debian/0000755000000000000000000000000012241754031007165 5ustar debian/menu0000644000000000000000000000027712214301263010055 0ustar ?package(adun.app):needs="X11" \ section="Applications/Science/Biology" \ title="Adun" command="/usr/bin/UL" \ longtitle="Biomolecular Simulator" \ icon="/usr/share/pixmaps/adun.xpm" debian/README.Debian0000644000000000000000000000260312214301263011222 0ustar 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 debian/manpages0000644000000000000000000000006212214301263010674 0ustar debian/UL.1 debian/AdunCore.1 debian/AdunServer.1 debian/source/0000755000000000000000000000000012241414124010461 5ustar debian/source/format0000644000000000000000000000001412214301263011666 0ustar 3.0 (quilt) debian/install0000644000000000000000000000010412241416570010554 0ustar debian/*.desktop usr/share/applications adun.xpm usr/share/pixmaps debian/dirs0000644000000000000000000000002112241416236010044 0ustar usr/lib/adun.app debian/README.source0000644000000000000000000000041512214301263011337 0ustar 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 debian/copyright0000644000000000000000000000310312214301263011110 0ustar 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'. debian/UL.10000644000000000000000000000116112214301263007561 0ustar .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). debian/upstream0000644000000000000000000000160012214301263010740 0ustar Archive: Gna Homepage: http://diana.imim.es/Adun Name: Adun Reference: Author: Michael A. Johnston and 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 DOI: 10.1002/jcc.20312 PMID: 16175583 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 debian/rules0000755000000000000000000001025012241753566010257 0ustar #!/usr/bin/make -f # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 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 %: dh $@ override_dh_auto_build: # 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 $(optim) \ messages=yes ADDITIONAL_CFLAGS="$(CFLAGS)" \ LDFLAGS="$(LDFLAGS)" \ $(mipsen-flags) convert UL/Resources/icon.tiff -resize 32x32 adun.xpm ## tried for hardening but does not help ## if all four variables below are set the build even fails # ADDITIONAL_LDFLAGS="$(LDFLAGS)" \ # ADDITIONAL_OBJC_LIBS="$(LDFLAGS)" \ # ADDITIONAL_TOOL_LIBS="$(LDFLAGS)" \ # ADDITIONAL_GUI_LIBS="$(LDFLAGS)" \ override_dh_auto_clean: 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 override_dh_clean: dh_clean adun.xpm override_dh_auto_install: $(MAKE) install messages=yes DESTDIR=$(d_app) \ GNUSTEP_SYSTEM_LIBRARIES=/usr/lib/adun.app \ GNUSTEP_INSTALLATION_DOMAIN=SYSTEM override_dh_install: dh_install # 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 override_dh_fixperms: dh_fixperms find $(d_app)/usr/share/GNUstep/UL.app -type f -exec chmod -x '{}' \; find $(d_app)/usr/lib/GNUstep/Applications/UL.app/Resources -type f -exec chmod -x '{}' \; chmod -x $(d_app)/usr/lib/GNUstep/Frameworks/ULFramework.framework/Versions/0/Resources/ForceFields/Enzymix/*.ffml # hack: no idea when and how to call dh_gnustep - just enforce it after dh_links override_dh_link: dh_link dh_gnustep ifeq ($(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 # lintian claims that postinst + postrm have useless call to ldconfig # the following code would remove these files totally but than update-menus # would be left out ... leaving the lintian warning for somebody else #override_dh_installdeb: # dh_installdeb # find debian \( -name postinst -o -name postrm \) -delete get-orig-source: mkdir -p ../tarballs uscan --verbose --force-download --destdir=../tarballs debian/patches/0000755000000000000000000000000012241745452010623 5ustar debian/patches/05_no-plugin-script.patch0000644000000000000000000000075012214301263015350 0ustar 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:: debian/patches/20_paths.patch0000644000000000000000000000275112214301263013255 0ustar 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 { debian/patches/fix-implicit-pointer.patch0000644000000000000000000000135512214301263015710 0ustar 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 debian/patches/15_link-properly.patch0000644000000000000000000000726412214301263014755 0ustar 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) debian/patches/series0000644000000000000000000000013312214301263012021 0ustar 05_no-plugin-script.patch 15_link-properly.patch 20_paths.patch fix-implicit-pointer.patch debian/AdunCore.10000644000000000000000000000423712214301263010750 0ustar .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). debian/watch0000644000000000000000000000057312214301263010216 0ustar 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 debian/changelog0000644000000000000000000001664612241753577011072 0ustar adun.app (0.81-6) unstable; urgency=low [ Charles Plessy ] * Renamed debian/upstream-metadata.yaml to debian/upstream [ Andreas Tille ] * debian/source/format: 3.0 (quilt) * debian/upstream: Small modifications to better match definition of References * debian/control: - cme fix dpkg-control * debian/rules: - dh - hardening [ Thorsten Alteholz ] * debian/rules: target get-orig-source added -- Andreas Tille Fri, 15 Nov 2013 13:54:30 +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 debian/AdunServer.10000644000000000000000000000137212214301263011323 0ustar .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). debian/UL.desktop0000644000000000000000000000030212214301263011066 0ustar [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 debian/compat0000644000000000000000000000000212241414740010363 0ustar 9 debian/control0000644000000000000000000000200512241420744010566 0ustar Source: adun.app Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Yavor Doganov Section: gnustep Priority: optional Build-Depends: debhelper (>= 9), gnustep-make, libgnustep-gui-dev, libgsl0-dev, imagemagick Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/adun.app/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/adun.app/trunk/ Homepage: http://diana.imim.es/Adun 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.