debian/0000775000000000000000000000000012255175442007177 5ustar debian/rules0000775000000000000000000000027012255174764010264 0ustar #!/usr/bin/make -f %: dh $@ override_dh_auto_clean: touch gdpc.o gdpc # ugly hack to let unpatched Makefile work $(MAKE) clean dh_clean override_dh_auto_install: # do nothing debian/watch0000664000000000000000000000012312255174764010232 0ustar version=3 http://www.frantz.fi/index.php?page=software software/gdpc-(.*)\.tar\.gz debian/gdpc-examples.dirs0000664000000000000000000000003512255174764012617 0ustar usr/share/doc/gdpc/examples/ debian/changelog0000664000000000000000000000567212255175211011055 0ustar gdpc (2.2.5-3ubuntu1) trusty; urgency=medium * Merge from Debian unstable. Remaining changes: - debian/patches/41_glib_deprecated_funcs.patch: Converted uses of deprecated glib functions, fixing FTBFS on amd64 buildds. * Drop 40_math_underlinkage.patch, as there is now a similar one in Debian. -- Logan Rosen Fri, 20 Dec 2013 21:17:44 -0500 gdpc (2.2.5-3) unstable; urgency=low * debian/control: - cme fix dpkg-control - debhelper 9 - Use anonscm in Vcs fields * debian/copyright: DEP5 * debian/patches/40_fix_gcc4.8_build.patch: Fix build with gcc4.8 Closes: #713652 -- Andreas Tille Tue, 15 Oct 2013 14:55:27 +0200 gdpc (2.2.5-2ubuntu2) raring; urgency=low * Converted uses of deprecated glib functions, fixing FTBFS on amd64 buildds. -- Daniel T Chen Sun, 07 Apr 2013 20:46:53 -0400 gdpc (2.2.5-2ubuntu1) raring; urgency=low * Added missing math lib to link, fixing FTBFS. -- Daniel T Chen Sun, 07 Apr 2013 18:21:13 -0400 gdpc (2.2.5-2) unstable; urgency=low * Do not use -DGDK_DISABLE_DEPRECATED (Thanks to Colin Watson for the patch) Closes: #642094 (LP: #770768) * Standards-Version: 3.9.2 (no changes needed) * debian/source/format: 3.0 (quilt) * Debhelper 8 (control+compat) -- Andreas Tille Fri, 09 Dec 2011 08:22:35 +0100 gdpc (2.2.5-1) unstable; urgency=low [ Charles Plessy ] * Removed category 'Utility' in debian/gdpc.desktop as it was making the entry appear in the 'Accessories' section of the GNOME menu. [ Andreas Tille ] * New upstream version * debian/control: - Added myself to uploaders - Standards-Version: 3.8.3 (added README.source) - Debhelper 7 - use quilt instead of simple-patchsys * debian/rules: short rules file using dh -- Andreas Tille Sun, 04 Oct 2009 09:59:31 +0200 gdpc (2.2.4-3) unstable; urgency=low * Updated gdpc homepage (Closes: #451920). Thanks Charles! * Updated Standards-Version; * Changed Maintainer to the Debian-Med Packaging Team; * Added Vcs-* fields. -- Nelson A. de Oliveira Thu, 21 Feb 2008 23:08:51 -0300 gdpc (2.2.4-2) unstable; urgency=low * Fix FTBS with newer libgtk2.0-0 versions (Launchpad #136973) Thanks to Stephan Hermann - Updated patches/Makefile.diff. * Updated debhelper compat level to 5; * Updated my email address; * Updated Standards-Version to 3.7.2; * Updated deprecated ${Source-Version} to ${source:Version}; * Updated menu file; * Updated watch file; * Updated FSF address in copyright file; * Added desktop file (Launchpad #36377) - Thanks to Phil Bull. -- Nelson A. de Oliveira Mon, 03 Sep 2007 12:06:20 -0300 gdpc (2.2.4-1) unstable; urgency=low * Initial Release (Closes: #306028). -- Nelson A. de Oliveira Sat, 23 Apr 2005 15:50:09 -0300 debian/gdpc.docs0000664000000000000000000000000712255174764010771 0ustar README debian/compat0000664000000000000000000000000212255175005010370 0ustar 9 debian/README.source0000664000000000000000000000026712255174764011371 0ustar This packages uses the quilt patch system. Please read /usr/share/doc/quilt/README.source for more information. -- Andreas Tille Mon, 31 Aug 2009 14:50:19 +0200 debian/copyright0000664000000000000000000000230012255175005011120 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: gdpc Source: http://www.frantz.fi/software/gdpc-2.2.5.tar.gz Files: * Copyright: © 1999-2009 Jonas Frantz License: GPL2+ Files: debian/* Copyright: © 2005-2008 Oliveira © 2009-2013 Andreas Tille License: GPL2+ License: GPL2+ This package 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 package 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 package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, 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-2'. debian/source/0000775000000000000000000000000012255175440010475 5ustar debian/source/format0000664000000000000000000000001412255174764011713 0ustar 3.0 (quilt) debian/manpages0000664000000000000000000000001612255174764010720 0ustar debian/gdpc.1 debian/gdpc.install0000664000000000000000000000011012255174764011502 0ustar debian/gdpc.desktop usr/share/applications/ gdpc usr/bin debian/gdpc.10000664000000000000000000000123212255174764010202 0ustar .TH GDPC 1 "Sun, 24 Apr 2005 02:40:13 -0300" .SH NAME gdpc \- program for visualising molecular dynamic simulations .SH DESCRIPTION This manual page documents briefly the .B gdpc command. .PP \fBgdpc\fP is a program, written in C and utilizing GTK, for visualising molecular dynamic simulations. It is a very versatile program and could easily be used for other purposes. \fBgdpc\fP reads \fIxyz\fP input and custom formats and can write out pictures of the frames. .SH AUTHOR gdpc was written by Jonas Frantz . .PP This manual page was written by Nelson A. de Oliveira , for the Debian project (but may be used by others). debian/gdpc.README.Debian0000664000000000000000000000236012255174764012163 0ustar gdpc for Debian --------------- EXAMPLES: --------- The gdpc-examples package contains 3 compressed files (liquid.test.gz, manytypes.test.gz and md.test.gz) located at /usr/share/doc/gdpc/examples/. They are included to demonstrate gdpc and to help in the process of learning how to use the program. KNOW CAVEATS: ------------- When opening a xyz file and "Arbitrary file format" is selected on "Input file format" (or the opposite), gdpc will quit. If you run gdpc from the command prompt, it will display a message like this: Error in input file : 976 Are you sure the input file isn't in xyz format ? Exiting. You must verify the type of file that you are using and that you selected before clicking on 'OK', or gdpc will quit if using a wrong combination of formats. KNOW PROBLEMS: -------------- Rare: There seems to be a problem with GTK+ stability on the alpha platform, gdpc exits on floating exception. Seems to depend on the value of the -O parameter used during compilation. Weird: There seems to be some strange bug in the rotation/reset orientation department, sometimes reset orientation kills restart and setup button. May be resolved, no confirmation. -- Nelson A. de Oliveira , Thu, 02 Jun 2005 20:40:35 -0300 debian/gdpc.desktop0000664000000000000000000000052712255174764011521 0ustar [Desktop Entry] Version=1.0 Name=GDPC Molecular Dynamic Simulator GenericName=Molecular Dynamic Simulator Comment=Visualize molecular dynamic simulations Comment[en_GB]=Visualise molecular dynamic simulations Comment[pt_BR]=Visualizador de simulações moleculares dinâmicas Type=Application Exec=gdpc Categories=Science;Chemistry;Education; debian/menu0000664000000000000000000000015412255174764010074 0ustar ?package(gdpc):needs="X11" section="Applications/Science/Chemistry"\ title="gdpc" command="/usr/bin/gdpc" debian/control0000664000000000000000000000274012255175214010602 0ustar Source: gdpc Maintainer: Ubuntu Developers XSBC-Original-Maintainer: Debian Med Packaging Team Uploaders: Nelson A. de Oliveira , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9), libgtk2.0-dev Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/gdpc/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/gdpc/trunk/ Homepage: http://www.frantz.fi/software/gdpc.php Package: gdpc Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: gdpc-examples (>= ${source:Version}), gqview Description: visualiser of molecular dynamic simulations gpdc is a graphical program for visualising output data from molecular dynamics simulations. It reads input in the standard xyz format, as well as other custom formats, and can output pictures of each frame in JPG or PNG format. Package: gdpc-examples Architecture: all Depends: ${misc:Depends} Recommends: gdpc (>= ${source:Version}) Description: example files for the gdpc program gpdc is a graphical program for visualising output data from molecular dynamics simulations. It reads input in the standard xyz format, as well as other custom formats, and can output pictures of each frame in JPG or PNG format. . This package contains examples to be used by the gdpc program. debian/gdpc-examples.install0000664000000000000000000000004412255174764013324 0ustar *.test usr/share/doc/gdpc/examples/ debian/dirs0000664000000000000000000000003712255174764010071 0ustar usr/bin usr/share/applications debian/patches/0000775000000000000000000000000012255175440010624 5ustar debian/patches/series0000664000000000000000000000016212255175044012040 0ustar 20_Makefile_options.patch 30_gdk_enable_deprecated.patch 40_fix_gcc4.8_build.patch 41_glib_deprecated_funcs.patch debian/patches/30_gdk_enable_deprecated.patch0000664000000000000000000000160212255174764016411 0ustar Description: Drop -DGDK_DISABLE_DEPRECATED gdpc uses GDK drawing functions, and needs to be converted to use Cairo instead. In the meantime, -DGDK_DISABLE_DEPRECATED unhelpfully breaks prototypes in release builds, so drop it. Author: Colin Watson Bug-Ubuntu: https://bugs.launchpad.net/bugs/770768 Forwarded: no Last-Update: 2011-09-19 Index: b/Makefile =================================================================== --- a/Makefile +++ b/Makefile @@ -1,5 +1,5 @@ CC = gcc -FLAGS=$(CFLAGS) -g -Wall `pkg-config --cflags gtk+-2.0 gthread-2.0` -DG_DISABLE_DEPRECATED -DGDK_DISABLE_DEPRECATED -DGDK_PIXBUF_DISABLE_DEPRECATED -DGTK_DISABLE_DEPRECATED +FLAGS=$(CFLAGS) -g -Wall `pkg-config --cflags gtk+-2.0 gthread-2.0` -DG_DISABLE_DEPRECATED -DGDK_PIXBUF_DISABLE_DEPRECATED -DGTK_DISABLE_DEPRECATED LIBS=`pkg-config --libs gtk+-2.0 gthread-2.0` bindir ?= /usr/bin debian/patches/41_glib_deprecated_funcs.patch0000664000000000000000000000275012255174764016460 0ustar Index: gdpc-2.2.5/main.c =================================================================== --- gdpc-2.2.5.orig/main.c 2009-04-21 14:03:07.000000000 -0400 +++ gdpc-2.2.5/main.c 2013-04-07 21:21:46.208492431 -0400 @@ -848,9 +848,9 @@ #endif for (i=0;iframeready[i] = g_mutex_new(); + g_mutex_init (params->frameready[i]); g_mutex_lock (params->frameready[i]); - params->framedrawn[i] = g_mutex_new(); + g_mutex_init (params->framedrawn[i]); g_mutex_unlock (params->framedrawn[i]); params->framedata[i] = NULL; } @@ -860,15 +860,15 @@ printf("Initialising filewait/EOF semaphores.\n"); #endif - params->filewait = g_mutex_new(); + g_mutex_init (params->filewait); g_mutex_lock (params->filewait); - params->atEnd = g_mutex_new(); + g_mutex_init (params->atEnd); #if Debug printf("Starting filereading thread.\n"); #endif - th_a = g_thread_create ((GThreadFunc) readinput, (gpointer) params, TRUE, NULL); + th_a = g_thread_try_new ("some_thread", (GThreadFunc) readinput, (gpointer) params, NULL); if (th_a == NULL) { fprintf(stderr, "Creating read thread failed.\n"); gtk_main_quit (); @@ -927,8 +927,6 @@ /* Start gtk initialization. */ gtk_init (&argc, &argv); - g_thread_init(NULL); - printf("\n gdpc version "GDPCVER", Copyright (C) 2000 Jonas Frantz\n"); printf(" gdpc comes with ABSOLUTELY NO WARRANTY; for details\n"); printf(" check out the documentation. This is free software, and\n"); debian/patches/40_fix_gcc4.8_build.patch0000664000000000000000000000103112255175005015153 0ustar Author: Andreas Tille Last-Update: Tue, 15 Oct 2013 14:55:27 +0200 Bug-Debian: http://bugs.debian.org/713652 Description: Add missing -lm to linker which is required when using gcc 4.8 --- a/Makefile +++ b/Makefile @@ -1,6 +1,6 @@ CC = gcc FLAGS=$(CFLAGS) -g -Wall `pkg-config --cflags gtk+-2.0 gthread-2.0` -DG_DISABLE_DEPRECATED -DGDK_PIXBUF_DISABLE_DEPRECATED -DGTK_DISABLE_DEPRECATED -LIBS=`pkg-config --libs gtk+-2.0 gthread-2.0` +LIBS=`pkg-config --libs gtk+-2.0 gthread-2.0` -lm bindir ?= /usr/bin .c.o: debian/patches/20_Makefile_options.patch0000664000000000000000000000164412255174764015453 0ustar Author: Andreas Tille (adopted from previous patch of Nelson A. de Oliveira ) Description: Enable Debian comppile options into upstream Makefile, Fix clean target to work also on already cleaned upstream source --- gdpc-2.2.5.orig/Makefile +++ gdpc-2.2.5/Makefile @@ -4,10 +4,10 @@ bindir ?= /usr/bin .c.o: - $(CC) -c $(FLAGS) $(CPPFLAGS) $< + $(CC) -c $(COPTIONS) $(FLAGS) $(CPPFLAGS) $< gdpc: main.o colors.o sort.o drawatoms.o readinput.o init.o rotate.o setup.o Makefile - $(CC) $(CFLAGS) -o gdpc main.o colors.o drawatoms.o init.o sort.o rotate.o setup.o readinput.o $(LIBS) + $(CC) $(COPTIONS) $(CFLAGS) -o gdpc main.o colors.o drawatoms.o init.o sort.o rotate.o setup.o readinput.o $(LIBS) main.o: main.c parameters.h @@ -26,7 +26,7 @@ setup.o: setup.c parameters.h tooltips.h clean: - rm *.o gdpc + rm -f *.o gdpc install: install -p -m 755 -D gdpc $(bindir)/gdpc