[med-svn] r1185 - in trunk/packages: . adun.app adun.app/trunk adun.app/trunk/debian adun.app/trunk/debian/patches
tille at alioth.debian.org
tille at alioth.debian.org
Mon Jan 21 17:48:45 UTC 2008
Author: tille
Date: 2008-01-21 17:48:44 +0000 (Mon, 21 Jan 2008)
New Revision: 1185
Added:
trunk/packages/adun.app/
trunk/packages/adun.app/trunk/
trunk/packages/adun.app/trunk/debian/
trunk/packages/adun.app/trunk/debian/AdunCore.1
trunk/packages/adun.app/trunk/debian/AdunServer.1
trunk/packages/adun.app/trunk/debian/README.Debian
trunk/packages/adun.app/trunk/debian/UL.1
trunk/packages/adun.app/trunk/debian/UL.desktop
trunk/packages/adun.app/trunk/debian/changelog
trunk/packages/adun.app/trunk/debian/compat
trunk/packages/adun.app/trunk/debian/control
trunk/packages/adun.app/trunk/debian/copyright
trunk/packages/adun.app/trunk/debian/manpages
trunk/packages/adun.app/trunk/debian/menu
trunk/packages/adun.app/trunk/debian/patches/
trunk/packages/adun.app/trunk/debian/patches/00list
trunk/packages/adun.app/trunk/debian/patches/05_no-plugin-script.dpatch
trunk/packages/adun.app/trunk/debian/patches/10_gcc-4.3-inline.dpatch
trunk/packages/adun.app/trunk/debian/patches/15_link-properly.dpatch
trunk/packages/adun.app/trunk/debian/patches/20_paths.dpatch
trunk/packages/adun.app/trunk/debian/patches/25_mipsel-ftbfs.dpatch
trunk/packages/adun.app/trunk/debian/rules
Log:
Checked adun.app as is, group maintainance stuff will follow
Added: trunk/packages/adun.app/trunk/debian/AdunCore.1
===================================================================
--- trunk/packages/adun.app/trunk/debian/AdunCore.1 (rev 0)
+++ trunk/packages/adun.app/trunk/debian/AdunCore.1 2008-01-21 17:48:44 UTC (rev 1185)
@@ -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 at gnu.org> for the
+Debian project (but may be used by others).
Added: trunk/packages/adun.app/trunk/debian/AdunServer.1
===================================================================
--- trunk/packages/adun.app/trunk/debian/AdunServer.1 (rev 0)
+++ trunk/packages/adun.app/trunk/debian/AdunServer.1 2008-01-21 17:48:44 UTC (rev 1185)
@@ -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 at gnu.org> for the
+Debian project (but may be used by others).
Added: trunk/packages/adun.app/trunk/debian/README.Debian
===================================================================
--- trunk/packages/adun.app/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/adun.app/trunk/debian/README.Debian 2008-01-21 17:48:44 UTC (rev 1185)
@@ -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 at gnu.org>, Sat, 19 Jan 2008 14:19:24 +0200
Added: trunk/packages/adun.app/trunk/debian/UL.1
===================================================================
--- trunk/packages/adun.app/trunk/debian/UL.1 (rev 0)
+++ trunk/packages/adun.app/trunk/debian/UL.1 2008-01-21 17:48:44 UTC (rev 1185)
@@ -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 at linuks.mine.nu>,
+for the Debian project (but may be used by others).
Added: trunk/packages/adun.app/trunk/debian/UL.desktop
===================================================================
--- trunk/packages/adun.app/trunk/debian/UL.desktop (rev 0)
+++ trunk/packages/adun.app/trunk/debian/UL.desktop 2008-01-21 17:48:44 UTC (rev 1185)
@@ -0,0 +1,7 @@
+[Desktop Entry]
+Type=Application
+Name=Adun
+Comment=Biomoleculal Simulator
+Version=0.94
+Categories=Education;Science;Biology;
+Exec=UL
Added: trunk/packages/adun.app/trunk/debian/changelog
===================================================================
--- trunk/packages/adun.app/trunk/debian/changelog (rev 0)
+++ trunk/packages/adun.app/trunk/debian/changelog 2008-01-21 17:48:44 UTC (rev 1185)
@@ -0,0 +1,72 @@
+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.
+
+ -- Yavor Doganov <yavor at gnu.org> Sat, 19 Jan 2008 15:21:59 +0200
+
+adun.app (0.6-3) unstable; urgency=low
+
+ * Fix the FTBFS for non-i386 properly.
+
+ -- Gürkan Sengün <gurkan at 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 at 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 at linuks.mine.nu> Sun, 3 Sep 2006 18:34:19 +0200
Added: trunk/packages/adun.app/trunk/debian/compat
===================================================================
--- trunk/packages/adun.app/trunk/debian/compat (rev 0)
+++ trunk/packages/adun.app/trunk/debian/compat 2008-01-21 17:48:44 UTC (rev 1185)
@@ -0,0 +1 @@
+6
Added: trunk/packages/adun.app/trunk/debian/control
===================================================================
--- trunk/packages/adun.app/trunk/debian/control (rev 0)
+++ trunk/packages/adun.app/trunk/debian/control 2008-01-21 17:48:44 UTC (rev 1185)
@@ -0,0 +1,18 @@
+Source: adun.app
+Section: science
+Priority: optional
+Maintainer: Debian QA Group <packages at qa.debian.org>
+Build-Depends: debhelper (>= 6),
+ dpatch,
+ libgnustep-gui-dev (>= 0.12.0),
+ libgsl0-dev
+Standards-Version: 3.7.3
+Homepage: http://diana.imim.es/Adun
+
+Package: adun.app
+Architecture: any
+Depends: ${shlibs:Depends}
+Recommends: gnuplot
+Description: Molecular Simulator for GNUstep
+ This is a new extendible molecular simulation program that also
+ includes data management and analysis capabilities.
Added: trunk/packages/adun.app/trunk/debian/copyright
===================================================================
--- trunk/packages/adun.app/trunk/debian/copyright (rev 0)
+++ trunk/packages/adun.app/trunk/debian/copyright 2008-01-21 17:48:44 UTC (rev 1185)
@@ -0,0 +1,37 @@
+This package was debianized by Gürkan Sengün <gurkan at 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)
+
+License:
+
+ Copyright (C) 2003-2007 Alexander V. Diemand (MolTalk)
+ Copyright (C) 2005-2007 Michael A. Johnston
+ Copyright (C) 2005-2007 Jordi Vill-Freixa
+
+ 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
+
+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 (C) 2006, Gürkan Sengün <gurkan at linuks.mine.nu> and
+is licensed under the GPL, see `/usr/share/common-licenses/GPL'.
Added: trunk/packages/adun.app/trunk/debian/manpages
===================================================================
--- trunk/packages/adun.app/trunk/debian/manpages (rev 0)
+++ trunk/packages/adun.app/trunk/debian/manpages 2008-01-21 17:48:44 UTC (rev 1185)
@@ -0,0 +1,3 @@
+debian/UL.1
+debian/AdunCore.1
+debian/AdunServer.1
Added: trunk/packages/adun.app/trunk/debian/menu
===================================================================
--- trunk/packages/adun.app/trunk/debian/menu (rev 0)
+++ trunk/packages/adun.app/trunk/debian/menu 2008-01-21 17:48:44 UTC (rev 1185)
@@ -0,0 +1,4 @@
+?package(adun.app):needs="X11" \
+ section="Applications/Science/Biology" \
+ title="Adun" command="/usr/bin/UL" \
+ longtitle="Biomolecular Simulator"
Added: trunk/packages/adun.app/trunk/debian/patches/00list
===================================================================
--- trunk/packages/adun.app/trunk/debian/patches/00list (rev 0)
+++ trunk/packages/adun.app/trunk/debian/patches/00list 2008-01-21 17:48:44 UTC (rev 1185)
@@ -0,0 +1,5 @@
+05_no-plugin-script
+10_gcc-4.3-inline
+15_link-properly
+20_paths
+25_mipsel-ftbfs
Added: trunk/packages/adun.app/trunk/debian/patches/05_no-plugin-script.dpatch
===================================================================
--- trunk/packages/adun.app/trunk/debian/patches/05_no-plugin-script.dpatch (rev 0)
+++ trunk/packages/adun.app/trunk/debian/patches/05_no-plugin-script.dpatch 2008-01-21 17:48:44 UTC (rev 1185)
@@ -0,0 +1,17 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 05_no-plugin-script.dpatch by Yavor Doganov <yavor at gnu.org>
+##
+## DP: Do not install the script for plugin installation.
+
+ at 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::
Added: trunk/packages/adun.app/trunk/debian/patches/10_gcc-4.3-inline.dpatch
===================================================================
--- trunk/packages/adun.app/trunk/debian/patches/10_gcc-4.3-inline.dpatch (rev 0)
+++ trunk/packages/adun.app/trunk/debian/patches/10_gcc-4.3-inline.dpatch 2008-01-21 17:48:44 UTC (rev 1185)
@@ -0,0 +1,404 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 10_gcc-4.3.dpatch by Yavor Doganov <yavor at gnu.org> and
+## Martin Michlmayr <tbm at cyrius.com>
+##
+## DP: Fixes FTBFS with GCC 4.3.
+
+ at DPATCH@
+diff -urNad adun.app-0.8.2~/Kernel/Base/AdBaseFunctions.h adun.app-0.8.2/Kernel/Base/AdBaseFunctions.h
+--- adun.app-0.8.2~/Kernel/Base/AdBaseFunctions.h 2006-11-02 15:40:06.000000000 +0200
++++ adun.app-0.8.2/Kernel/Base/AdBaseFunctions.h 2008-01-13 19:34:21.000000000 +0200
+@@ -9,6 +9,6 @@
+ masses \e masses.
+ */
+
+-inline double AdCalculateKineticEnergy(DoubleMatrix* velocities, double* masses);
++extern double AdCalculateKineticEnergy(DoubleMatrix* velocities, double* masses);
+
+ #endif
+diff -urNad adun.app-0.8.2~/Kernel/Base/AdForceFieldFunctions.h adun.app-0.8.2/Kernel/Base/AdForceFieldFunctions.h
+--- adun.app-0.8.2~/Kernel/Base/AdForceFieldFunctions.h 2008-01-13 19:33:38.000000000 +0200
++++ adun.app-0.8.2/Kernel/Base/AdForceFieldFunctions.h 2008-01-13 19:33:48.000000000 +0200
+@@ -64,10 +64,10 @@
+ extern bool __GRFNonbondedEnergyDebug__;
+ extern bool __GRFNonbondedForceDebug__;
+
+-inline void AdNonbondedEnergyLog(char* cutType, char* ljType, int a1, int a2, double ljA,
++extern void AdNonbondedEnergyLog(char* cutType, char* ljType, int a1, int a2, double ljA,
+ double ljB, double charge, double sep, double estPot, double ljPot,
+ bool flag);
+-inline void AdNonbondedForceLog(char* cutType, char* ljType, int a1, int a2, double ljA,
++extern void AdNonbondedForceLog(char* cutType, char* ljType, int a1, int a2, double ljA,
+ double ljB, double charge, double sep, double estPot, double ljPot, double force,
+ bool flag);
+ /**
+@@ -93,78 +93,78 @@
+ */
+
+ /** Calculates the energy of a bond using a harmonic bond function */
+-inline void AdHarmonicBondEnergy(double *bond, double **coordinates, double *bnd_pot);
++extern void AdHarmonicBondEnergy(double *bond, double **coordinates, double *bnd_pot);
+ /** Calculates the energy and force of a bond using a harmonic bond function */
+-inline void AdHarmonicBondForce(double* bond, double **coordinates, double **forces, double* bnd_pot);
++extern void AdHarmonicBondForce(double* bond, double **coordinates, double **forces, double* bnd_pot);
+ /**
+ Enzymix force field uses k*(x-x0)² instead of k/2*(x-xo)² like other force fields
+ */
+-inline void AdEnzymixBondEnergy(double* bond, double **coordinates, double* bnd_pot);
++extern void AdEnzymixBondEnergy(double* bond, double **coordinates, double* bnd_pot);
+ /**
+ As harmonic force except force magnitude is 2k*(x-x0) instead of k*(x-xo) like other force fields
+ */
+-inline void AdEnzymixBondForce(double* bond, double **coordinates, double **forces, double* bnd_pot);
++extern void AdEnzymixBondForce(double* bond, double **coordinates, double **forces, double* bnd_pot);
+
+ /*
+ * Harmonic Angle
+ */
+
+ /** Calculates the energy of an angle using a harmonic angle function */
+-inline void AdHarmonicAngleEnergy(double *interaction, double **coordinates, double *ang_pot);
+-inline void AdHarmonicAngleForce(double *interaction, double **coordinates, double **forces, double *ang_pot);
++extern void AdHarmonicAngleEnergy(double *interaction, double **coordinates, double *ang_pot);
++extern void AdHarmonicAngleForce(double *interaction, double **coordinates, double **forces, double *ang_pot);
+ /**
+ Enzymix force field uses k*(x-x0)² instead of k/2*(x-xo)² like other force fields
+ Where x is the angle.
+ */
+-inline void AdEnzymixAngleEnergy(double *interaction, double** coordinates, double *ang_pot);
+-inline void AdEnzymixAngleForce(double *interaction, double **coordinates, double **forces, double *ang_pot);
++extern void AdEnzymixAngleEnergy(double *interaction, double** coordinates, double *ang_pot);
++extern void AdEnzymixAngleForce(double *interaction, double **coordinates, double **forces, double *ang_pot);
+
+ /*
+ * fourier torsion
+ */
+
+ /** calculates the energy of a proper torsion using a fourier torsion function */
+-inline void AdFourierTorsionEnergy(double *interaction, double **coordinates, double *tor_pot);
+-inline void AdFourierTorsionForce(double *interaction, double **coordinates, double **forces, double *tor_pot);
++extern void AdFourierTorsionEnergy(double *interaction, double **coordinates, double *tor_pot);
++extern void AdFourierTorsionForce(double *interaction, double **coordinates, double **forces, double *tor_pot);
+ /*
+ Calculate the torsion angle for four atoms. Torsion 4 element array each element an atom index. The
+ atoms position must be given by the corresponding row in coordinates.
+ */
+-inline double AdCalculateTorsionAngle(int* torsion, double** coordinates);
++extern double AdCalculateTorsionAngle(int* torsion, double** coordinates);
+
+ /*
+ * harmonic improper torsion
+ */
+
+ /** calculates the energy of an improper torsion using a harmonic function */
+-inline void AdHarmonicImproperTorsionEnergy(double *interaction, double **coordinates , double *itor_pot);
+-inline void AdHarmonicImproperTorsionForce(double *interaction, double **coordinates, double **forces, double *itor_pot);
++extern void AdHarmonicImproperTorsionEnergy(double *interaction, double **coordinates , double *itor_pot);
++extern void AdHarmonicImproperTorsionForce(double *interaction, double **coordinates, double **forces, double *itor_pot);
+
+ /** Calculates the combined energy of a coloumb electrostatic and lennard jones A term.
+ Lennard Jones A uses parameters A and B. These functions are optimised for use in
+ Adun AdForceField obects.
+ \todo Possibly move the separation and cutoff rejection code to AdunKernel classes */
+-inline void AdCoulombAndLennardJonesAEnergy(ListElement* interaction,
++extern void AdCoulombAndLennardJonesAEnergy(ListElement* interaction,
+ double** coordinates,
+ double EPSILON_RP,
+ double cutoff,
+ double* vdw_pot,
+ double* est_pot);
+-inline void AdCoulombAndLennardJonesAForce(ListElement* interaction,
++extern void AdCoulombAndLennardJonesAForce(ListElement* interaction,
+ double** coordinates,
+ double** forces,
+ double EPSILON_RP,
+ double cutoff,
+ double* vdw_pot,
+ double* est_pot);
+-inline void AdShiftedCoulombAndLennardJonesAEnergy(ListElement* interaction,
++extern void AdShiftedCoulombAndLennardJonesAEnergy(ListElement* interaction,
+ double** coordinates,
+ double EPSILON_RP,
+ double cut,
+ double r_cutoff2,
+ double* vdw_pot,
+ double* est_pot);
+-inline void AdShiftedCoulombAndLennardJonesAForce(ListElement* interaction,
++extern void AdShiftedCoulombAndLennardJonesAForce(ListElement* interaction,
+ double** coordinates,
+ double** forces,
+ double EPSILON_RP,
+@@ -172,7 +172,7 @@
+ double r_cutoff2,
+ double* vdw_pot,
+ double* est_pot);
+-inline void AdGRFCoulombAndLennardJonesAEnergy(ListElement* interaction,
++extern void AdGRFCoulombAndLennardJonesAEnergy(ListElement* interaction,
+ double** coordinates,
+ double EPSILON_RP,
+ double cutoff,
+@@ -180,7 +180,7 @@
+ double b1,
+ double* vdw_pot,
+ double* est_pot);
+-inline void AdGRFCoulombAndLennardJonesAForce(ListElement* interaction,
++extern void AdGRFCoulombAndLennardJonesAForce(ListElement* interaction,
+ double** coordinates,
+ double** forces,
+ double EPSILON_RP,
+@@ -192,20 +192,20 @@
+ /** Calculates the combined energy of a coloumb electrostatic and lennard jones B term.
+ Lennard Jones A uses parameters well depth and equilibrium separation.
+ These functions are optimised for use in Adun AdForceField obects.*/
+-inline void AdCoulombAndLennardJonesBEnergy(ListElement* interaction,
++extern void AdCoulombAndLennardJonesBEnergy(ListElement* interaction,
+ double** coordinates,
+ double EPSILON_RP,
+ double cutoff,
+ double* vdw_pot,
+ double* est_pot);
+-inline void AdCoulombAndLennardJonesBForce(ListElement* interaction,
++extern void AdCoulombAndLennardJonesBForce(ListElement* interaction,
+ double** coordinates,
+ double** forces,
+ double EPSILON_RP,
+ double cutoff,
+ double* vdw_pot,
+ double* est_pot);
+-inline void AdShiftedCoulombAndLennardJonesBForce(ListElement* interaction,
++extern void AdShiftedCoulombAndLennardJonesBForce(ListElement* interaction,
+ double** coordinates,
+ double** forces,
+ double EPSILON_RP,
+@@ -213,14 +213,14 @@
+ double r_cutoff2,
+ double* vdw_pot,
+ double* est_pot);
+-inline void AdShiftedCoulombAndLennardJonesBEnergy(ListElement* interaction,
++extern void AdShiftedCoulombAndLennardJonesBEnergy(ListElement* interaction,
+ double** coordinates,
+ double EPSILON_RP,
+ double cut,
+ double r_cutoff2,
+ double* vdw_pot,
+ double* est_pot);
+-inline void AdGRFCoulombAndLennardJonesBEnergy(ListElement* interaction,
++extern void AdGRFCoulombAndLennardJonesBEnergy(ListElement* interaction,
+ double** coordinates,
+ double EPSILON_RP,
+ double cutoff,
+@@ -228,7 +228,7 @@
+ double b1,
+ double* vdw_pot,
+ double* est_pot);
+-inline void AdGRFCoulombAndLennardJonesBForce(ListElement* interaction,
++extern void AdGRFCoulombAndLennardJonesBForce(ListElement* interaction,
+ double** coordinates,
+ double** forces,
+ double EPSILON_RP,
+@@ -238,7 +238,7 @@
+ double* vdw_pot,
+ double* est_pot);
+ //test
+-inline void AdCoulombAndLennardJonesAForceTest(ListElement* interaction,
++extern void AdCoulombAndLennardJonesAForceTest(ListElement* interaction,
+ Vector3D* seperation_s,
+ double** forces,
+ double EPSILON_RP,
+diff -urNad adun.app-0.8.2~/Kernel/Base/AdLinkedList.h adun.app-0.8.2/Kernel/Base/AdLinkedList.h
+--- adun.app-0.8.2~/Kernel/Base/AdLinkedList.h 2008-01-13 19:33:38.000000000 +0200
++++ adun.app-0.8.2/Kernel/Base/AdLinkedList.h 2008-01-13 19:33:48.000000000 +0200
+@@ -71,25 +71,25 @@
+ \param index The index at which to insert the list. Currently not implemented
+ \return 0 on success, -1 on failure
+ **/
+-inline int AdSafeLinkedListAdd(ListElement*, ListElement*, int);
++extern int AdSafeLinkedListAdd(ListElement*, ListElement*, int);
+ /**
+ Same as AdSafeLinkedListAdd but doesn't check if you've passed
+ the last element.
+ **/
+-inline int AdUnsafeLinkedListAdd(ListElement*, ListElement*, int);
++extern int AdUnsafeLinkedListAdd(ListElement*, ListElement*, int);
+ /**
+ Reinserts an element extracted with AdUnsafeLinkedListExtract
+ Does not check that ListElement actually points to an element
+ in a real list
+ **/
+-inline int AdUnsafeLinkedListReinsert(ListElement*);
++extern int AdUnsafeLinkedListReinsert(ListElement*);
+ /**
+ Removes the element passed from the list. You CANNOT remove the first and last
+ element (big trouble if you do)
+ \param list_el Pointer to the list element to be removed
+ \returns 0 if succeds. -1 if you tried to remove the first or last list elements.
+ **/
+-inline int AdSafeLinkedListRemove(ListElement*);
++extern int AdSafeLinkedListRemove(ListElement*);
+ /**
+ The same as AdUnsafeLinkedListRemove except doesnt set the remove
+ elements previous and next pointer to nil
+@@ -97,17 +97,17 @@
+ \returns 0 if succeds. -1 if you tried to remove the first or last list elements.
+ **/
+
+-inline int AdUnsafeLinkedListExtract(ListElement *list_el);
++extern int AdUnsafeLinkedListExtract(ListElement *list_el);
+ /**
+ Same as safe_linked_list_remove() but doesn't check if the
+ element is the first or last. Use with care.
+ **/
+-inline int AdUnsafeLinkedListRemove(ListElement*);
++extern int AdUnsafeLinkedListRemove(ListElement*);
+ /** Returns a pointer to the last element of the list. **/
+-inline ListElement* AdLinkedListEnd(ListElement*);
++extern ListElement* AdLinkedListEnd(ListElement*);
+ /** Returns a pointer to the first element of the list **/
+-inline ListElement* AdLinkedListStart(ListElement*);
+-inline int AdLinkedListCount(ListElement*);
++extern ListElement* AdLinkedListStart(ListElement*);
++extern int AdLinkedListCount(ListElement*);
+
+ /** \@}**/
+
+diff -urNad adun.app-0.8.2~/Kernel/Base/AdMatrix.h adun.app-0.8.2/Kernel/Base/AdMatrix.h
+--- adun.app-0.8.2~/Kernel/Base/AdMatrix.h 2008-01-13 19:33:38.000000000 +0200
++++ adun.app-0.8.2/Kernel/Base/AdMatrix.h 2008-01-13 19:33:48.000000000 +0200
+@@ -76,36 +76,36 @@
+ @{
+ **/
+
+-inline void AdSetDoubleMatrixWithValue(DoubleMatrix *, double);
+-inline void AdSetFloatMatrixWithValue(FloatMatrix *, float);
+-inline void AdSetIntMatrixWithValue(IntMatrix *, int);
++extern void AdSetDoubleMatrixWithValue(DoubleMatrix *, double);
++extern void AdSetFloatMatrixWithValue(FloatMatrix *, float);
++extern void AdSetIntMatrixWithValue(IntMatrix *, int);
+
+-inline IntMatrix* AdIntMatrixFromRowSection(IntMatrix *, int , int);
+-inline FloatMatrix* AdFloatMatrixFromRowSection(FloatMatrix *, int , int);
+-inline DoubleMatrix* AdDoubleMatrixFromRowSection(DoubleMatrix *, int , int);
++extern IntMatrix* AdIntMatrixFromRowSection(IntMatrix *, int , int);
++extern FloatMatrix* AdFloatMatrixFromRowSection(FloatMatrix *, int , int);
++extern DoubleMatrix* AdDoubleMatrixFromRowSection(DoubleMatrix *, int , int);
+
+-inline IntMatrix* AdIntMatrixFromRowSelection(IntMatrix *, int* , int);
+-inline FloatMatrix* AdFloatMatrixFromRowSelection(FloatMatrix *, int* , int);
+-inline DoubleMatrix* AdDoubleMatrixFromRowSelection(DoubleMatrix *, int* , int);
++extern IntMatrix* AdIntMatrixFromRowSelection(IntMatrix *, int* , int);
++extern FloatMatrix* AdFloatMatrixFromRowSelection(FloatMatrix *, int* , int);
++extern DoubleMatrix* AdDoubleMatrixFromRowSelection(DoubleMatrix *, int* , int);
+
+-inline IntMatrix* AdIntMatrixFromColumnSection(IntMatrix *, int , int);
+-inline FloatMatrix* AdFloatMatrixFromColumnSection(FloatMatrix *, int , int);
+-inline DoubleMatrix* AdDoubleMatrixFromColumnSection(DoubleMatrix *, int , int);
++extern IntMatrix* AdIntMatrixFromColumnSection(IntMatrix *, int , int);
++extern FloatMatrix* AdFloatMatrixFromColumnSection(FloatMatrix *, int , int);
++extern DoubleMatrix* AdDoubleMatrixFromColumnSection(DoubleMatrix *, int , int);
+
+-inline IntMatrix* AdIntMatrixFromColumnSelection(IntMatrix *, int* , int);
+-inline FloatMatrix* AdFloatMatrixFromColumnSelection(FloatMatrix *, int* , int);
+-inline DoubleMatrix* AdDoubleMatrixFromColumnSelection(DoubleMatrix *, int* , int);
++extern IntMatrix* AdIntMatrixFromColumnSelection(IntMatrix *, int* , int);
++extern FloatMatrix* AdFloatMatrixFromColumnSelection(FloatMatrix *, int* , int);
++extern DoubleMatrix* AdDoubleMatrixFromColumnSelection(DoubleMatrix *, int* , int);
+
+-inline void AdFreeDoubleMatrix(DoubleMatrix*);
+-inline void AdFreeIntMatrix(IntMatrix*);
+-inline void AdFreeFloatMatrix(FloatMatrix*);
++extern void AdFreeDoubleMatrix(DoubleMatrix*);
++extern void AdFreeIntMatrix(IntMatrix*);
++extern void AdFreeFloatMatrix(FloatMatrix*);
+
+-inline IntMatrix* AdAllocateIntMatrix(int, int);
+-inline FloatMatrix* AdAllocateFloatMatrix(int, int);
+-inline DoubleMatrix* AdAllocateDoubleMatrix(int, int);
++extern IntMatrix* AdAllocateIntMatrix(int, int);
++extern FloatMatrix* AdAllocateFloatMatrix(int, int);
++extern DoubleMatrix* AdAllocateDoubleMatrix(int, int);
+
+ /**
+ AdMatrix copy function.
+ */
+-inline void AdCopyAdMatrixToAdMatrix(DoubleMatrix*, DoubleMatrix*);
++extern void AdCopyAdMatrixToAdMatrix(DoubleMatrix*, DoubleMatrix*);
+ #endif
+diff -urNad adun.app-0.8.2~/Kernel/Base/AdSorter.h adun.app-0.8.2/Kernel/Base/AdSorter.h
+--- adun.app-0.8.2~/Kernel/Base/AdSorter.h 2008-01-13 19:33:38.000000000 +0200
++++ adun.app-0.8.2/Kernel/Base/AdSorter.h 2008-01-13 19:33:48.000000000 +0200
+@@ -41,7 +41,7 @@
+ @{
+ */
+
+-inline int AdIndexSorter(const void* el_one, const void* el_two);
++extern int AdIndexSorter(const void* el_one, const void* el_two);
+ int AdAscendingIntSort(const void* numberOne, const void* numberTwo);
+
+ /** \@}**/
+diff -urNad adun.app-0.8.2~/Kernel/Base/AdVector.h adun.app-0.8.2/Kernel/Base/AdVector.h
+--- adun.app-0.8.2~/Kernel/Base/AdVector.h 2008-01-13 19:33:38.000000000 +0200
++++ adun.app-0.8.2/Kernel/Base/AdVector.h 2008-01-13 19:33:48.000000000 +0200
+@@ -73,26 +73,26 @@
+ \param vector_two Pointer to a Vector3D structs
+ \return The dot product of the two vectors
+ **/
+-inline double Ad3DDotProduct(Vector3D*, Vector3D*);
++extern double Ad3DDotProduct(Vector3D*, Vector3D*);
+ /**
+ Calculates the cross product of two vectors.
+ \param v_one Pointer to a Vector3D struct.
+ \param v_two Pointer to a Vector3D struct.
+ \param result Pointer to a Vector3D struct where the result vector will be stored.
+ **/
+-inline void Ad3DCrossProduct(Vector3D*, Vector3D*, Vector3D*);
++extern void Ad3DCrossProduct(Vector3D*, Vector3D*, Vector3D*);
+ /**
+ Calculates the length of the vector represented by Vector3D.
+ struct vector and then assigns the result to vector->length.
+ \param vector A pointer to a Vector3D struct.
+ **/
+-inline void Ad3DVectorLength(Vector3D*);
++extern void Ad3DVectorLength(Vector3D*);
+ /**
+ Finds the unit vector related to a given vector.
+ \param vector A pointer to a Vector3D struct.
+ \param unit_vector Pointer to the Vector3D struct where the unit vector is to be stored.
+ **/
+-inline void AdGet3DUnitVector(Vector3D*, Vector3D*);
++extern void AdGet3DUnitVector(Vector3D*, Vector3D*);
+ /**
+ In essence generates uniformly distributed points on the unit sphere using \e generator
+ via the trig-method.
+@@ -100,25 +100,25 @@
+ \param generator Pointer to a previously allocated gsl_rng instance which will be used
+ to generate the necessary random numbers.
+ */
+-inline void AdGetRandom3DUnitVector(Vector3D* vector, gsl_rng* generator);
+-inline void Ad3DVectorLengthSquared(Vector3D*);
++extern void AdGetRandom3DUnitVector(Vector3D* vector, gsl_rng* generator);
++extern void Ad3DVectorLengthSquared(Vector3D*);
+ /**
+ Return the index of the minimium element in a standard double array.
+ If there is more than one entry with the same value the smallest
+ index is returned
+ **/
+-inline int AdDoubleArrayMin(double*, int);
++extern int AdDoubleArrayMin(double*, int);
+ /**
+ Return the index of the maximum element in a standard double array.
+ If there is more than one entry with the same value the smallest
+ index is returned
+ **/
+-inline int AdDoubleArrayMax(double*, int);
++extern int AdDoubleArrayMax(double*, int);
+
+
+-inline void AdIntArrayIntersectionAndDifference(IntArrayStruct *prime, IntArrayStruct *query, IntArrayStruct *intersection, IntArrayStruct *complement);
+-inline void AdIntArrayIntersection(IntArrayStruct *prime, IntArrayStruct *query, IntArrayStruct *intersection);
+-inline void AdIntArrayDifference(IntArrayStruct *prime, IntArrayStruct *query, IntArrayStruct *difference);
++extern void AdIntArrayIntersectionAndDifference(IntArrayStruct *prime, IntArrayStruct *query, IntArrayStruct *intersection, IntArrayStruct *complement);
++extern void AdIntArrayIntersection(IntArrayStruct *prime, IntArrayStruct *query, IntArrayStruct *intersection);
++extern void AdIntArrayDifference(IntArrayStruct *prime, IntArrayStruct *query, IntArrayStruct *difference);
+
+ /** \@}**/
+
Added: trunk/packages/adun.app/trunk/debian/patches/15_link-properly.dpatch
===================================================================
--- trunk/packages/adun.app/trunk/debian/patches/15_link-properly.dpatch (rev 0)
+++ trunk/packages/adun.app/trunk/debian/patches/15_link-properly.dpatch 2008-01-21 17:48:44 UTC (rev 1185)
@@ -0,0 +1,142 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 15_build.dpatch by Yavor Doganov <yavor at gnu.org>
+##
+## DP: Link all objects with the libs they use symbols from. The
+## DP: `--no-as-needed' option is a workaround for #456898, which was
+## DP: incorrectly tagged `wontfix'.
+
+ at 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 = 0.11
+ 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) $(OBJC_LIBS)
+ endif
+
+ AdunKernel_OBJCFLAGS = -W -O3 -fconstant-string-class=NSConstantString
+diff -urNad adun.app-0.8.2~/Kernel/AdunKernel/GNUmakefile.preamble adun.app-0.8.2/Kernel/AdunKernel/GNUmakefile.preamble
+--- adun.app-0.8.2~/Kernel/AdunKernel/GNUmakefile.preamble 2008-01-17 12:37:12.000000000 +0200
++++ adun.app-0.8.2/Kernel/AdunKernel/GNUmakefile.preamble 2008-01-17 12:38:28.000000000 +0200
+@@ -8,7 +8,7 @@
+ ADDITIONAL_CFLAGS +=
+
+ # Additional flags to pass to the linker
+-ADDITIONAL_LDFLAGS +=
++ADDITIONAL_LDFLAGS += -Wl,--no-as-needed -lgsl -lgslcblas
+
+ # Additional include directories the compiler should search
+ ADDITIONAL_INCLUDE_DIRS +=
+diff -urNad adun.app-0.8.2~/Kernel/Base/GNUmakefile.preamble adun.app-0.8.2/Kernel/Base/GNUmakefile.preamble
+--- adun.app-0.8.2~/Kernel/Base/GNUmakefile.preamble 2008-01-17 12:37:12.000000000 +0200
++++ adun.app-0.8.2/Kernel/Base/GNUmakefile.preamble 2008-01-17 12:38:28.000000000 +0200
+@@ -17,7 +17,8 @@
+ ADDITIONAL_CFLAGS +=
+
+ # Additional flags to pass to the linker
+-ADDITIONAL_LDFLAGS += -lgsl -lgslcblas
++ADDITIONAL_LDFLAGS += -Wl,--no-as-needed -lgsl -lgslcblas
++LIBRARIES_DEPEND_UPON += -lgsl -lgslcblas -lm
+
+ # Additional include directories the compiler should search
+ ADDITIONAL_INCLUDE_DIRS += -I$(GSL_INCLUDE_DIR)
+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/ULFramework/GNUmakefile.preamble adun.app-0.8.2/UL/ULFramework/GNUmakefile.preamble
+--- adun.app-0.8.2~/UL/ULFramework/GNUmakefile.preamble 2008-01-17 12:37:12.000000000 +0200
++++ adun.app-0.8.2/UL/ULFramework/GNUmakefile.preamble 2008-01-17 12:38:28.000000000 +0200
+@@ -12,7 +12,7 @@
+ ADDITIONAL_CFLAGS +=
+
+ # Additional flags to pass to the linker
+-ADDITIONAL_LDFLAGS +=
++ADDITIONAL_LDFLAGS += -Wl,--no-as-needed -lgsl -lgslcblas -lm
+
+ # Additional include directories the compiler should search
+ ifeq ($(MAKELEVEL),3)
+diff -urNad adun.app-0.8.2~/UL/XMLLib/GNUmakefile.preamble adun.app-0.8.2/UL/XMLLib/GNUmakefile.preamble
+--- adun.app-0.8.2~/UL/XMLLib/GNUmakefile.preamble 2008-01-17 12:37:12.000000000 +0200
++++ adun.app-0.8.2/UL/XMLLib/GNUmakefile.preamble 2008-01-17 12:38:28.000000000 +0200
+@@ -18,5 +18,6 @@
+ ADDITIONAL_INCLUDE_DIRS += -I../ -I../../Kernel -I../../Kernel/AdunKernel/Headers -I$(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)
Added: trunk/packages/adun.app/trunk/debian/patches/20_paths.dpatch
===================================================================
--- trunk/packages/adun.app/trunk/debian/patches/20_paths.dpatch (rev 0)
+++ trunk/packages/adun.app/trunk/debian/patches/20_paths.dpatch 2008-01-21 17:48:44 UTC (rev 1185)
@@ -0,0 +1,50 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 20_paths.dpatch by Yavor Doganov <yavor at gnu.org>
+##
+## DP: Adjust some essential paths.
+
+ at 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/ViewController.m adun.app-0.8.2/UL/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 @@
+ forKey: @"BuildOutput"];
+ [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/buildOutput"]
+ forKey: @"BuildOutput"];
+@@ -95,8 +95,7 @@
+ //This is because when installing from xcode its easier to install locally.
+ //While with PackageMaker the opposite is true.
+ //We set a default to $HOME/bin which we override during the package install process
+- [defaults setObject: [NSHomeDirectory() stringByAppendingPathComponent: @"bin"]
+- forKey: @"AdunServerPath"];
++ [defaults setObject: @"/usr/bin" forKey: @"AdunServerPath"];
+ #endif
+ [defaults setObject: [NSNumber numberWithDouble: 300] forKey: @"AutoUpdateInterval"];
+ [defaults setObject: [NSNumber numberWithBool: YES] forKey: @"AutoUpdate"];
+@@ -434,8 +433,7 @@
+ stringForKey: @"AdunServerPath"];
+ launchPath = [launchPath stringByAppendingPathComponent: @"AdunServer"];
+ #else
+- launchPath = [NSHomeDirectory()
+- stringByAppendingPathComponent: @"GNUstep/Tools/AdunServer"];
++ launchPath = @"/usr/bin/AdunServer";
+ #endif
+ NS_DURING
+ {
Added: trunk/packages/adun.app/trunk/debian/patches/25_mipsel-ftbfs.dpatch
===================================================================
--- trunk/packages/adun.app/trunk/debian/patches/25_mipsel-ftbfs.dpatch (rev 0)
+++ trunk/packages/adun.app/trunk/debian/patches/25_mipsel-ftbfs.dpatch 2008-01-21 17:48:44 UTC (rev 1185)
@@ -0,0 +1,18 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 25_mipsel-ftbfs.dpatch by Yavor Doganov <yavor at gnu.org>
+##
+## DP: Fixes FTBFS on mipsel where $HOME is not accessible.
+
+ at DPATCH@
+diff -urNad adun.app-0.8.2~/UL/XMLLib/GNUmakefile.preamble adun.app-0.8.2/UL/XMLLib/GNUmakefile.preamble
+--- adun.app-0.8.2~/UL/XMLLib/GNUmakefile.preamble 2008-01-18 23:08:33.000000000 +0200
++++ adun.app-0.8.2/UL/XMLLib/GNUmakefile.preamble 2008-01-18 23:09:26.000000000 +0200
+@@ -15,7 +15,7 @@
+ ADDITIONAL_LDFLAGS +=
+
+ # Additional include directories the compiler should search
+-ADDITIONAL_INCLUDE_DIRS += -I../ -I../../Kernel -I../../Kernel/AdunKernel/Headers -I$(HOME)/GNUstep/Library/Headers
++ADDITIONAL_INCLUDE_DIRS += -I../ -I../../Kernel -I../../Kernel/AdunKernel/Headers
+
+ # Additional library directories the linker should search
+ ADDITIONAL_LIB_DIRS += -L$(ADUN_SOURCE_DIR)/Kernel/AdunKernel/AdunKernel.framework/Versions/Current
Added: trunk/packages/adun.app/trunk/debian/rules
===================================================================
--- trunk/packages/adun.app/trunk/debian/rules (rev 0)
+++ trunk/packages/adun.app/trunk/debian/rules 2008-01-21 17:48:44 UTC (rev 1185)
@@ -0,0 +1,87 @@
+#!/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
+
+d_app := $(CURDIR)/debian/adun.app
+LDFLAGS := -Wl,-z,defs -Wl,--as-needed -Wl,-rpath,/usr/lib/adun.app
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+OPTFLAG := -O0
+else
+OPTFLAG := -O2
+endif
+
+build: patch build-stamp
+
+build-stamp:
+ dh_testdir
+ GNUSTEP_MAKEFILES=/usr/share/GNUstep/Makefiles MAKELEVEL=0 \
+ $(MAKE) OPTFLAG=$(OPTFLAG) LDFLAGS="$(LDFLAGS)" messages=yes
+ touch $@
+
+clean: clean-patched unpatch
+
+clean-patched:
+ dh_testdir
+ dh_testroot
+ $(RM) build-stamp
+ gs_make clean distclean
+ dh_clean
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+# Install private libraries in /usr/lib/adun.app; fixes a Policy
+# `SHOULD' violation (10.2).
+ dh_installdirs usr/lib/adun.app
+ gs_make install messages=yes DESTDIR=$(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 $(CURDIR)/debian/*.app/usr/lib/GNUstep/Applications/*.app/Resources/*.desktop
+ install -D -m 644 debian/*.desktop \
+ $(d_app)/usr/share/applications/UL.desktop
+
+# Build architecture-independent files here.
+binary-indep: build install
+# We have nothing to do by default.
+
+# Build architecture-dependent files here.
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs
+ dh_installmenu
+ dh_installman
+ dh_link
+ gsdh_gnustep
+ifeq ($(GS_USE_FHS),yes)
+ 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
Property changes on: trunk/packages/adun.app/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
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