debian/0000755000000000000000000000000012262735033007171 5ustar debian/sofa-apps.install0000644000000000000000000000014311761714730012454 0ustar debian/sofa.desktop usr/share/applications debian/sofa.xpm usr/share/pixmaps debian/sofa usr/bin debian/libsofa1-dev.install0000644000000000000000000000005211761714730013036 0ustar #lib/lib*.a usr/lib lib/*/lib*.so usr/lib debian/sofa.menu0000644000000000000000000000021611622751360011006 0ustar ?package(sofa):needs="X11" section="Applications/Science/Medicine"\ title="SOFA" command="/usr/bin/sofa" icon="/usr/share/pixmaps/sofa.xpm" debian/sofa-doc.install0000644000000000000000000000005711761714730012262 0ustar debian/index.html usr/share/doc/sofa-doc/html debian/copyright0000644000000000000000000000510511725665773011145 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Contact: Francois Faure Debianized-By: Dominique Belhachemi Debianized-Date: Tue, 24 Jun 2008 20:51:56 +0200 Original-Source: http://www.sofa-framework.org/ Files: framework/* Copyright: 2006-2008 MGH, INRIA, USTL, UJF, CNRS License: LGPL-2.1+ see `/usr/share/common-licenses/LGPL-2.1' Files: modules/* Copyright: 2006-2008 MGH, INRIA, USTL, UJF, CNRS License: LGPL-2.1+ see `/usr/share/common-licenses/LGPL-2.1' Files: applications/* Copyright: 2006-2008 MGH, INRIA, USTL, UJF, CNRS License: GPL-2+ see `/usr/share/common-licenses/GPL-2' Files: extlibs/LML/* Copyright: 2003 TIMC (Emmanuel Promayon) License: GPL-2+ see `/usr/share/common-licenses/GPL-2' Files: extlibs/miniFlowVR/* Copyright: 2005 Laboratoire Informatique et Distribution (UMR5132), INRIA Project MOVI. License: LGPL see `/usr/share/common-licenses/LGPL' Files: extlibs/miniFlowVR/src/librender/* Copyright: 2005 Laboratoire Informatique et Distribution (UMR5132), INRIA Project MOVI. License: GPL see `/usr/share/common-licenses/GPL' Files: extlibs/PML/* Copyright: 2001 TIMC (Emmanuel Promayon, Matthieu Chabanas) License: GPL-2+ see `/usr/share/common-licenses/GPL-2' Files: extlibs/csparse/* Copyright: 2006, Timothy A. Davis. License: LGPL-2.1+ see `/usr/share/common-licenses/LGPL-2.1' Files: extlibs/tinyxml/* Copyright: 2000-2006 Lee Thomason (www.grinninglizard.com) License: ZLIB This software is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software. . Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions: . 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required. . 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. . 3. This notice may not be removed or altered from any source distribution. Files: * Copyright: 2006-2008 MGH, INRIA, USTL, UJF, CNRS License: LGPL see `/usr/share/common-licenses/LGPL' Files: debian/* Copyright: 2008, Dominique Belhachemi License: GPL-2+ The Debian packaging is licensed under the GPL, see `/usr/share/common-licenses/GPL-2' debian/sofa-tutorials.install0000644000000000000000000000003111761714730013533 0ustar tutorials usr/share/sofa debian/get-orig-source0000755000000000000000000000443411761714730012143 0ustar #!/bin/sh # get source for sofa-framework which assembles sofa-framework, sofa-modules and sofa-applications set -e # set -x NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` if ! echo $@ | grep -q upstream-version ; then VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'` # regard dversionmangle VERSION=`echo ${VERSION} | sed 's/\([0-9]\)~\([br]\)/\1-\2/'` else VERSION=`echo $@ | sed 's?^.*--upstream-version \([-0-9.rcbeta]\+\) .*sofa-framework.*?\1?'` if echo "$VERSION" | grep -q "upstream-version" ; then echo "Unable to parse version number" exit fi fi TARBALLDIR=../tarballs mkdir -p ${TARBALLDIR} indexpage=`grep www.sofa-framework.org debian/watch | sed 's/^.*\(http:[^[:space:]]\+\)[[:space:]].*$/\1/'` cd ${TARBALLDIR} wget -q -N "$indexpage" if [ -e ../${NAME}-${VERSION}.zip ] ; then mv ../${NAME}-${VERSION}.zip . else wget -q -N --no-check-certificate `grep framework.*\.zip download | sed "s?^.*\(https://gforge.inria.fr/frs/download.php/[0-9]\+/sofa-framework-${VERSION}\.zip\).*?\1?"` fi wget -q -N --no-check-certificate `grep modules.*\.zip download | sed "s?^.*\(https://gforge.inria.fr/frs/download.php/[0-9]\+/sofa-modules-${VERSION}\.zip\).*?\1?"` wget -q -N --no-check-certificate `grep applications.*\.zip download | sed "s?^.*\(https://gforge.inria.fr/frs/download.php/[0-9]\+/sofa-applications-${VERSION}\.zip\).*?\1?"` rm download OUTPUTDIR=sofa-${VERSION} rm -rf ${OUTPUTDIR} mkdir -p ${OUTPUTDIR} cd ${OUTPUTDIR} find .. -mindepth 1 -maxdepth 1 -name "sofa-*.zip" -exec unzip -q \{\} \; find .. -mindepth 1 -maxdepth 1 -name "sofa-*.zip" -delete rm -rf extlibs/miniBoost # libboost-dev rm -rf extlibs/libQGLViewer* # libqglviewer-dev rm -rf extlibs/eigen* # libeigen3-dev # rm -rf extlibs/qwt* # libqwt5-qt4-dev rm -rf extlibs/newmat # libnewmat10-dev rm -rf extlibs/csparse # libsuitesparse-dev rm -rf extlibs/tinyxml # libtinyxml-dev (>= 2.6) # the external libraries are still there: # LML miniFlowVR PML tinyxml cd .. # might need to mangle version (untested) VERSION=`echo ${VERSION} | sed 's/\([0-9]\)-\([br]\)/\1~\2/'` GZIP="--best --no-name" tar czf sofa-framework_${VERSION}.orig.tar.gz ${OUTPUTDIR} rm -rf ${OUTPUTDIR} debian/libsofa1.install0000644000000000000000000000003511761714730012263 0ustar lib/*/lib*.so.[0-9]* usr/lib debian/changelog0000644000000000000000000001544712262735033011056 0ustar sofa-framework (1.0~beta4-8build1) trusty; urgency=medium * Rebuild against glew 1.10. -- Matthias Klose Tue, 07 Jan 2014 09:25:27 +0100 sofa-framework (1.0~beta4-8) unstable; urgency=low * Team upload. * Drop "-mt" suffix from boost lib, in the 50_all_changes.diff (Closes: #701288) * Add missing include which causes undefined symbols (Closes: #560104) (Closes: #701360) -- Dmitrijs Ledkovs Wed, 10 Jul 2013 00:56:09 +0100 sofa-framework (1.0~beta4-7.1) unstable; urgency=low * Non-maintainer upload. * Remove build-dep on quilt. * Change build-dep from libqglviewer-qt4-dev to libqglviewer-dev. * Remove obsolete DM-Upload flag. * Fix FTBFS against libpng1.5. (Closes: #650568) -- Anton Gladky Mon, 20 May 2013 19:44:00 +0200 sofa-framework (1.0~beta4-7) unstable; urgency=low * debian/watch: also seek for https URLs * debian/get-orig-source: - Fetch any new version not only one hard coded version - Make sure also versioned external library sources will be removed * debian/rules - debian/*.{install,manpages} (make more use of dh_* helper files) - Fixed clean target - use short dh to simplify further packaging including hardening * debian/control: - Build-Depends: libeigen3-dev, libqglviewer-qt4-dev, libsuitesparse-dev - Build-Depends: s/libpng12-dev/libpng-dev/ Closes: #662508 - Standards-Version: 3.9.3 (no changes needed) - Do not build sofa-doc by default (see README.source) * debian/copyright: ensure DEP5 by fixing using cme fix dpkg-copyright * debian/patches/sofa-framework-gcc-4.7.diff: Fix gcc-4.7 build issue Thanks to Matej Vela for the patch Closes: #673841 * debian/README.source: - delete remark about quilt which is redundant these days - add remark why sofa-doc is not builded any more and how the package could be build for private use * debhelper 9 (control+compat) -- Andreas Tille Thu, 31 May 2012 16:19:59 +0200 sofa-framework (1.0~beta4-6.1) unstable; urgency=low * Non maintainer upload. * Fix build failure with GCC 4.7 (Matej Vela). Closes: #673841. -- Matthias Klose Tue, 29 May 2012 09:18:41 +0000 sofa-framework (1.0~beta4-6) unstable; urgency=low [ Nelson A. de Oliveira ] * Fix menu file * Updated build-dependency on libqwt-dev (Closes: #638170) [ Andreas Tille ] * debian/control: - Standards-Version: 3.9.2 (no changes needed) - Fixed Vcs-Svn - Build-Depends: + s/libpng-dev/libpng12-dev/ + s/libqwt-dev/libqwt5-qt4-dev/ * debian/rules - Do not remove extlibs/tinyxml in clean target which is just part of the upstream source. The proper place to remove things like this would be in get-orig-source. - Polishing after clean target which leaves several files hanging around * debian/patches/qwt5-qt4.patch: Sofa does not build properly with libqwt-dev so adjusting include directory and fixing some header file is needed * debian/sofa.1: Fixed spelling error -- Andreas Tille Tue, 13 Dec 2011 12:55:52 +0100 sofa-framework (1.0~beta4-5.1) unstable; urgency=high * Non-maintainer upload. * Fix build failure due to new TinyXML 2.6 (Closes: #628114). Thanks to Felix Geyer for the patch. * Bump build-dep on libtinyxml-dev to 2.6. -- Mehdi Dogguy Sun, 29 May 2011 18:02:12 +0200 sofa-framework (1.0~beta4-5) unstable; urgency=low * Switch to dpkg-source 3.0 (quilt) format * debian/rules: drop the quilt patch/unpatch logic * patches/fix_mutable_serr_sout.diff: remove mutable keyword (Closes: #625059) * bump Standards-Version: 3.9.1 (no changes) * set debian/compat to 8 * debian/control: removed duplicated "section" fields * Changed debian/sofa.desktop's category to Education;Science * (Closes: #594671, LP: #605497) -- Dominique Belhachemi Sat, 07 May 2011 20:21:51 -0400 sofa-framework (1.0~beta4-4) unstable; urgency=low * use Debian's libtinyxml-dev (Closes: #573941) * reduce optimization level to -O1 as a workaround for linking failure (Thanks to Ilya Barygi) (Closes: #560104) * fixed FTBFS for SuperH (Thanks to Nobuhiro Iwamatsu) (Closes: #567223) -- Dominique Belhachemi Tue, 16 Mar 2010 17:42:22 -0400 sofa-framework (1.0~beta4-3) unstable; urgency=low [Dominique Belhachemi] * added linker option --no-add-needed (Closes: #556352) libdl had to be added to the list of libraries * switched from dpatch to quilt * added debain/README.source * removed dh_desktop from debian/rules [Andreas Tille] * debian/control: - Added missing Vcs tags - Standards-Version: 3.8.3 (no changes) -- Dominique Belhachemi Sun, 06 Dec 2009 20:18:59 -0500 sofa-framework (1.0~beta4-2) unstable; urgency=low * csparse support disabled because it conflicts with the newer version in libsuitesparse-dev (Closes: #532693) * Build-Conflicts: qt3-dev-tools added * lost GCC 4.4 patches added (Closes: #532396) -- Dominique Belhachemi Wed, 17 Jun 2009 23:10:35 -0400 sofa-framework (1.0~beta4-1) unstable; urgency=low * new upstream release * Qt OGRE 3D viewer disabled (Closes: #527706) * MIPS/ARM patch, AMD64 patch and Newmat patch removed because they have been applied by upstream (Thanks to Everton Hermann) -- Dominique Belhachemi Sun, 07 Jun 2009 14:35:15 -0400 sofa-framework (1.0~beta3-5) unstable; urgency=low * set SOFA_QT4 explicitly * added #include headers required by GCC 4.4 (Closes: #505953) * added missing PML files * fixed sofa wrapper -- Dominique Belhachemi Sat, 15 Nov 2008 19:45:47 +0100 sofa-framework (1.0~beta3-4) unstable; urgency=low * PML/LML support enabled * PNG support enabled * Qt OGRE 3D viewer enabled * debian/control: doxygen & graphviz moved to Build-Depends-Indep -- Dominique Belhachemi Wed, 12 Nov 2008 20:36:57 +0100 sofa-framework (1.0~beta3-3) unstable; urgency=low * fixed build-indep issue (Closes: #503555) * fixed MIPS and ARM build error (sqrt/sqrtl) * fixed installation for man page (Closes: #504927) -- Dominique Belhachemi Sat, 08 Nov 2008 01:50:23 +0100 sofa-framework (1.0~beta3-2) unstable; urgency=low * fixed segfault on amd64 * build arch all packages only in the binary-indep target (Closes: #503555) * fixed MIPS and ARM build error (sqrt/sqrtl) -- Dominique Belhachemi Thu, 30 Oct 2008 19:23:49 +0100 sofa-framework (1.0~beta3-1) unstable; urgency=low * Initial release (Closes: #455064) -- Dominique Belhachemi Wed, 13 Aug 2008 10:26:03 +0100 debian/sofa-data.install0000644000000000000000000000005611761714730012425 0ustar share usr/share/sofa examples usr/share/sofa debian/sofa-apps.manpages0000644000000000000000000000001311675211474012576 0ustar debian/*.1 debian/compat0000644000000000000000000000000211622747433010375 0ustar 8 debian/sofa-doc.doc-base0000644000000000000000000000101011064025703012246 0ustar Document: sofa-doc Title: SOFA class documentation Author: Various Abstract: GUI for the Simulation Open Framework Architecture (SOFA) SOFA is an Open Source framework primarily targeted at real-time simulation, with an emphasis on medical simulation. It is mostly intended for the research community to help develop newer algorithms, but can also be used as an efficient prototyping tool. Section: Programming Format: HTML Index: /usr/share/doc/sofa-doc/html/index.html Files: /usr/share/doc/sofa-doc/html/*.html debian/patches/0000755000000000000000000000000012171756325010626 5ustar debian/patches/fix-undefined-symbol.patch0000644000000000000000000000117312171755331015675 0ustar Description: missing include of template function definitons Bug-Debian: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=701360 Bug-Debian: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=560104 Author: Dmitrijs Ledkovs --- sofa-framework-1.0~beta4.orig/modules/sofa/simulation/tree/GNode.cpp +++ sofa-framework-1.0~beta4/modules/sofa/simulation/tree/GNode.cpp @@ -26,6 +26,7 @@ #include #include #include +#include #include using std::cerr; debian/patches/55_fix_mips_sqrt.diff0000644000000000000000000000204011761714730014652 0ustar #! /bin/sh /usr/share/dpatch/dpatch-run ## 55_fix_mips_sqrt.dpatch by ## ## All lines beginning with `## DP:' are a description of the patch. ## DP: fixes a build error on MIPS, ARM, and SuperH (sqrt/sqrtl) @DPATCH@ Index: sofa-framework-1.0~beta4/framework/sofa/helper/rmath.h =================================================================== --- sofa-framework-1.0~beta4.orig/framework/sofa/helper/rmath.h 2009-12-06 14:23:24.000000000 -0500 +++ sofa-framework-1.0~beta4/framework/sofa/helper/rmath.h 2009-12-06 14:23:29.000000000 -0500 @@ -132,8 +132,8 @@ inline double rsqrt(const double& a) { -#if defined(__GNUC__) - return sqrt(a); +#if defined(__arm__) || defined(__mips__) || defined(__sh__) + return sqrt((double)a); #else return (double)sqrtl((long double)a); #endif @@ -141,7 +141,11 @@ inline long double rsqrt(const long double& a) { +#if defined(__arm__) || defined(__mips__) || defined(__sh__) + return (long double)sqrt((double)a); +#else return sqrtl(a); +#endif } template debian/patches/78_atomicity.diff0000644000000000000000000000203311761714730013774 0ustar ## 78_atomicity.dpatch by ## ## All lines beginning with `## DP:' are a description of the patch. ## DP: fix: error: bits/atomicity.h: No such file or directory Index: sofa-framework-1.0~beta4/framework/sofa/helper/system/atomic.h =================================================================== --- sofa-framework-1.0~beta4.orig/framework/sofa/helper/system/atomic.h 2009-12-06 14:20:15.000000000 -0500 +++ sofa-framework-1.0~beta4/framework/sofa/helper/system/atomic.h 2009-12-06 14:20:36.000000000 -0500 @@ -31,9 +31,10 @@ #if defined(SOFA_USE_ASM_ATOMIC) #include -#include // for __exchange_and_add -#elif defined(__GNUC__) && (defined(i386) || defined(__i386__) || defined(__x86_64__)) -// custom ASM code, no include +#endif + +#if defined( __GNUC__ ) && ( __GNUC__ * 100 + __GNUC_MINOR__ >= 402 ) +# include #elif defined(__GNUC__) // Fall-back mode: stdc++ atomic operations (should be available on all gcc-supported platforms) #include debian/patches/sofa-framework-1.0~beta4.libpng15.patch0000644000000000000000000000116612171755331017624 0ustar Description: fixes FTBFS against libpng1.5 Author: Nobuhiro Iwamatsu Origin: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=650568#12 Bug-Debian: http://bugs.debian.org/650568 Acked-by: Anton Gladky Last-Update: 2013-05-20 --- a/framework/sofa/helper/io/ImagePNG.cpp +++ b/framework/sofa/helper/io/ImagePNG.cpp @@ -129,7 +129,11 @@ if (color_type == PNG_COLOR_TYPE_GRAY && bit_depth < 8) { +#if PNG_LIBPNG_VER_MAJOR >= 1 && PNG_LIBPNG_VER_MINOR >= 4 + png_set_expand_gray_1_2_4_to_8(PNG_reader); +#else png_set_gray_1_2_4_to_8(PNG_reader); +#endif changed = true; } debian/patches/sofa-framework-gcc-4.7.diff0000644000000000000000000003270111761714730015444 0ustar Description: Fix build issue when using gcc-4.7 Author: Matej Vela Date: Sat, 26 May 2012 23:09:58 +0100 Bug-Debian: http://bugs.debian.org/673841 --- sofa-framework-1.0~beta4~/framework/sofa/core/componentmodel/behavior/MechanicalMapping.inl +++ sofa-framework-1.0~beta4/framework/sofa/core/componentmodel/behavior/MechanicalMapping.inl @@ -88,14 +88,14 @@ void MechanicalMapping::propagateX() { if (this->fromModel!=NULL && this->toModel->getX()!=NULL && this->fromModel->getX()!=NULL) - apply(*this->toModel->getX(), *this->fromModel->getX()); + this->apply(*this->toModel->getX(), *this->fromModel->getX()); } template void MechanicalMapping::propagateV() { if (this->fromModel!=NULL && this->toModel->getV()!=NULL && this->fromModel->getV()!=NULL) - applyJ(*this->toModel->getV(), *this->fromModel->getV()); + this->applyJ(*this->toModel->getV(), *this->fromModel->getV()); } template @@ -110,14 +110,14 @@ void MechanicalMapping::propagateDx() { if (this->fromModel!=NULL && this->toModel->getDx()!=NULL && this->fromModel->getDx()!=NULL) - applyJ(*this->toModel->getDx(), *this->fromModel->getDx()); + this->applyJ(*this->toModel->getDx(), *this->fromModel->getDx()); } template void MechanicalMapping::propagateXfree() { if (this->fromModel!=NULL && this->toModel->getXfree()!=NULL && this->fromModel->getXfree()!=NULL) - apply(*this->toModel->getXfree(), *this->fromModel->getXfree()); + this->apply(*this->toModel->getXfree(), *this->fromModel->getXfree()); } --- sofa-framework-1.0~beta4~/modules/sofa/component/constraint/DistanceConstraint.inl +++ sofa-framework-1.0~beta4/modules/sofa/component/constraint/DistanceConstraint.inl @@ -147,9 +147,9 @@ V2.insert(idx2,V12);c2.push_back(V2); } - core::componentmodel::behavior::BaseLMConstraint::constraintGroup *constraintAcc = addGroupConstraint(this->ACC); - core::componentmodel::behavior::BaseLMConstraint::constraintGroup *constraintVel = addGroupConstraint(this->VEL); - core::componentmodel::behavior::BaseLMConstraint::constraintGroup *constraintPos = addGroupConstraint(this->POS); + core::componentmodel::behavior::BaseLMConstraint::constraintGroup *constraintAcc = this->addGroupConstraint(this->ACC); + core::componentmodel::behavior::BaseLMConstraint::constraintGroup *constraintVel = this->addGroupConstraint(this->VEL); + core::componentmodel::behavior::BaseLMConstraint::constraintGroup *constraintPos = this->addGroupConstraint(this->POS); //BaseLMConstraint interface constraintAcc->addConstraint(idxInVecConst[0], idxInVecConst[1], --- sofa-framework-1.0~beta4~/modules/sofa/component/constraint/UnilateralInteractionConstraint.inl +++ sofa-framework-1.0~beta4/modules/sofa/component/constraint/UnilateralInteractionConstraint.inl @@ -71,7 +71,7 @@ c.contactId = id; - if (rabs(delta - deltaFree) > 0.001 * delta) + if (helper::rabs(delta - deltaFree) > 0.001 * delta) { dt = delta / (delta - deltaFree); if (dt > 0.0 && dt < 1.0 ){ --- sofa-framework-1.0~beta4~/modules/sofa/component/container/MappedObject.inl +++ sofa-framework-1.0~beta4/modules/sofa/component/container/MappedObject.inl @@ -36,8 +36,8 @@ template MappedObject::MappedObject() -: f_X( initData(&f_X, "position", "position vector") ) -, f_V( initData(&f_V, "velocity", "velocity vector") ) +: f_X( this->initData(&f_X, "position", "position vector") ) +, f_V( this->initData(&f_V, "velocity", "velocity vector") ) { } --- sofa-framework-1.0~beta4~/modules/sofa/component/forcefield/BoxStiffSpringForceField.inl +++ sofa-framework-1.0~beta4/modules/sofa/component/forcefield/BoxStiffSpringForceField.inl @@ -48,8 +48,8 @@ template BoxStiffSpringForceField::BoxStiffSpringForceField(MechanicalState* object1, MechanicalState* object2, double ks, double kd) : StiffSpringForceField(object1, object2, ks, kd), - box_object1( initData( &box_object1, Vec6(0,0,0,1,1,1), "box_object1", "Box for the object1 where springs will be attached") ), - box_object2( initData( &box_object2, Vec6(0,0,0,1,1,1), "box_object2", "Box for the object2 where springs will be attached") ) + box_object1( this->initData( &box_object1, Vec6(0,0,0,1,1,1), "box_object1", "Box for the object1 where springs will be attached") ), + box_object2( this->initData( &box_object2, Vec6(0,0,0,1,1,1), "box_object2", "Box for the object2 where springs will be attached") ) { } @@ -57,8 +57,8 @@ template BoxStiffSpringForceField::BoxStiffSpringForceField(double ks, double kd) : StiffSpringForceField(ks, kd), - box_object1( initData( &box_object1, Vec6(0,0,0,1,1,1), "box_object1", "Box for the object1 where springs will be attached") ), - box_object2( initData( &box_object2, Vec6(0,0,0,1,1,1), "box_object2", "Box for the object2 where springs will be attached") ) + box_object1( this->initData( &box_object1, Vec6(0,0,0,1,1,1), "box_object1", "Box for the object1 where springs will be attached") ), + box_object2( this->initData( &box_object2, Vec6(0,0,0,1,1,1), "box_object2", "Box for the object2 where springs will be attached") ) { } --- sofa-framework-1.0~beta4~/modules/sofa/component/forcefield/HexahedronFEMForceFieldAndMass.inl +++ sofa-framework-1.0~beta4/modules/sofa/component/forcefield/HexahedronFEMForceFieldAndMass.inl @@ -48,8 +48,8 @@ HexahedronFEMForceFieldAndMass::HexahedronFEMForceFieldAndMass() : MassT() , HexahedronFEMForceFieldT() - ,_elementMasses(initData(&_elementMasses,"massMatrices", "Mass matrices per element (M_i)")) - , _density(initData(&_density,(Real)1.0,"density","density == volumetric mass in english (kg.m-3)")) + ,_elementMasses(this->initData(&_elementMasses,"massMatrices", "Mass matrices per element (M_i)")) + , _density(this->initData(&_density,(Real)1.0,"density","density == volumetric mass in english (kg.m-3)")) { _lumpedMass = this->initData(&_lumpedMass,false,"lumpedMass","Does it use lumped masses?"); } --- sofa-framework-1.0~beta4~/modules/sofa/component/forcefield/RegularGridSpringForceField.h +++ sofa-framework-1.0~beta4/modules/sofa/component/forcefield/RegularGridSpringForceField.h @@ -63,32 +63,32 @@ public: RegularGridSpringForceField(core::componentmodel::behavior::MechanicalState* object1, core::componentmodel::behavior::MechanicalState* object2) : StiffSpringForceField(object1, object2), - linesStiffness (initData(&linesStiffness,Real(100),"linesStiffness","Lines Stiffness")) - , linesDamping (initData(&linesDamping ,Real(5),"linesDamping" ,"Lines Damping")) - , quadsStiffness(initData(&quadsStiffness,Real(100),"quadsStiffness","Quads Stiffness")) - , quadsDamping (initData(&quadsDamping ,Real(5),"quadsDamping" ,"Quads Damping")) - , cubesStiffness(initData(&cubesStiffness,Real(100),"cubesStiffness","Cubes Stiffness")) - , cubesDamping (initData(&cubesDamping ,Real(5),"cubesDamping" ,"Cubes Damping")) + linesStiffness (this->initData(&linesStiffness,Real(100),"linesStiffness","Lines Stiffness")) + , linesDamping (this->initData(&linesDamping ,Real(5),"linesDamping" ,"Lines Damping")) + , quadsStiffness(this->initData(&quadsStiffness,Real(100),"quadsStiffness","Quads Stiffness")) + , quadsDamping (this->initData(&quadsDamping ,Real(5),"quadsDamping" ,"Quads Damping")) + , cubesStiffness(this->initData(&cubesStiffness,Real(100),"cubesStiffness","Cubes Stiffness")) + , cubesDamping (this->initData(&cubesDamping ,Real(5),"cubesDamping" ,"Cubes Damping")) , topology(NULL) { - addAlias(&linesStiffness, "stiffness");addAlias(&linesDamping, "damping"); - addAlias(&quadsStiffness, "stiffness");addAlias(&quadsDamping, "damping"); - addAlias(&cubesStiffness, "stiffness");addAlias(&cubesDamping, "damping"); + this->addAlias(&linesStiffness, "stiffness");this->addAlias(&linesDamping, "damping"); + this->addAlias(&quadsStiffness, "stiffness");this->addAlias(&quadsDamping, "damping"); + this->addAlias(&cubesStiffness, "stiffness");this->addAlias(&cubesDamping, "damping"); } RegularGridSpringForceField() : - linesStiffness (initData(&linesStiffness,Real(100),"linesStiffness","Lines Stiffness")) - , linesDamping (initData(&linesDamping ,Real(5),"linesDamping" ,"Lines Damping")) - , quadsStiffness(initData(&quadsStiffness,Real(100),"quadsStiffness","Quads Stiffness")) - , quadsDamping (initData(&quadsDamping ,Real(5),"quadsDamping" ,"Quads Damping")) - , cubesStiffness(initData(&cubesStiffness,Real(100),"cubesStiffness","Cubes Stiffness")) - , cubesDamping (initData(&cubesDamping ,Real(5),"cubesDamping" ,"Cubes Damping")) + linesStiffness (this->initData(&linesStiffness,Real(100),"linesStiffness","Lines Stiffness")) + , linesDamping (this->initData(&linesDamping ,Real(5),"linesDamping" ,"Lines Damping")) + , quadsStiffness(this->initData(&quadsStiffness,Real(100),"quadsStiffness","Quads Stiffness")) + , quadsDamping (this->initData(&quadsDamping ,Real(5),"quadsDamping" ,"Quads Damping")) + , cubesStiffness(this->initData(&cubesStiffness,Real(100),"cubesStiffness","Cubes Stiffness")) + , cubesDamping (this->initData(&cubesDamping ,Real(5),"cubesDamping" ,"Cubes Damping")) , topology(NULL) { - addAlias(&linesStiffness, "stiffness");addAlias(&linesDamping, "damping"); - addAlias(&quadsStiffness, "stiffness");addAlias(&quadsDamping, "damping"); - addAlias(&cubesStiffness, "stiffness");addAlias(&cubesDamping, "damping"); + this->addAlias(&linesStiffness, "stiffness");this->addAlias(&linesDamping, "damping"); + this->addAlias(&quadsStiffness, "stiffness");this->addAlias(&quadsDamping, "damping"); + this->addAlias(&cubesStiffness, "stiffness");this->addAlias(&cubesDamping, "damping"); } Real getStiffness() const { return linesStiffness.getValue(); } --- sofa-framework-1.0~beta4~/modules/sofa/component/mass/MatrixMass.h +++ sofa-framework-1.0~beta4/modules/sofa/component/mass/MatrixMass.h @@ -78,11 +78,11 @@ MatrixMass() - : f_mass( initData(&f_mass, "massMatrices", "values of the particles masses") ) - , _defaultValue( initData(&_defaultValue, (Real)1.0,"defaultValue", "real default value") ) + : f_mass( this->initData(&f_mass, "massMatrices", "values of the particles masses") ) + , _defaultValue( this->initData(&_defaultValue, (Real)1.0,"defaultValue", "real default value") ) ,_usingDefaultDiagonalMatrices(false) { - _lumped = initData( &this->_lumped, false, "lumped", ""); + _lumped = this->initData( &this->_lumped, false, "lumped", ""); }; ~MatrixMass(); --- sofa-framework-1.0~beta4~/modules/sofa/component/topology/DynamicSparseGridGeometryAlgorithms.inl +++ sofa-framework-1.0~beta4/modules/sofa/component/topology/DynamicSparseGridGeometryAlgorithms.inl @@ -96,7 +96,7 @@ it = regular2topo.find( regularGridIndex); if( it != regular2topo.end()) { - const Real d = computeElementRestDistanceMeasure(it->second, pos); + const Real d = this->computeElementRestDistanceMeasure(it->second, pos); // std::cout << "Distance : " << d << "\n"; if(d::findNearestElementInRestPos( pos, baryC, distance); } - distance = computeElementRestDistanceMeasure( index, pos); + distance = this->computeElementRestDistanceMeasure( index, pos); - baryC = computeHexahedronRestBarycentricCoeficients(index, pos); + baryC = this->computeHexahedronRestBarycentricCoeficients(index, pos); return index; } --- sofa-framework-1.0~beta4~/modules/sofa/component/topology/EdgeSubsetData.inl +++ sofa-framework-1.0~beta4/modules/sofa/component/topology/EdgeSubsetData.inl @@ -137,7 +137,7 @@ // test that there are no item with the key = s+i assert(this->find(s+i)==this->end()); - insert(std::pair(s+i,t)); + this->insert(std::pair(s+i,t)); } lastEdgeIndex+=nbEdges; } @@ -160,10 +160,10 @@ { /// change the key of the item associated with key lastEdgeIndex T tmp=(*itend).second; - erase(itend); - insert(std::pair(index[i],tmp)); + this->erase(itend); + this->insert(std::pair(index[i],tmp)); } - erase(it); + this->erase(it); } --lastEdgeIndex; } --- sofa-framework-1.0~beta4~/modules/sofa/component/topology/TriangleSubsetData.inl +++ sofa-framework-1.0~beta4/modules/sofa/component/topology/TriangleSubsetData.inl @@ -115,7 +115,7 @@ // test that there are no item with the key = s+i assert(this->find(s+i)==this->end()); - insert(std::pair(s+i,t)); + this->insert(std::pair(s+i,t)); } lastTriangleIndex+=nbTriangles; } @@ -138,10 +138,10 @@ { /// change the key of the item associated with key lastTriangleIndex T tmp=(*itend).second; - erase(itend); - insert(std::pair(index[i],tmp)); + this->erase(itend); + this->insert(std::pair(index[i],tmp)); } - erase(it); + this->erase(it); } --lastTriangleIndex; } debian/patches/tinyxml26.diff0000644000000000000000000000260511761714730013335 0ustar --- a/applications/sofa/gui/qt/GraphVisitor.cpp +++ b/applications/sofa/gui/qt/GraphVisitor.cpp @@ -207,10 +207,10 @@ Q3ListViewItem *graphNode=NULL; switch (typeOfNode) { - case TiXmlNode::DOCUMENT: + case TiXmlNode::TINYXML_DOCUMENT: break; - case TiXmlNode::ELEMENT: + case TiXmlNode::TINYXML_ELEMENT: if (nameOfNode == "Time") { openTime( node, parent); @@ -222,17 +222,17 @@ } break; - case TiXmlNode::COMMENT: + case TiXmlNode::TINYXML_COMMENT: graphNode = addComment(parent, elementAbove, nameOfNode); break; - case TiXmlNode::UNKNOWN: + case TiXmlNode::TINYXML_UNKNOWN: break; - case TiXmlNode::TEXT: + case TiXmlNode::TINYXML_TEXT: break; - case TiXmlNode::DECLARATION: + case TiXmlNode::TINYXML_DECLARATION: break; default: break; --- a/modules/sofa/simulation/tree/xml/XML.cpp +++ b/modules/sofa/simulation/tree/xml/XML.cpp @@ -84,7 +84,7 @@ BaseElement* createNode(TiXmlNode* root, const char *basefilename, bool isRoot = false) { //if (!xmlStrcmp(root->name,(const xmlChar*)"text")) return NULL; - if (root->Type() != TiXmlNode::ELEMENT) return NULL; + if (root->Type() != TiXmlNode::TINYXML_ELEMENT) return NULL; TiXmlElement* element = root->ToElement(); if (!element || !element->Value() || !element->Value()[0]) return NULL; debian/patches/fix_mutable_serr_sout.diff0000644000000000000000000000262311761714730016065 0ustar ## 78_atomicity.dpatch by ## ## All lines beginning with `## DP:' are a description of the patch. ## DP: fix #625059 , error: reference 'serr' cannot be declared 'mutable' [-fpermissive] Index: sofa-framework-1.0~beta4/framework/sofa/core/objectmodel/Base.h =================================================================== --- sofa-framework-1.0~beta4.orig/framework/sofa/core/objectmodel/Base.h 2011-05-07 16:18:02.000000000 -0400 +++ sofa-framework-1.0~beta4/framework/sofa/core/objectmodel/Base.h 2011-05-07 16:18:06.000000000 -0400 @@ -279,8 +279,8 @@ std::multimap< std::string, BaseData* > getAliases() { return m_aliasData; } mutable sofa::helper::system::SofaOStream sendl; - mutable std::ostringstream &serr; - mutable std::ostringstream &sout; + std::ostringstream &serr; + std::ostringstream &sout; protected: Index: sofa-framework-1.0~beta4/framework/sofa/core/core.h =================================================================== --- sofa-framework-1.0~beta4.orig/framework/sofa/core/core.h 2011-05-07 16:21:56.000000000 -0400 +++ sofa-framework-1.0~beta4/framework/sofa/core/core.h 2011-05-07 16:22:12.000000000 -0400 @@ -28,6 +28,7 @@ #define SOFA_CORE_H #include +#include #ifdef SOFA_BUILD_CORE # define SOFA_CORE_API SOFA_EXPORT_DYNAMIC_LIBRARY debian/patches/qwt5-qt4.patch0000644000000000000000000000147411761714730013261 0ustar Author: Andreas Tille Last-Changed: Tue, 13 Dec 2011 12:55:52 +0100 Description: Sofa does not build properly with libqwt-dev so adjusting include directory and fixing some header file is needed --- sofa-framework-1.0~beta4.orig/applications/sofa/gui/qt/GraphDataWidget.h +++ sofa-framework-1.0~beta4/applications/sofa/gui/qt/GraphDataWidget.h @@ -33,6 +33,8 @@ #include #include #include +#include +#include namespace sofa { --- sofa-framework-1.0~beta4.orig/sofa.cfg +++ sofa-framework-1.0~beta4/sofa.cfg @@ -212,7 +212,7 @@ $$SOFA_DIR/modules \ $$SOFA_DIR/applications \ /usr/include/qt4 \ - /usr/include/qwt + /usr/include/qwt-qt4 debian/patches/50_all_changes.diff0000644000000000000000000001531512171756305014227 0ustar #! /bin/sh /usr/share/dpatch/dpatch-run ## 50_all_changes.dpatch by ## ## All lines beginning with `## DP:' are a description of the patch. ## DP: Link sofa to Debians newmat, boost, xml2 and qwt library. ## DP: Use OGRE >= 1.6.0 if switched on. @DPATCH@ --- a/Sofa.pro +++ b/Sofa.pro @@ -3,13 +3,13 @@ include($${SOFA_DIR}/sofa.cfg) -SUBDIRS += extlibs/newmat +#SUBDIRS += extlibs/newmat -SUBDIRS += extlibs/qwt +#SUBDIRS += extlibs/qwt contains(DEFINES,SOFA_XML_PARSER_TINYXML){ - SUBDIRS += extlibs/tinyxml +# SUBDIRS += extlibs/tinyxml } # FlowVR @@ -21,14 +21,15 @@ #CSParse contains(DEFINES,SOFA_HAVE_CSPARSE){ - SUBDIRS += extlibs/csparse +# use Debian's system library instead of the one in extlibs +# SUBDIRS += extlibs/csparse } #QGLViewer contains(DEFINES,SOFA_GUI_QGLVIEWER){ - SUBDIRS += extlibs/libQGLViewer/QGLViewer +# SUBDIRS += extlibs/libQGLViewer/QGLViewer } # PML --- a/framework/sofa/helper/gl/DrawManager.cpp +++ b/framework/sofa/helper/gl/DrawManager.cpp @@ -517,7 +517,7 @@ node->scale(radius/50.0,radius/50.0,radius/50.0); node->translate(p[0],p[1],p[2]); node->attachObject(sph); - sph->setNormaliseNormals(true); + //sph->setNormaliseNormals(true); break; #endif } --- a/sofa-default.cfg +++ b/sofa-default.cfg @@ -47,7 +47,7 @@ # DEFINES += SOFA_HAVE_FLOWVR # Uncomment if you want to use Boost lib for multithread computing -# DEFINES += SOFA_HAVE_BOOST + DEFINES += SOFA_HAVE_BOOST # Uncomment if you want to compile CUDA GPU prototype (require NVIDIA CUDA SDK) # DEFINES += SOFA_GPU_CUDA @@ -61,10 +61,10 @@ # DEFINES += SOFA_GPU_CUDA_DOUBLE # Uncomment if you want to use SofaPML to load PML and LML files -# DEFINES += SOFA_PML +DEFINES += SOFA_PML # Uncomment if you want to use LAPACK for Matrix Solvers -#DEFINES += SOFA_HAVE_LAPACK +# DEFINES += SOFA_HAVE_LAPACK # Uncomment if you want to use MKL for Matrix Solvers #DEFINES += SOFA_HAVE_MKL @@ -77,7 +77,7 @@ # DEFINES += SOFA_HAVE_CHAI3D # Uncomment if you want to support moving frames when computing inertia forces in Mass -# DEFINES += SOFA_SUPPORT_MOVING_FRAMES + DEFINES += SOFA_SUPPORT_MOVING_FRAMES # Uncomment if you want to have the possibility to trave the visitor execution DEFINES += DUMP_VISITOR_INFO @@ -110,6 +110,8 @@ # Choose if you want to compile the debug or release version #CONFIG = debug CONFIG = release +QMAKE_CXXFLAGS += -W +QMAKE_CFLAGS += -W # Uncomment if you want debug symbols even in release build # QMAKE_CXXFLAGS += -g --- a/sofa.cfg +++ b/sofa.cfg @@ -19,7 +19,8 @@ # Auto-detect Qt 4.x # The QT variable was introduced in Qt 4 -!isEmpty(QT): DEFINES += SOFA_QT4 +#!isEmpty(QT): DEFINES += SOFA_QT4 +DEFINES += SOFA_QT4 !include( sofa-local.cfg ) { # Copy sofa-default.cfg to sofa-local.cfg and modify it to change local options @@ -197,12 +198,10 @@ OBJECTS_DIR = OBJ/$$join(CONFIGDEBUG,,,) CONFIGLIBRARIES+= \ - warn_on \ stl \ rtti \ thread -CONFIGPROJECT += warn_on CONFIGPROJECTGUI = $$CONFIGPROJECT CONFIGPROJECTCMD = $$CONFIGPROJECT CONFIGPROJECTCMD += console @@ -211,7 +210,11 @@ $$SOFA_DIR/include \ $$SOFA_DIR/framework \ $$SOFA_DIR/modules \ - $$SOFA_DIR/applications + $$SOFA_DIR/applications \ + /usr/include/qt4 \ + /usr/include/qwt + + DEPENDPATH *= \ $$SOFA_DIR/framework \ @@ -251,9 +254,9 @@ # CSPARSE ######################################################################## contains(DEFINES,SOFA_HAVE_CSPARSE){ - SOFA_EXT_LIBS *= -lcsparse$$LIBSUFFIX + SOFA_EXT_LIBS *= -lcsparse # use csparse headers included in extlibs - INCLUDEPATH *= $$SOFA_DIR/extlibs/csparse + # INCLUDEPATH *= $$SOFA_DIR/extlibs/csparse } ######################################################################## @@ -267,7 +270,7 @@ contains(DEFINES,SOFA_XML_PARSER_TINYXML){ # DEFINES *= TIXML_USE_STL SOFA_EXT_LIBS += -ltinyxml$$LIBSUFFIX - INCLUDEPATH *= $$SOFA_DIR/extlibs/tinyxml +# INCLUDEPATH *= $$SOFA_DIR/extlibs/tinyxml } ######################################################################## @@ -322,8 +325,8 @@ # NewMAT ######################################################################## -INCLUDEPATH *= $$SOFA_DIR/extlibs/newmat -SOFA_EXT_LIBS *= -lnewmat$$LIBSUFFIX +#INCLUDEPATH *= $$SOFA_DIR/extlibs/newmat +SOFA_EXT_LIBS *= -lnewmat ######################################################################## # METIS @@ -377,8 +380,9 @@ else { QT += opengl } - INCLUDEPATH += $$SOFA_DIR/extlibs/qwt - SOFA_GUI_EXT_LIBS *= -lqwt$${LIBSUFFIX} +# INCLUDEPATH += $$SOFA_DIR/extlibs/qwt +# SOFA_GUI_EXT_LIBS *= -lqwt + SOFA_GUI_EXT_LIBS *= -lqwt-qt4 } ######################################################################## @@ -398,10 +402,10 @@ else { QT += opengl } - unix:SOFA_GUI_EXT_LIBS *= -lQGLViewer$${LIBSUFFIX} + unix:SOFA_GUI_EXT_LIBS *= -lqglviewer-qt4$${LIBSUFFIX} win32:SOFA_GUI_EXT_LIBS *= -lQGLViewer2$${LIBSUFFIX} - INCLUDEPATH += $$SOFA_DIR/extlibs/qwt $$SOFA_DIR/extlibs/libQGLViewer - SOFA_GUI_EXT_LIBS *= -lqwt$${LIBSUFFIX} + INCLUDEPATH += /usr/include/qglviewer-qt4 + SOFA_GUI_EXT_LIBS *= -lqwt-qt4 } ######################################################################## @@ -428,8 +432,8 @@ QMAKE_LIBDIR += $(OGRE_HOME)/lib LIBS += OgreMain.lib } - INCLUDEPATH += $$SOFA_DIR/extlibs/qwt - SOFA_GUI_EXT_LIBS *= -lqwt$${LIBSUFFIX} +# INCLUDEPATH += $$SOFA_DIR/extlibs/qwt + SOFA_GUI_EXT_LIBS *= -lqwt-qt4 unix { macx: QMAKE_CXXFLAGS += -Wno-unused @@ -601,6 +605,9 @@ SOFA_GUI_LIBS *= -lsofagui$$LIBSUFFIX -lsofaguimain$$LIBSUFFIX +# for binutils-gold +SOFA_EXTRA_LIBS += -ldl + # When using staticlib, rebuild applications if a library has changed contains(CONFIGLIBRARIES,staticlib){ contains(TEMPLATE,app){ @@ -619,7 +626,7 @@ } } -SOFA_LIBS = $${SOFA_MODULES_LIBS} $${SOFA_MODULES_LIBS} $${SOFA_FRAMEWORK_LIBS} $${SOFA_FRAMEWORK_LIBS} $${SOFA_EXT_LIBS} +SOFA_LIBS = $${SOFA_MODULES_LIBS} $${SOFA_MODULES_LIBS} $${SOFA_FRAMEWORK_LIBS} $${SOFA_FRAMEWORK_LIBS} $${SOFA_EXT_LIBS} $${SOFA_EXTRA_LIBS} SOFA_GUI_LIBS += $${SOFA_GUI_EXT_LIBS} --- a/applications/sofa/gui/qt/GraphVisitor.cpp +++ b/applications/sofa/gui/qt/GraphVisitor.cpp @@ -28,10 +28,7 @@ #include -#include -#include -#include -#include +#include #include --- a/applications/sofa/gui/qt/GraphVisitor.h +++ b/applications/sofa/gui/qt/GraphVisitor.h @@ -43,7 +43,6 @@ //Tinyxml library #include -#include #include #include debian/patches/13_gcc4.4.diff0000644000000000000000000000633411761714730012751 0ustar #! /bin/sh /usr/share/dpatch/dpatch-run ## 13_gcc4.4.dpatch by ## ## All lines beginning with `## DP:' are a description of the patch. ## DP: added #include headers required by GCC 4.4 (Closes: #505953) @DPATCH@ diff -urNad sofa-framework-1.0~beta4~/framework/sofa/helper/LCPSolver.inl sofa-framework-1.0~beta4/framework/sofa/helper/LCPSolver.inl --- sofa-framework-1.0~beta4~/framework/sofa/helper/LCPSolver.inl 2009-06-09 21:10:29.000000000 -0400 +++ sofa-framework-1.0~beta4/framework/sofa/helper/LCPSolver.inl 2009-06-09 21:10:49.000000000 -0400 @@ -28,6 +28,7 @@ #define SOFA_HELPER_LCPSOLVER_INL #include +#include namespace sofa { diff -urNad sofa-framework-1.0~beta4~/framework/sofa/helper/Quater.inl sofa-framework-1.0~beta4/framework/sofa/helper/Quater.inl --- sofa-framework-1.0~beta4~/framework/sofa/helper/Quater.inl 2009-06-09 21:10:29.000000000 -0400 +++ sofa-framework-1.0~beta4/framework/sofa/helper/Quater.inl 2009-06-09 21:10:49.000000000 -0400 @@ -28,6 +28,7 @@ #define SOFA_HELPER_QUATER_INL #include "Quater.h" +#include #include #include diff -urNad sofa-framework-1.0~beta4~/framework/sofa/helper/gl/Capture.cpp sofa-framework-1.0~beta4/framework/sofa/helper/gl/Capture.cpp --- sofa-framework-1.0~beta4~/framework/sofa/helper/gl/Capture.cpp 2009-06-09 21:10:29.000000000 -0400 +++ sofa-framework-1.0~beta4/framework/sofa/helper/gl/Capture.cpp 2009-06-09 21:10:49.000000000 -0400 @@ -30,6 +30,7 @@ #include #endif +#include #include #include diff -urNad sofa-framework-1.0~beta4~/framework/sofa/helper/io/ImageBMP.cpp sofa-framework-1.0~beta4/framework/sofa/helper/io/ImageBMP.cpp --- sofa-framework-1.0~beta4~/framework/sofa/helper/io/ImageBMP.cpp 2009-06-09 21:10:29.000000000 -0400 +++ sofa-framework-1.0~beta4/framework/sofa/helper/io/ImageBMP.cpp 2009-06-09 21:10:49.000000000 -0400 @@ -26,6 +26,7 @@ ******************************************************************************/ #include #include +#include #include namespace sofa diff -urNad sofa-framework-1.0~beta4~/framework/sofa/helper/io/ImageRAW.cpp sofa-framework-1.0~beta4/framework/sofa/helper/io/ImageRAW.cpp --- sofa-framework-1.0~beta4~/framework/sofa/helper/io/ImageRAW.cpp 2009-06-09 21:10:29.000000000 -0400 +++ sofa-framework-1.0~beta4/framework/sofa/helper/io/ImageRAW.cpp 2009-06-09 21:10:49.000000000 -0400 @@ -27,6 +27,7 @@ #include #include #include +#include namespace sofa { diff -urNad sofa-framework-1.0~beta4~/framework/sofa/helper/io/MeshTrian.cpp sofa-framework-1.0~beta4/framework/sofa/helper/io/MeshTrian.cpp --- sofa-framework-1.0~beta4~/framework/sofa/helper/io/MeshTrian.cpp 2009-06-09 21:10:29.000000000 -0400 +++ sofa-framework-1.0~beta4/framework/sofa/helper/io/MeshTrian.cpp 2009-06-09 21:10:49.000000000 -0400 @@ -27,6 +27,7 @@ #include #include #include +#include #include #include debian/patches/series0000644000000000000000000000034412171755350012041 0ustar 13_gcc4.4.diff 50_all_changes.diff 55_fix_mips_sqrt.diff 78_atomicity.diff fix_mutable_serr_sout.diff tinyxml26.diff qwt5-qt4.patch sofa-framework-gcc-4.7.diff sofa-framework-1.0~beta4.libpng15.patch fix-undefined-symbol.patch debian/README.Debian0000644000000000000000000000340011622747433011235 0ustar sofa-framework for Debian ------------------------- beta3: Project MESSAGE: ====== SOFA Build Configuration ====== Project MESSAGE: | Platform: Linux/Unix Project MESSAGE: | Mode: RELEASE Project MESSAGE: | Qt version: 4.x Project MESSAGE: | RDTSC timer: DISABLED Project MESSAGE: | PNG support: ENABLED Project MESSAGE: | OpenGL Extensions support using GLEW: ENABLED Project MESSAGE: | GPU support using CUDA: DISABLED Project MESSAGE: | PML/LML support: ENABLED Project MESSAGE: | GLUT GUI: ENABLED Project MESSAGE: | Qt GUI: ENABLED Project MESSAGE: | - Qt OpenGL viewer: ENABLED Project MESSAGE: | - Qt QGLViewer viewer: DISABLED Project MESSAGE: | - Qt OGRE 3D viewer: ENABLED Project MESSAGE: ====================================== beta4: Project MESSAGE: ====== SOFA Build Configuration ====== Project MESSAGE: | Platform: Linux/Unix Project MESSAGE: | Mode: RELEASE with debug symbols Project MESSAGE: | Qt version: 4.x Project MESSAGE: | RDTSC timer: DISABLED Project MESSAGE: | BOOST libraries: ENABLED Project MESSAGE: | TinyXML parser: ENABLED Project MESSAGE: | LibXML parser: DISABLED Project MESSAGE: | PNG support: ENABLED Project MESSAGE: | OpenGL Extensions support using GLEW: ENABLED Project MESSAGE: | GPU support using CUDA: DISABLED Project MESSAGE: | PML/LML support: ENABLED Project MESSAGE: | CSPARSE library : DISABLED Project MESSAGE: | METIS library : DISABLED Project MESSAGE: | TAUCS library : DISABLED Project MESSAGE: | GLUT GUI: ENABLED Project MESSAGE: | Qt GUI: ENABLED Project MESSAGE: | - Qt OpenGL viewer: ENABLED Project MESSAGE: | - Qt QGLViewer viewer: DISABLED Project MESSAGE: | - Qt OGRE 3D viewer: ENABLED Project MESSAGE: ====================================== -- Dominique Belhachemi Sat, 16 Feb 2008 10:26:03 +0100 debian/sofa0000644000000000000000000000162311622747433010054 0ustar #!/bin/sh # # SOFA wrapper script # # Copyright (C) 2008 Dominique Belhachemi (domibel@debian.org) # # 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 program; if not, write to the Free Software # Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA export SOFA_DATA_PATH=/usr/share/sofa/share:/usr/share/sofa/examples /usr/lib/sofa-framework/sofa $* exit 0 debian/control0000644000000000000000000000770612146473270010611 0ustar Source: sofa-framework Section: graphics Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Build-Depends: debhelper (>= 9), freeglut3-dev, libboost-dev, libboost-graph-dev, libboost-thread-dev, libboost-system-dev, libeigen3-dev, libglew-dev, libnewmat10-dev, libpng-dev, libqglviewer-dev, libqt4-dev, libqt4-opengl-dev, libqwt5-qt4-dev, libtinyxml-dev (>= 2.6), libsuitesparse-dev, libxml2-dev, pkg-config, Build-Depends-Indep: doxygen, graphviz Build-Conflicts: qt3-dev-tools Standards-Version: 3.9.3 Homepage: http://www.sofa-framework.org/ Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/sofa-framework/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/sofa-framework/trunk/ Package: sofa-apps Architecture: any Depends: libsofa1 (= ${binary:Version}), sofa-data, ${misc:Depends}, ${shlibs:Depends} Description: GUI for the Simulation Open Framework Architecture (SOFA) SOFA is an Open Source framework primarily targeted at real-time simulation, with an emphasis on medical simulation. It is mostly intended for the research community to help develop newer algorithms, but can also be used as an efficient prototyping tool. . This package contains the SOFA main application. Package: libsofa1-dev Section: libdevel Architecture: any Depends: libsofa1 (= ${binary:Version}), ${misc:Depends} Suggests: sofa-tutorials Description: Simulation Open Framework Architecture - development SOFA is an Open Source framework primarily targeted at real-time simulation, with an emphasis on medical simulation. It is mostly intended for the research community to help develop newer algorithms, but can also be used as an efficient prototyping tool. . This package contains the development files needed to build your own SOFA applications. Package: libsofa1 Section: libs Architecture: any Depends: ${misc:Depends}, ${shlibs:Depends} Description: Simulation Open Framework Architecture - runtime SOFA is an Open Source framework primarily targeted at real-time simulation, with an emphasis on medical simulation. It is mostly intended for the research community to help develop newer algorithms, but can also be used as an efficient prototyping tool. . This package contains the libraries needed to run SOFA applications. Package: sofa-tutorials Architecture: all Depends: ${misc:Depends} Description: Simulation Open Framework Architecture - tutorials SOFA is an Open Source framework primarily targeted at real-time simulation, with an emphasis on medical simulation. It is mostly intended for the research community to help develop newer algorithms, but can also be used as an efficient prototyping tool. . This package contains tutorials from the SOFA source. Package: sofa-data Architecture: all Depends: ${misc:Depends} Description: Simulation Open Framework Architecture - data SOFA is an Open Source framework primarily targeted at real-time simulation, with an emphasis on medical simulation. It is mostly intended for the research community to help develop newer algorithms, but can also be used as an efficient prototyping tool. . This package contains data for the SOFA applications. #Package: sofa-doc #Section: doc #Architecture: all #Depends: ${misc:Depends} #Description: SOFA class reference documentation # SOFA is an Open Source framework primarily targeted at # real-time simulation, with an emphasis on medical simulation. # It is mostly intended for the research community to help # develop newer algorithms, but can also be used as an efficient # prototyping tool. # . # This package contains exhaustive HTML documentation for the all the # documented C++ classes. debian/Notes0000644000000000000000000000332311350044643010202 0ustar 1) $ grep -r "1.0 beta 3" . ./modules/sofa/component/topology/ManifoldTriangleSetTopologyAlgorithms.h: * SOFA, Simulation Open-Framework Architecture, version 1.0 beta 3 * 2) please provide a copyright file for extlibs/miniFlowVR/ 3) please provide a make install 4) Sometimes it is better to link against: libqt3-mt-dev, qt3-dev-tools, libqglviewer-dev, libqwt-dev, 5) * debian/copyright: MKL removed 6) * Example files can be find in /usr/share/sofa * Use a shell script to set the environment variable SOFA_DATA_PATH and to start the sofa gui 7) * $$LIBSUFFIX for the debug target not needed because we are using Debian libraries 8) update "man page", update "sofa -h" because "sofa myscene.scn" works, but it is not documented 9) libogre-dev (>= 1.6.0) because of removed Entity::setNormaliseNormals * By default now, renormalisation of normals is automatic if there is a non-unit scale on the main world matrix rather than the Entity::setNormaliseNormals option. If the user wants to optimise this, they can prevent the SceneManager doing it in all cases by calling SceneManager::setNormaliseNormalsOnScale(false) and then explicitly enabling the option per Pass instead. In the case of an array of world matrices being used, if the first world matrix isn't a guide then the shader writer should handle the renormalisation. 10) doesn't work # Uncomment if you want to use LibXML instead of built-in TinyXML # DEFINES += SOFA_XML_PARSER_LIBXML ./applications/sofa/gui/qt/GraphVisitor.h contains //Tinyxml library #include #include 11) since libtinyxml-dev is in Debian we can remove ./extlibs/tinyxml debian/copyright has to be updated as well debian/rules0000755000000000000000000000640011761714730010255 0ustar #!/usr/bin/make -f # Uncomment this to turn on verbose mode. # export DH_VERBOSE=1 PACKAGE := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p') DEB_SOURCE_PACKAGE:=$(PACKAGE) devpkg := libsofa1-dev apppkg := sofa-apps docpkg := sofa-doc %: dh $@ get-orig-source: . debian/get-orig-source override_dh_auto_configure: qmake (cd applications/projects/runSofa; qmake -o Makefile runSofa.pro) # create a folder without object files cp -a $(CURDIR)/applications/tutorials $(CURDIR)/tutorials override_dh_auto_build: dh_auto_build # Create the documentation files if debian/control does include the package definition if grep -q "^Package: sofa-doc$$" debian/control ; then \ mkdir -p $(CURDIR)/doc/doxygen ; \ doxygen -u Doxyfile ; \ doxygen ; \ fi # remove zero byte files find $(CURDIR)/doc/doxygen/ -depth -empty | xargs rm -rf override_dh_clean: rm -rf bin lib tutorials doc OBJ # - rm -rf extlibs/tinyxml/ dh_clean # some packages might remain after clean find . -name "*.o" -delete find . -name "Makefile" -delete find . -name "Makefile.lib*" -delete find . -name "Makefile.sofa_*" -delete find . -name "moc_*" -delete find . -type d -empty -delete rm -rf applications/sofa/gui/qt/PluginManager.h \ applications/sofa/gui/qt/VisitorGUI.cpp \ applications/sofa/gui/qt/GUI.cpp \ applications/sofa/gui/qt/GUI.h \ applications/sofa/gui/qt/DialogAddObject.h \ applications/sofa/gui/qt/PluginManager.cpp \ applications/sofa/gui/qt/BaseGenGraphForm.h \ applications/sofa/gui/qt/VisitorGUI.h \ applications/sofa/gui/qt/DialogAddObject.cpp \ applications/sofa/gui/qt/BaseGenGraphForm.cpp \ applications/projects/Modeler/lib/PluginManager.h \ applications/projects/Modeler/lib/Modeler.cpp \ applications/projects/Modeler/lib/DialogAddPreset.cpp \ applications/projects/Modeler/lib/PluginManager.cpp \ applications/projects/Modeler/lib/DialogAddPreset.h \ applications/projects/Modeler/lib/Modeler.h \ applications/sofa/gui/qt/UI \ applications/projects/Modeler/lib/UI rm -f Sofa.tag doxygen.log override_dh_install: find tutorials -name "*.kdevelop" | xargs chmod 644 find share -type f -exec chmod 644 \{\} \; find share -name "*.sh" -exec chmod 755 \{\} \; find examples -type f -exec chmod 644 \{\} \; find examples -name "*.sh" -exec chmod 755 \{\} \; dh_install # try only if doxygen was called above if [ -d doc/doxygen/html ] ; then mv doc/doxygen/html/* $(CURDIR)/debian/$(docpkg)/usr/share/doc/sofa-doc/html ; fi # install some files directly into development package mkdir -p $(CURDIR)/debian/$(devpkg)/usr/include for dir in framework modules applications ; do \ for header in `find $$dir -name "*.h" -o -name "*.inl"` ; do \ target=`echo $$header | sed "s?^$${dir}/??"`; \ mkdir -p `dirname debian/$(devpkg)/usr/include/$$target`; \ cp -a $$header debian/$(devpkg)/usr/include/$$target ; \ done ; \ done # rename runSofa mkdir -p $(CURDIR)/debian/$(apppkg)/usr/lib/sofa-framework mv $(CURDIR)/bin/runSofa $(CURDIR)/debian/$(apppkg)/usr/lib/sofa-framework/sofa debian/sofa.desktop0000644000000000000000000000026211622747433011522 0ustar [Desktop Entry] GenericName=SOFA Name=SOFA Comment=Open Source Framework for Medical Simulation Exec=sofa Icon=sofa Terminal=false Type=Application Categories=Education;Science; debian/source/0000755000000000000000000000000012171756325010477 5ustar debian/source/format0000644000000000000000000000001411622747433011705 0ustar 3.0 (quilt) debian/README.source0000644000000000000000000000126111761714730011354 0ustar Doxygen documentation for sofa ------------------------------ Formerly a package sofa-doc was created which contained exhaustive documentation created automatically by using doxygen. The process to generate the documentation lasts more than one hour on recent hardware and the results are close to 20.000 Files consuming nearly 1GB of disk space (0.75GB compressed in *.deb file). This seems to be a waste of resources and thus the package was dropped. If you intend to build the documentation locally from the Debian package source feel free to uncomment the sofa-doc package section in the debian/control file. -- Andreas Tille Tue, 29 May 2012 10:55:43 +0200 debian/sofa.xpm0000644000000000000000000001561011056537707010662 0ustar /* XPM */ static char * soffaaaa_xpm[] = { "32 32 301 2", " c None", ". c #383846", "+ c #363746", "@ c #373846", "# c #7E5A48", "$ c #CD6A36", "% c #BF6436", "& c #5A4444", "* c #744D40", "= c #F3722C", "- c #F2712C", "; c #F2702B", "> c #E76F2F", ", c #433C46", "' c #BC6236", ") c #7B4E3F", "! c #4C4246", "~ c #965A3C", "{ c #98593B", "] c #4F4044", "^ c #393947", "/ c #3A3A47", "( c #BE6336", "_ c #F3742E", ": c #7C5544", "< c #504245", "[ c #E77130", "} c #F2712B", "| c #EA702E", "1 c #524244", "2 c #7A4F40", "3 c #E87130", "4 c #ED7631", "5 c #95583C", "6 c #7E5040", "7 c #F3712B", "8 c #E8702F", "9 c #453D46", "0 c #A95D39", "a c #A55B39", "b c #493F46", "c c #EF712D", "d c #F2702C", "e c #F57730", "f c 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", ". . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ", ". . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ", ". . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ", ". . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . "}; debian/sofa.10000644000000000000000000000303111671701760010203 0ustar .TH "sofa" "1" "August 2008" "" "" .SH "NAME" sofa \- SOFA GUI .SH "SYNOPSIS" sofa [OPTIONS] .SH "DESCRIPTION" SOFA is an Open Source framework primarily targeted at real\-time simulation, with an emphasis on medical simulation. It is mostly intended for the research community to help develop newer algorithms, but can also be used as an efficient prototyping tool. Based on an advanced software architecture, it allows one to: * create complex and evolving simulations by combining new algorithms with algorithms already included in SOFA * modify most parameters of the simulation – deformable behavior, surface representation, solver, constraints, collision algorithm, etc. – by simply editing an XML file * build complex models from simpler ones using a scene\-graph description * efficiently simulate the dynamics of interacting objects using abstract equation solvers * reuse and easily compare a variety of available methods .SH "OPTIONS" .IP "\-h \-\-help" this help .IP "\-s \-\-start" start the animation loop (default: 0 ) .IP "\-p \-\-factory" In addition to the baz segments, also parse the blurfl headers. .IP "\-g \-\-gui" choose the UI (batch|qt|glut) (default: qt ) .IP "\-l \-\-load" load given plugins (default: ) .SH "AUTHORS" SOFA is currently developed by 3 INRIA teams: Alcove, Evasion and Asclepios but the project also benefited from the help of the CIMIT Sim Group, ETH Zurich and CSIRO. .SH "SEE ALSO" The full documentation for .B sofa is available at <\fBhttp://www.sofa\-framework.org\fR> debian/index.html0000644000000000000000000000131711213027540011160 0ustar Sofa API Documentation <body><a href="http://www.sofa-framework.org/sofa/doc/doxygen/html/main.html">Frames are disabled. Click here to go to the main page.</a></body> debian/watch0000644000000000000000000000027211673647150010232 0ustar version=3 opts="dversionmangle=s/~/-/" \ http://www.sofa-framework.org/download \ https*://gforge.inria.fr/frs/download.php/.*/sofa-framework-(.*)\.zip \ debian debian/get-orig-source debian/libsofa1.lintian-overrides0000644000000000000000000000133611350044643014251 0ustar libsofa1: package-name-doesnt-match-sonames libload1 libminiFlowVR1 libphysicalmodel1 libsofacomponent1 libsofacomponentbase1 libsofacomponentbehaviormodel1 libsofacomponentcollision1 libsofacomponentconstraint1 libsofacomponentcontextobject1 libsofacomponentcontroller1 libsofacomponentengine1 libsofacomponentfem1 libsofacomponentforcefield1 libsofacomponentinteractionforcefield1 libsofacomponentlinearsolver1 libsofacomponentmapping1 libsofacomponentmass1 libsofacomponentmastersolver1 libsofacomponentmisc1 libsofacomponentodesolver1 libsofacomponentvisualmodel1 libsofacore1 libsofadefaulttype1 libsofagui1 libsofaguiglut1 libsofaguimain1 libsofaguiqt1 libsofahelper1 libsofamodeler1 libsofapml1 libsofasimulation1 libsofatree1