--- 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 for the +Debian project (but may be used by others). --- 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/quilt/quilt.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/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 for the +Debian project (but may be used by others). --- adun.app-0.81.orig/debian/changelog +++ adun.app-0.81/debian/changelog @@ -0,0 +1,182 @@ +adun.app (0.81-5build1) raring; urgency=low + + * Rebuild for gnustep-gui 0.22 transition. + + -- Benjamin Drung Wed, 21 Nov 2012 16:47:08 +0100 + +adun.app (0.81-5) unstable; urgency=low + + * Use quilt instead of dpatch + * Apply patch provided by Andreas Moog (Thanks + to Andreas) to fix a build failure + Closes: 631641 (LP: 771041) + * Standards-Version: 3.9.2 (no changes needed) + * Debhelper 8 (control+compat) + * Corrected Vcs-URLs + + -- Andreas Tille Tue, 28 Jun 2011 10:38:55 +0200 + +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 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 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 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 ) + 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 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 + + Closes: #454459 + * Added watch file + * Added Vcs-Browser, Vcs-Svn, XS-DM-Upload-Allowed + * Uploaders: Andreas Tille + * debian/rules: ifdef GS_MAKE_DIR condition to avoid problems on + systems that do not have gnustep-make installed + + -- Andreas Tille 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 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 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 Sun, 3 Sep 2006 18:34:19 +0200 --- 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/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.$2/, \ + http://download.gna.org/adun/Adun-([\d.]+)\.tar\.gz --- adun.app-0.81.orig/debian/manpages +++ adun.app-0.81/debian/manpages @@ -0,0 +1,3 @@ +debian/UL.1 +debian/AdunCore.1 +debian/AdunServer.1 --- adun.app-0.81.orig/debian/README.Debian +++ adun.app-0.81/debian/README.Debian @@ -0,0 +1,41 @@ +Adun for Debian +--------------- + +The Debian package adun.app is capable of running simulations, but to +perform analysis on the results you need to build and install various +plugins. Upstream's build system and the operation of Adun are +designed in a way that assumes plugins to be installed under +$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 , Sat, 19 Jan 2008 14:19:24 +0200 --- 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 +DM-Upload-Allowed: yes +Uploaders: Andreas Tille , + Yavor Doganov +Build-Depends: debhelper (>= 8), + quilt, + libgnustep-gui-dev, + libgsl0-dev, + imagemagick +Standards-Version: 3.9.2 +Homepage: http://diana.imim.es/Adun +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/adun.app/trunk/ +Vcs-Svn: svn://svn.debian.org/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/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/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 , +for the Debian project (but may be used by others). --- adun.app-0.81.orig/debian/compat +++ adun.app-0.81/debian/compat @@ -0,0 +1 @@ +8 --- adun.app-0.81.orig/debian/copyright +++ adun.app-0.81/debian/copyright @@ -0,0 +1,42 @@ +This package was debianized by Gürkan Sengün 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 and + © 2009, Yavor Doganov +is licensed under the GPL, see `/usr/share/common-licenses/GPL'. --- 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/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 , Thu, 8 Oct 2009 00:59:53 +0300 --- adun.app-0.81.orig/debian/patches/20_paths.patch +++ adun.app-0.81/debian/patches/20_paths.patch @@ -0,0 +1,38 @@ +Name: 20_paths.patch +Author: Yavor Doganov +Forwarded: no +Description: This patch contains x-terminal-emulator, which is specific to Debian. + Adjust some essential paths. + +--- Adun-0.81.orig/UL/AdunServer/main.m ++++ Adun-0.81/UL/AdunServer/main.m +@@ -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"]; +--- Adun-0.81.orig/UL/ViewController.m ++++ Adun-0.81/UL/ViewController.m +@@ -82,7 +82,7 @@ + #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"]; +@@ -444,8 +444,7 @@ + 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/series +++ adun.app-0.81/debian/patches/series @@ -0,0 +1,4 @@ +05_no-plugin-script.patch +15_link-properly.patch +20_paths.patch +fix-implicit-pointer.patch --- adun.app-0.81.orig/debian/patches/05_no-plugin-script.patch +++ adun.app-0.81/debian/patches/05_no-plugin-script.patch @@ -0,0 +1,15 @@ +Name: 05_no-plugin-script.patch +Author: Yavor Doganov +Forwarded: no +Description: This patch is specific to Debian. + +--- Adun-0.81.orig/GNUmakefile.postamble ++++ Adun-0.81/GNUmakefile.postamble +@@ -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/fix-implicit-pointer.patch +++ adun.app-0.81/debian/patches/fix-implicit-pointer.patch @@ -0,0 +1,19 @@ +Description: AdunCellListHandler.m was missing a include for the function + AdCreateError, resulting in a forced-FTBFS on 64 bit archs. See + http://wiki.debian.org/ImplicitPointerConversions for more information. +Origin: Upstream CVS +Bug-Ubuntu: https://bugs.launchpad.net/bugs/771041 +Name: fix-implicit-pointer.patch +Author: Andreas Moog +Bug: 631641 + +--- Adun-0.81.orig/Kernel/AdunKernel/Framework/AdunCellListHandler.m ++++ Adun-0.81/Kernel/AdunKernel/Framework/AdunCellListHandler.m +@@ -22,6 +22,7 @@ + Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111 USA. + */ + #include "AdunKernel/AdunCellListHandler.h" ++#include "AdunKernel/AdFrameworkFunctions.h" + + /* + Category containing methods for creating and --- adun.app-0.81.orig/debian/patches/15_link-properly.patch +++ adun.app-0.81/debian/patches/15_link-properly.patch @@ -0,0 +1,105 @@ +Name: 15_build.patch +Author: Yavor Doganov +Forwarded: not yet + +--- Adun-0.81.orig/Kernel/AdunKernel/GNUmakefile ++++ Adun-0.81/Kernel/AdunKernel/GNUmakefile +@@ -10,7 +10,7 @@ + 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) $(OBJC_LIBS) + endif + + export KERNEL_COMPILER ?= gcc +--- Adun-0.81.orig/Kernel/GNUmakefile ++++ Adun-0.81/Kernel/GNUmakefile +@@ -22,7 +22,7 @@ + ifeq ($(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 +--- Adun-0.81.orig/MolTalk/GNUmakefile.preamble ++++ Adun-0.81/MolTalk/GNUmakefile.preamble +@@ -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) $(OBJC_LIBS) + + # + # Flags dealing with installing and uninstalling +--- Adun-0.81.orig/UL/AdunServer/GNUmakefile ++++ Adun-0.81/UL/AdunServer/GNUmakefile +@@ -18,7 +18,7 @@ + # + + AdunServer_LIB_DIRS += -L../ULFramework/ULFramework.framework/Versions/Current -L../XMLLib/obj +-AdunServer_TOOL_LIBS += -lXMLLib -lULFramework ++AdunServer_TOOL_LIBS += -lXMLLib -lULFramework -ladun_base -lAdunKernel -lMolTalk + + # + # Resource files +--- Adun-0.81.orig/UL/AdunServer/GNUmakefile.preamble ++++ Adun-0.81/UL/AdunServer/GNUmakefile.preamble +@@ -15,9 +15,7 @@ + ADDITIONAL_CFLAGS += + + # Additional flags to pass to the linker +-ifeq ($(MAKELEVEL), 3) +-ADDITIONAL_LDFLAGS += -ladun_base -lAdunKernel -lMolTalk +-endif ++ADDITIONAL_LDFLAGS += + + # Additional include directories the compiler should search + ifeq ($(MAKELEVEL),3) +--- Adun-0.81.orig/UL/GNUmakefile ++++ Adun-0.81/UL/GNUmakefile +@@ -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 + # +--- Adun-0.81.orig/UL/ULFramework/GNUmakefile ++++ Adun-0.81/UL/ULFramework/GNUmakefile +@@ -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 +--- Adun-0.81.orig/UL/XMLLib/GNUmakefile.preamble ++++ Adun-0.81/UL/XMLLib/GNUmakefile.preamble +@@ -18,5 +18,6 @@ + ADDITIONAL_INCLUDE_DIRS += -I../ -I../../Kernel -I../../Kernel/AdunKernel/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) $(OBJC_LIBS) +--- Adun-0.81.orig/Kernel/Base/GNUmakefile.preamble ++++ Adun-0.81/Kernel/Base/GNUmakefile.preamble +@@ -17,7 +17,8 @@ + ADDITIONAL_CFLAGS += + + # Additional flags to pass to the linker +-ADDITIONAL_LDFLAGS += -lgsl -lgslcblas ++ADDITIONAL_LDFLAGS += ++LIBRARIES_DEPEND_UPON += -lgsl -lm + + # Additional include directories the compiler should search + ADDITIONAL_INCLUDE_DIRS += -I$(GSL_INCLUDE_DIR) --- adun.app-0.81.orig/debian/source/format +++ adun.app-0.81/debian/source/format @@ -0,0 +1 @@ +1.0