debian/0000755000000000000000000000000011716101062007161 5ustar debian/source/0000755000000000000000000000000011716101062010461 5ustar debian/source/format0000644000000000000000000000001411716101062011667 0ustar 3.0 (quilt) debian/dirs0000644000000000000000000000001111716101062010035 0ustar usr/bin debian/watch0000644000000000000000000000015611716101062010214 0ustar version=3 opts="dversionmangle=s/.dfsg$//" \ http://www.math.pitt.edu/~bard/bardware/xppaut([\d.]+)\.tar\.gz debian/patches/0000755000000000000000000000000011716101062010610 5ustar debian/patches/fix_makefile.diff0000644000000000000000000000256411716101062014074 0ustar diff --git a/Makefile b/Makefile index 38af165..06f046c 100644 --- a/Makefile +++ b/Makefile @@ -249,8 +249,6 @@ mkI77: cd libI77 ; make mkcvode: cd cvodesrc ; make -mkmkavi: - cd mkavi ; make # # Edited for Debian GNU/Linux. install: xppaut @@ -291,8 +289,7 @@ tarfile: tar cvf xppaut$(VERSION).tar $(SOURCES) $(AUTOSRC) $(HEADERS) $(BITMAPS) default.opt \ xpp_doc.tex README Makefile Makefile.nice Makefile.lib Makefile.avi Makefile.old \ ode/*.* xpp_doc.ps xpp_doc.pdf xpp_sum.tex xpp_sum.pdf xpp_sum.ps nullcline_bw.c \ - xppaut.1\ - mkavi/*.cc mkavi/*.h mkavi/Makefile mkavi/drive.c help/*.html \ + xppaut.1 help/*.html \ help/odes/*.ode help/odes/*.c install.pdf install.tex LICENSE HISTORY \ Makefile.s2x sbml2xpp.c *.xbm *.jar changes.txt gzip xppaut$(VERSION).tar @@ -301,8 +298,7 @@ otarfile: xpp_doc.tex README Makefile Makefile.nice Makefile.lib Makefile.avi Makefile.old \ ode/*.* xpp_doc.ps xpp_doc.pdf xpp_sum.tex xpp_sum.pdf xpp_sum.ps nullcline_bw.c \ libI77/*.c libI77/*.h libI77/Makefile \ - cvodesrc/*.c cvodesrc/*.h cvodesrc/Makefile xppaut.1\ - mkavi/*.cc mkavi/*.h mkavi/Makefile mkavi/drive.c help/*.html \ + cvodesrc/*.c cvodesrc/*.h cvodesrc/Makefile xppaut.1 help/*.html \ help/odes/*.ode help/odes/*.c install.pdf install.tex LICENSE HISTORY \ Makefile.s2x sbml2xpp.c *.xbm *.jar gzip xppaut$(VERSION).tar debian/patches/series0000644000000000000000000000004711716101062012026 0ustar 010_makefile.diff 040_menudrive_c.diff debian/patches/040_menudrive_c.diff0000644000000000000000000000221111716101062014321 0ustar diff --git a/menudrive.c b/menudrive.c index 0973452..1d43431 100644 --- a/menudrive.c +++ b/menudrive.c @@ -2,6 +2,7 @@ #include #include +#include /* the menu for XPP commands this calls any command it also has lots of the direct X Gui stuff @@ -118,20 +119,28 @@ void xpp_hlp() { char cmd[256]; - - if(getenv("XPPHELP")==NULL) - { - err_msg("Environment variable XPPHELP undefined."); - return; + char *helpPath; + helpPath = getenv("XPPHELP"); + + if(helpPath==NULL){ + struct stat* statBuff = (struct stat*) malloc(sizeof(struct stat)); + /* This is the default path on the Debian GNU/Linux system: */ + stat ("/usr/share/doc/xppaut/html", statBuff); + if (S_ISDIR (statBuff->st_mode)) + helpPath = "/usr/share/doc/xppaut/html"; + else { + err_msg("Environment variable XPPHELP undefined."); + return; + } } - + if (getenv("XPPBROWSER")==NULL) { err_msg("Environment variable XPPBROWSER undefined."); return; } - sprintf(cmd,"file:///%s",getenv("XPPHELP")); + sprintf(cmd,"file:///%s",helpPath); if(fork()==0){ debian/patches/010_makefile.diff0000644000000000000000000000345711716101062013610 0ustar --- a/Makefile +++ b/Makefile @@ -2,9 +2,9 @@ # Edited for Debian GNU/Linux. #BINDIR = /usr/X11R6/bin DESTDIR = -BINDIR = /usr/local/bin +BINDIR = /usr/bin DOCDIR = /usr/share/doc/xppaut -MANDIR = /usr/local/man/man1 +MANDIR = /usr/share/man/man1 # End Debian Edit ################################# # @@ -20,7 +20,7 @@ HELP=help/*.html # Use Gnu compiler #CC= gcc # Use c99 to compile according to newer ISO C standards (IEEE Std 1003.1-2001) -CC= gcc -std=c99 -pedantic -D_XOPEN_SOURCE=600 -Wall +CC= gcc -O -std=c99 -pedantic -D_XOPEN_SOURCE=600 -Wall #AUTLIBS= -lsundials_cvode -lX11 -lm #These are the 32bit compat libraries. AUTLIBS= -lm @@ -36,9 +36,9 @@ AUTLIBS= -lm #CFLAGS= -g -O -m32 -DNON_UNIX_STDIO -DAUTO -DCVODE_YES -DHAVEDLL -DMYSTR1=$(MAJORVER) -DMYSTR2=$(MINORVER) -I/usr/X11R6/include #CFLAGS= -g -O -m64 -DNOERRNO -DNON_UNIX_STDIO -DAUTO -DCVODE_YES -DHAVEDLL -DMYSTR1=$(MAJORVER) -DMYSTR2=$(MINORVER) -I/usr/include/X11 -CFLAGS= -g -pedantic -O -m32 -DNOERRNO -DNON_UNIX_STDIO -DAUTO -DCVODE_YES -DHAVEDLL -DMYSTR1=$(MAJORVER) -DMYSTR2=$(MINORVER) -I/usr/include/X11 +CFLAGS = -g -pedantic -O -DNOERRNO -DNON_UNIX_STDIO -DAUTO -DCVODE_YES -DHAVEDLL -DMYSTR1=$(MAJORVER) -DMYSTR2=$(MINORVER) -I/usr/include/X11 #LDFLAGS= -m64 -L/usr/lib -L/usr/lib64 -LDFLAGS= -m32 -L/usr/X11R6/lib +LDFLAGS= -L/usr/lib LIBS= -lX11 -lm -ldl # NOTE: Recent (RedHat 8) versions of GCC seem to no longer have # the integer errno, so compile with the -DNOERRNO option as well @@ -266,7 +266,7 @@ install: xppaut install -m 755 xppaut $(DESTDIR)$(BINDIR) cp -r ode* $(DESTDIR)$(DOCDIR)/examples cp -r help/* $(DESTDIR)$(DOCDIR)/html - cp README *.pdf $(DESTDIR)$(DOCDIR) + #cp README *.pdf $(DESTDIR)$(DOCDIR) cp *.xbm $(DESTDIR)$(DOCDIR)/xbm cp xppaut.1 $(DESTDIR)$(MANDIR) debian/patches/fix_macdirent.diff0000644000000000000000000000277011716101062014264 0ustar diff --git a/Makefile b/Makefile index a6c8cca..44d1c5a 100644 --- a/Makefile +++ b/Makefile @@ -113,8 +113,8 @@ HEADERS = abort.h comline.h extra.h kinescope.h newhome.h stiff.h\ array_print.h cvspgmr.h fmt.h local.h toons.h\ autevd.h dae_fun.h form_ode.h lread.h open.h torus.h\ autlib1.h delay_handle.h fp.h lunch-new.h parser.h txtread.h\ - autlib2.h del_stab.h gear.h macdirent.h parserslow.h uio.h\ - autlim.h dense.h getvar.h macsysdirent.h phsplan.h userbut.h\ + autlib2.h del_stab.h gear.h parserslow.h uio.h\ + autlim.h dense.h getvar.h phsplan.h userbut.h\ auto_define.h derived.h ggets.h main.h pop_list.h util.h\ auto.h dfe.h graf_par.h many_pops.h pp_shoot.h vector.h\ auto_nox.h diagram.h graphics.h markov.h rdfmt.h volterra2.h\ diff --git a/load_eqn.c b/load_eqn.c index 67b7724..e3611f8 100644 --- a/load_eqn.c +++ b/load_eqn.c @@ -16,7 +16,9 @@ #include "adj2.h" #include "arrayplot.h" #include "lunch-new.h" -#include "macdirent.h" +//#include "macdirent.h" +//SUbstitued with system dirent.h +#include #include "userbut.h" #include "volterra2.h" #include "storage.h" diff --git a/read_dir.c b/read_dir.c index 07e378a..b374e35 100644 --- a/read_dir.c +++ b/read_dir.c @@ -44,11 +44,12 @@ and save the file. */ -#ifdef MACOSX -#include "macdirent.h" -#else +//#ifdef MACOSX +//#include "macdirent.h" +//#else +// Just system dirent.h should work #include -#endif +//#endif #include #include #define MAXPATHLEN 1024 debian/changelog0000644000000000000000000001244211716101062011036 0ustar xppaut (6.11b+1.dfsg-1) unstable; urgency=low [ Jakub Nowacki ] * New upstream release; cleaned (DFSG) version [ Yaroslav Halchenko ] * debian/control: placed into 'science' section due to better fit * debian/copyright: added copyright information on debian/* content -- Yaroslav Halchenko Sun, 12 Feb 2012 22:02:27 -0500 xppaut (6.11b+1-1) UNRELEASED; urgency=low * New upstream release * Fixed patches dropped * menudrive.c patch fixed -- Jakub Nowacki Mon, 06 Feb 2012 21:48:57 +0000 xppaut (6.11b-1) UNRELEASED; urgency=low * New upstream release (fixed #216089, #448531) * Quilt related fixes: added debian/source/format and debian/README.source; minor fix to debian/changelog * Fixing lintian warning: debhelper-but-no-misc-depends * Application compiles and works well on 32 and 64-bits (fixed #412102, #557980, #566495, #293517) * Patches removing unused macdirent.h and mkavi added * Not used files deleted; debian/copyright updated -- Jakub Nowacki Sun, 30 Oct 2011 21:12:18 +0000 xppaut (6.11-1) UNRELEASED; urgency=low * New upstream release * Reviving from the dead (was removed from the archive, see #566638) * Switched to use dh7 * Patches fixed or dropped if not needed * Adjusted debian/copyright to be DEP-5 compliant * Git-related fields added to debian/control -- Jakub Nowacki Sat, 17 Sep 2011 22:45:11 +0100 xppaut (5.98-1) unstable; urgency=low * QA upload. * New upstream release. (Closes: #448531). * Move old source changes to quilt. * 050_manpage_section.diff - Fix manpage header entry for section 1. * Don't ship shared objects in /usr/share/doc/examples dir. * Watch file is OK. (Closes: #453576). * Bump Standards Version to 3.8.1. -- Barry deFreese Fri, 08 May 2009 15:51:50 -0400 xppaut (5.85-5) unstable; urgency=low * QA upload. * Makefile, Makefile.64: Let dh_strip do the stripping (honoring DEB_BUILD_OPTIONS=nostrip). Closes: #438314. * debian/rules: Doh, `MAKE +=', not `$(MAKE) +='. Closes: #412102. * debian/rules: Don't ignore errors from `$(MAKE) clean'. * debian/menu: Update section to Applications/Science/Mathematics. -- Matej Vela Tue, 21 Aug 2007 11:32:24 +0200 xppaut (5.85-4) unstable; urgency=low * QA upload. * Package is orphaned (#419087); set maintainer to Debian QA Group. * Switch to debhelper 5. * Update build dependencies for modular X. Closes: #419019. - Replace xlibs-data with xbitmaps. - Remove x-dev. * Makefile, Makefile.64: Fix bashism. * debian/menu: Add quotes to placate Lintian. * debian/rules: - Use perl to detect 64-bit machines. - Let dh_strip handle DEB_BUILD_OPTIONS=nostrip. * debian/watch: Fix pattern. * Conforms to Standards version 3.7.2. -- Matej Vela Sat, 28 Apr 2007 15:46:23 +0200 xppaut (5.85-3.3) unstable; urgency=low * Non-maintainer upload. * Implement alternative Makefile for 64 bit to fix segfaults on integration on amd64.(Closes: #412102) -- Neil Williams Wed, 28 Feb 2007 23:43:59 +0000 xppaut (5.85-3.2) unstable; urgency=low * Non-maintainer upload to help with xlibs-dev transition. * debian/control: Replace xlibs-dev build-dep. (Closes: #346836) -- Marc 'HE' Brockschmidt Fri, 20 Jan 2006 17:12:37 +0100 xppaut (5.85-3.1) unstable; urgency=low * Non-maintainer upload. * Fix FTBFS with gcc-4.0 (missing #include of ): Applied patch from Andreas Jochens . (closes: #306173) -- Rob Bradford Sat, 10 Sep 2005 00:51:41 +0100 xppaut (5.85-3) unstable; urgency=low * debian/doc-base - HTML help integrated with doc-base, closes: #222148 * new maintainer -- Balbir Thomas Thu, 5 Aug 2004 01:54:31 -0400 xppaut (5.85-2) unstable; urgency=low * debian/control - Updated to debhelper 4 - Updated the standards version * debian/rules - Reordered some lines in the clean rule so stamps are removed first - cleaned up comments - removed debhelper commands that did nothing: - commented ones - dh_installexamples - dh_clean -k - dh_installcron - dh_installinfo - dh_installman * debian/dirs - removed empty /usr/sbin directory -- Isaac Jones Fri, 7 Nov 2003 22:52:01 -0500 xppaut (5.85-1) unstable; urgency=low * New upstream release, closes: #216089 * Upstream Changelog: VERSION 5.85 July 2003 - added crosscorrelation - fixed some bugs - added clone which sort of works - added postscript options like font size, font type, line width * And From VERSION 5.6 Sept 2002 - added POISSON(t) function - nullclines in the animator -- Isaac Jones Sat, 18 Oct 2003 21:11:02 -0400 xppaut (5.57-1) unstable; urgency=low * New upstream release * Added some more information to the man page * Updated the standards version -- Isaac Jones Wed, 23 Apr 2003 22:46:07 -0400 xppaut (5.56-1) unstable; urgency=low * Initial Release. * Altered Makefile to add install target and DESTDIR -- Isaac Jones Mon, 20 October 2002 23:44:47 -0500 debian/copyright0000644000000000000000000000447111716101062011122 0ustar Format: http://dep.debian.net/deps/dep5/ Upstream-name: XPPAUT Upstream-contact: Bard Ermentraut Source: http://www.math.pitt.edu/~bard/xpp/download.html Files: * Copyright: 2002-2011 Bard Ermentrout & Daniel Dougherty License: GPL-2+ Files: fftn.c Copyright: 1995,97 Mark Olesen Queen's Univ at Kingston (Canada) Licence: custom Permission to use, copy, modify, and distribute this software for any purpose without fee is hereby granted, provided that this entire notice is included in all copies of any software which is or includes a copy or modification of this software and in all copies of the supporting documentation for such software. . THIS SOFTWARE IS BEING PROVIDED "AS IS", WITHOUT ANY EXPRESS OR IMPLIED WARRANTY. IN PARTICULAR, NEITHER THE AUTHOR NOR QUEEN'S UNIVERSITY AT KINGSTON MAKES ANY REPRESENTATION OR WARRANTY OF ANY KIND CONCERNING THE MERCHANTABILITY OF THIS SOFTWARE OR ITS FITNESS FOR ANY PARTICULAR PURPOSE. . All of which is to say that you can do what you like with this source code provided you don't try to sell it as your own and you include an unaltered copy of this message (including the copyright). . It is also implicitly understood that bug fixes and improvements should make their way back to the general Internet community so that everyone benefits. Files: debian/* Copyright: 2002-2003, Isaac Jones , 2011-2012, Jakub Nowacki License: GPL-2+ License: GPL-2+ This program 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 package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the full text of the GNU General Public License version 2 can be found in the file `/usr/share/common-licenses/GPL-2'. debian/xppaut.doc-base0000644000000000000000000000043111716101062012077 0ustar Document: xppaut Title: Xppaut Manual Author: Bard Ermentrout Abstract: A Brief description of Xppaut ode file syntax and interative command reference Section: Science/Mathematics Format:HTML Index: /usr/share/doc/xppaut/html/xpphelp.html Files: /usr/share/doc/xppaut/html/*.html debian/rules0000755000000000000000000000011111716101062010232 0ustar #!/usr/bin/make -f # Sample debian/rules that uses debhelper. %: dh $@ debian/README.source0000644000000000000000000000036111716101062011340 0ustar This package uses quilt to manage all modifications to the upstream source. Changes are stored in the source package as diffs in debian/patches and applied during the build. See /usr/share/doc/quilt/README.source for a detailed explanation. debian/docs0000644000000000000000000000000711716101062010031 0ustar README debian/blends0000644000000000000000000000020511716101062010350 0ustar Format: extended Source: xppaut Tasks: debian-science/neuroscience-modeling Pkg-URL: http://neuro.debian.net/pkgs/%(Pkg-Name)s.html debian/menu0000644000000000000000000000016111716101062010046 0ustar ?package(xppaut):needs="X11" section="Applications/Science/Mathematics" title="xppaut" command="/usr/bin/xppaut" debian/TODO0000644000000000000000000000011511716101062007646 0ustar * git-buildpackage git-pbuilder create git-buildpackage --git-pbuilder debian/control0000644000000000000000000000177311716101062010574 0ustar Source: xppaut Section: science Priority: optional Maintainer: Jakub Nowacki Uploaders: Yaroslav Halchenko , Michael Hanke Build-Depends: debhelper (>= 7), quilt, libx11-dev, xbitmaps Standards-Version: 3.9.2 Vcs-Git: git://github.com/neurodebian/pkg-xppaut.git Vcs-browser: https://github.com/neurodebian/pkg-xppaut Homepage: http://www.math.pitt.edu/~bard/xpp/xpp.html Package: xppaut Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: Phase Plane Plus Auto: Solves many kinds of equations XPPAUT is a tool for solving * differential equations, * difference equations, * delay equations, * functional equations, * boundary value problems, and * stochastic equations. . The code brings together a number of useful algorithms and is extremely portable. All the graphics and interface are written completely in Xlib which explains the somewhat idiosyncratic and primitive widgets interface. debian/compat0000644000000000000000000000000211716101062010357 0ustar 7