/UL/GNUmakefile	2008-01-17 12:38:28.000000000 +0200
+@@ -25,7 +25,7 @@
+ 
+ UL_LIB_DIRS += -L./XMLLib/obj -L. -L./ULFramework/ULFramework.framework/Versions/Current
+ UL_HEADER_FILES_INSTALL_DIR = UL/
+-UL_OBJC_LIBS =  -lXMLLib -lULFramework -lAdunKernel -lMolTalk -ladun_base  -lgsl -lgslcblas
++UL_GUI_LIBS =  -lXMLLib -lULFramework -lAdunKernel -lMolTalk -ladun_base
+ 
+ GNUSTEP_INSTALLATION_DOMAIN = USER
+ #
+diff -urNad adun.app-0.8.2~/UL/ULFramework/GNUmakefile adun.app-0.8.2/UL/ULFramework/GNUmakefile
+--- adun.app-0.8.2~/UL/ULFramework/GNUmakefile	2008-01-17 12:37:12.000000000 +0200
++++ adun.app-0.8.2/UL/ULFramework/GNUmakefile	2008-01-17 12:38:28.000000000 +0200
+@@ -14,7 +14,7 @@
+ #
+ # Libraries
+ #
+-ULFramework_LIBRARIES_DEPEND_UPON += -lAdunKernel -lMolTalk -lXMLLib
++ULFramework_LIBRARIES_DEPEND_UPON += -lAdunKernel -lMolTalk -lXMLLib -lgsl -lgslcblas -lm $(FND_LIBS) $(OBJC_LIBS)
+ 
+ ifeq ($(MAKELEVEL),3)
+ ULFramework_LIB_DIRS =  -L$(ADUN_SOURCE_DIR)/Kernel/AdunKernel/AdunKernel.framework/Versions/Current -L$(ADUN_SOURCE_DIR)/MolTalk/MolTalk.framework/Versions/Current 
+diff -urNad adun.app-0.8.2~/UL/XMLLib/GNUmakefile.preamble adun.app-0.8.2/UL/XMLLib/GNUmakefile.preamble
+--- adun.app-0.8.2~/UL/XMLLib/GNUmakefile.preamble	2008-01-17 12:37:12.000000000 +0200
++++ adun.app-0.8.2/UL/XMLLib/GNUmakefile.preamble	2008-01-17 12:38:28.000000000 +0200
+@@ -18,5 +18,6 @@
+ ADDITIONAL_INCLUDE_DIRS += -I../ -I../../Kernel -I../../Kernel/AdunKernel/Headers -I$(HOME)/GNUstep/Library/Headers
+ 
+ # Additional library directories the linker should search
+-ADDITIONAL_LIB_DIRS += 
++ADDITIONAL_LIB_DIRS += -L$(ADUN_SOURCE_DIR)/Kernel/AdunKernel/AdunKernel.framework/Versions/Current
+ 
++LIBRARIES_DEPEND_UPON += -lAdunKernel $(FND_LIBS) $(OBJC_LIBS)
+diff -urNad adun.app-0.8.2~/Kernel/Base/GNUmakefile.preamble adun.app-0.8.2/Kernel/Base/GNUmakefile.preamble
+--- adun.app-0.8.2~/Kernel/Base/GNUmakefile.preamble	2008-01-17 12:37:12.000000000 +0200
++++ adun.app-0.8.2/Kernel/Base/GNUmakefile.preamble	2008-01-17 12:38:28.000000000 +0200
+@@ -17,7 +17,8 @@
+ ADDITIONAL_CFLAGS += 
+ 
+ # Additional flags to pass to the linker
+-ADDITIONAL_LDFLAGS +=  -lgsl -lgslcblas
++ADDITIONAL_LDFLAGS +=
++LIBRARIES_DEPEND_UPON += -lgsl -lm
+ 
+ # Additional include directories the compiler should search
+ ADDITIONAL_INCLUDE_DIRS += -I$(GSL_INCLUDE_DIR)
--- adun.app-0.81.orig/debian/patches/05_no-plugin-script.dpatch
+++ adun.app-0.81/debian/patches/05_no-plugin-script.dpatch
@@ -0,0 +1,18 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 05_no-plugin-script.dpatch by Yavor Doganov <yavor@gnu.org>
+## Forwarded: no
+##  This patch is specific to Debian.
+## DP: Do not install the script for plugin installation.
+
+@DPATCH@
+diff -urNad adun.app-0.8.2~/GNUmakefile.postamble adun.app-0.8.2/GNUmakefile.postamble
+--- adun.app-0.8.2~/GNUmakefile.postamble	2007-06-04 14:11:12.000000000 +0300
++++ adun.app-0.8.2/GNUmakefile.postamble	2007-12-17 23:09:18.000000000 +0200
+@@ -16,7 +16,6 @@
+ # ResultsConverter depends on EnergyConverter & ConformationConverter plugins.
+ # Things to do after installing
+  after-install::
+-	cp Tools/InstallPlugin.py $(GNUSTEP_HOME)/$(GNUSTEP_USER_DIR_TOOLS)
+ 
+ # Things to do before uninstalling
+ # before-uninstall::
--- adun.app-0.81.orig/debian/patches/00list
+++ adun.app-0.81/debian/patches/00list
@@ -0,0 +1,3 @@
+05_no-plugin-script
+15_link-properly
+20_paths