diff options
| -rw-r--r-- | academic/avogadro/avogadro-1.1.1-eigen3.patch | 51 | ||||
| -rw-r--r-- | academic/avogadro/avogadro-1.1.1-python_openbabel.patch | 14 | ||||
| -rw-r--r-- | academic/avogadro/avogadro-1.2.0-libmsym.patch | 29 | ||||
| -rw-r--r-- | academic/avogadro/avogadro-cmake-3.2.patch | 12 | ||||
| -rw-r--r-- | academic/avogadro/avogadro.SlackBuild | 31 | ||||
| -rw-r--r-- | academic/avogadro/avogadro.info | 6 | ||||
| -rw-r--r-- | academic/avogadro/boost-1.53.patch | 60 | ||||
| -rw-r--r-- | academic/avogadro/gcc-4.7.patch | 209 |
8 files changed, 59 insertions, 353 deletions
diff --git a/academic/avogadro/avogadro-1.1.1-eigen3.patch b/academic/avogadro/avogadro-1.1.1-eigen3.patch deleted file mode 100644 index dc07d6974e12..000000000000 --- a/academic/avogadro/avogadro-1.1.1-eigen3.patch +++ /dev/null @@ -1,51 +0,0 @@ ---- avogadro-1.1.1/CMakeLists.txt.omv~ 2014-01-30 13:58:22.999443609 +0100 -+++ avogadro-1.1.1/CMakeLists.txt 2014-01-30 13:59:31.086106925 +0100 -@@ -230,13 +230,15 @@ if(NOT Linguist_FOUND) - message(WARNING " Qt4 Linguist not found, please install it if you want Avogadro translations") - endif() - --find_package(Eigen3) # find and setup Eigen3 if available -+find_package(Eigen3 REQUIRED) # find and setup Eigen3 if available - if(NOT EIGEN3_FOUND) - message(STATUS "Cannot find Eigen3, trying Eigen2") -- find_package(Eigen2 REQUIRED) # Some version is required -+ find_package(Eigen2) # Some version is required - else() - # Use Stage10 Eigen3 support - set (EIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API TRUE) -+ add_definitions (-DEIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API) -+ set (EIGEN2_INCLUDE_DIR ${EIGEN3_INCLUDE_DIR}) - endif() - - find_package(ZLIB REQUIRED) ---- avogadro-1.1.1/libavogadro/src/extensions/qtaim/CMakeLists.txt.omv~ 2014-01-30 14:12:33.859401753 +0100 -+++ avogadro-1.1.1/libavogadro/src/extensions/qtaim/CMakeLists.txt 2014-01-30 14:15:07.652727522 +0100 -@@ -4,6 +4,8 @@ set(LINK_LIBS avogadro) - set(PLUGIN_LABEL extensions) - set(PLUGIN_TARGET extensions) - -+add_definitions(-DEIGEN2_SUPPORT_STAGE20_RESOLVE_API_CONFLICTS -std=gnu++11) -+ - set(qtaimextension_SRCS - qtaimextension.cpp - # qtaimdialog.cpp ---- avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/CMakeLists.txt.omv~ 2014-01-30 13:59:05.889441500 +0100 -+++ avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/CMakeLists.txt 2014-01-30 13:59:08.832774688 +0100 -@@ -1,5 +1,5 @@ - find_package(Qt4 4.6 REQUIRED) --find_package(Eigen2 REQUIRED) -+find_package(Eigen3 REQUIRED) - - include_directories(${QT_INCLUDE_DIR} ${EIGEN2_INCLUDE_DIR}) - ---- avogadro-1.1.1/cmake/modules/AvogadroUse.cmake.orig 2014-10-13 20:13:59.909828034 +0100 -+++ avogadro-1.1.1/cmake/modules/AvogadroUse.cmake 2014-10-13 20:15:09.492822908 +0100 -@@ -12,7 +12,7 @@ - - # Add the Avogadro modules directory to the CMake module path - set(CMAKE_MODULE_PATH ${Avogadro_PLUGIN_DIR}/cmake ${CMAKE_MODULE_PATH}) --find_package(Eigen2 REQUIRED) -+find_package(Eigen3 REQUIRED) - include_directories(${EIGEN2_INCLUDE_DIR}) - if(Avogadro_ENABLE_GLSL) - find_package(GLEW) diff --git a/academic/avogadro/avogadro-1.1.1-python_openbabel.patch b/academic/avogadro/avogadro-1.1.1-python_openbabel.patch new file mode 100644 index 000000000000..c819b08502e6 --- /dev/null +++ b/academic/avogadro/avogadro-1.1.1-python_openbabel.patch @@ -0,0 +1,14 @@ +diff -up avogadro-1.1.1/libavogadro/src/python/CMakeLists.txt.openbabel avogadro-1.1.1/libavogadro/src/python/CMakeLists.txt +--- avogadro-1.1.1/libavogadro/src/python/CMakeLists.txt.openbabel 2013-12-06 09:50:04.000000000 -0600 ++++ avogadro-1.1.1/libavogadro/src/python/CMakeLists.txt 2016-01-25 13:50:10.469758655 -0600 +@@ -20,8 +20,8 @@ if (WIN32) + set_target_properties(python-module PROPERTIES SUFFIX ".pyd") + target_link_libraries(python-module avogadro ${PYTHON_LIBRARIES}) + else() +- target_link_libraries(python-module stdc++ avogadro +- ${QT_LIBRARIES} ${PYTHON_LIBRARIES} ${Boost_LIBRARIES}) ++ target_link_libraries(python-module stdc++ avogadro ++ ${QT_LIBRARIES} ${PYTHON_LIBRARIES} ${OPENBABEL2_LIBRARIES} ${Boost_LIBRARIES}) + endif() + + # Let's try to use this instead: diff --git a/academic/avogadro/avogadro-1.2.0-libmsym.patch b/academic/avogadro/avogadro-1.2.0-libmsym.patch new file mode 100644 index 000000000000..818b2e434bb4 --- /dev/null +++ b/academic/avogadro/avogadro-1.2.0-libmsym.patch @@ -0,0 +1,29 @@ +diff -Naur avogadro-1.2.0.orig/libavogadro/src/extensions/symmetry/libmsym/CMakeLists.txt avogadro-1.2.0/libavogadro/src/extensions/symmetry/libmsym/CMakeLists.txt +--- avogadro-1.2.0.orig/libavogadro/src/extensions/symmetry/libmsym/CMakeLists.txt 2016-06-08 14:19:45.000000000 +0000 ++++ avogadro-1.2.0/libavogadro/src/extensions/symmetry/libmsym/CMakeLists.txt 2016-08-01 04:18:55.910888721 +0000 +@@ -7,13 +7,13 @@ + set(LIBMSYM_PATCH_VERSION 0) + set(LIBMSYM_VERSION ${LIBMSYM_MAJOR_VERSION}.${LIBMSYM_MINOR_VERSION}.${LIBMSYM_PATCH_VERSION}) + +-set(INSTALL_LIB_DIR lib CACHE PATH "Installation directory for msym library") ++set(INSTALL_LIB_DIR lib${LIB_SUFFIX} CACHE PATH "Installation directory for msym library") + set(INSTALL_INCLUDE_DIR include CACHE PATH "Installation directory for header files") + + if(WIN32 AND NOT CYGWIN) + set(DEF_INSTALL_CMAKE_DIR CMake) + else() +- set(DEF_INSTALL_CMAKE_DIR lib/cmake/libmsym) ++ set(DEF_INSTALL_CMAKE_DIR lib${LIB_SUFFIX}/cmake/libmsym) + endif() + set(INSTALL_CMAKE_DIR ${DEF_INSTALL_CMAKE_DIR} CACHE PATH "Installation directory for CMake files") + +@@ -29,6 +29,9 @@ + file (GLOB source src/*.c) + add_library (msym ${source}) + if (BUILD_SHARED_LIBS) ++ if(CMAKE_SYSTEM_NAME MATCHES Linux) ++ target_link_libraries(msym m) ++ endif() + set_target_properties (msym PROPERTIES + POSITION_INDEPENDENT_CODE "TRUE") + endif () diff --git a/academic/avogadro/avogadro-cmake-3.2.patch b/academic/avogadro/avogadro-cmake-3.2.patch deleted file mode 100644 index 1c6a38d4ca9b..000000000000 --- a/academic/avogadro/avogadro-cmake-3.2.patch +++ /dev/null @@ -1,12 +0,0 @@ -Index: avogadro-1.1.1/CMakeLists.txt -=================================================================== ---- avogadro-1.1.1.orig/CMakeLists.txt -+++ avogadro-1.1.1/CMakeLists.txt -@@ -225,6 +225,7 @@ set(I18N_LANGUAGE "" CACHE STRING "Build - - find_package(Qt4 4.6.0 REQUIRED) # find and setup Qt4 for this project - find_package(OpenGL REQUIRED) # find and setup OpenGL -+find_package(X11 REQUIRED) # find and setup X11 - find_package(Linguist) # find and setup Linguist - if(NOT Linguist_FOUND) - message(WARNING " Qt4 Linguist not found, please install it if you want Avogadro translations") diff --git a/academic/avogadro/avogadro.SlackBuild b/academic/avogadro/avogadro.SlackBuild index 070bf3f192bd..481347fe3c0c 100644 --- a/academic/avogadro/avogadro.SlackBuild +++ b/academic/avogadro/avogadro.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for Avogadro -# Copyright 2010-2013 Larry Hajali <larryhaja[at]gmail[dot]com> +# Copyright 2010-2016 Larry Hajali <larryhaja[at]gmail[dot]com> # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=avogadro -VERSION=${VERSION:-1.1.1} +VERSION=${VERSION:-1.2.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -60,30 +60,23 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.bz2 +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ -o -perm 511 \) -exec chmod 755 {} \; -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# Fix gcc-4.7.x build issues. -patch -p1 < $CWD/gcc-4.7.patch -# Fix boost 1.53 build issues. -patch -p1 < $CWD/boost-1.53.patch # Fix manpage directory. sed -i 's|share/man|man|' doc/CMakeLists.txt +# Fix install directory and linking for libmsym library. +patch -p1 < $CWD/avogadro-1.2.0-libmsym.patch -# Fix eigen3 support (thanks slack_jack, ponce and Fedora) -# http://pkgs.fedoraproject.org/cgit/avogadro.git/plain/avogadro-1.1.1-eigen3.patch -patch -p1 < $CWD/avogadro-1.1.1-eigen3.patch - -# Fix underlinking (gcc-5.2) thanks Fedora -patch -p1 < $CWD/avogadro-cmake-3.2.patch -# Fix more underlinking (gcc-5.3) -SLKCFLAGS="$SLKCFLAGS -lopenbabel" +# fix build (with recent swig/linker/python?) +# http://pkgs.fedoraproject.org/cgit/rpms/avogadro.git/tree/avogadro-1.1.1-python_openbabel.patch +patch -p1 < $CWD/avogadro-1.1.1-python_openbabel.patch mkdir -p build cd build @@ -96,6 +89,8 @@ cd build -DCMAKE_SKIP_RPATH=YES \ -DENABLE_GLSL:BOOL=ON \ -DENABLE_UPDATE_CHECKER=OFF \ + -DENABLE_VERSIONED_PLUGIN_DIR:BOOL=OFF \ + -DBUILD_SHARED_LIBS:BOOL=ON \ -DQT_MKSPECS_RELATIVE=lib${LIBDIRSUFFIX}/qt/mkspecs \ -DCMAKE_BUILD_TYPE=Release .. @@ -103,14 +98,14 @@ cd build make install DESTDIR=$PKG cd - -find $PKG | xargs file | grep -e "executable" -e "shared object" | grep ELF \ +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true find $PKG/usr/man -type f -exec gzip -9 {} \; mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - AUTHORS ChangeLog COPYING INSTALL README \ + AUTHORS COPYING INSTALL README \ libavogadro/src/extensions/gl2ps/{COPYING*,*.txt,*.pdf} \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild diff --git a/academic/avogadro/avogadro.info b/academic/avogadro/avogadro.info index 2faa4a6baa4b..226b33bef06e 100644 --- a/academic/avogadro/avogadro.info +++ b/academic/avogadro/avogadro.info @@ -1,8 +1,8 @@ PRGNAM="avogadro" -VERSION="1.1.1" +VERSION="1.2.0" HOMEPAGE="http://avogadro.openmolecules.net/wiki/Main_Page" -DOWNLOAD="http://downloads.sourceforge.net/avogadro/avogadro-1.1.1.tar.bz2" -MD5SUM="1223bb18f50dccd2c60538aa90d58c7a" +DOWNLOAD="http://downloads.sourceforge.net/avogadro/avogadro-1.2.0.tar.gz" +MD5SUM="3206068fc27bd3b717c568ee72f1e5ec" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="openbabel" diff --git a/academic/avogadro/boost-1.53.patch b/academic/avogadro/boost-1.53.patch deleted file mode 100644 index fd8685974c2e..000000000000 --- a/academic/avogadro/boost-1.53.patch +++ /dev/null @@ -1,60 +0,0 @@ ---- avogadro-1.1.0/libavogadro/src/pythonengine_p.h~ 2013-03-29 12:46:16.306165881 +0000 -+++ avogadro-1.1.0/libavogadro/src/pythonengine_p.h 2013-03-29 12:45:43.123089622 +0000 -@@ -27,7 +27,9 @@ - - #include <avogadro/global.h> - #include <avogadro/engine.h> -+#ifndef Q_MOC_RUN - #include <boost/python.hpp> -+#endif - - namespace Avogadro { - ---- avogadro-1.1.0/libavogadro/src/pythonextension_p.h~ 2013-03-29 12:46:32.156043085 +0000 -+++ avogadro-1.1.0/libavogadro/src/pythonextension_p.h 2013-03-29 12:47:07.265771087 +0000 -@@ -29,7 +29,9 @@ - #include <avogadro/extension.h> - #include <avogadro/primitive.h> - #include <avogadro/glwidget.h> -+#ifndef Q_MOC_RUN - #include <boost/python.hpp> -+#endif - - #include <QWidget> - #include <QList> ---- avogadro-1.1.0/libavogadro/src/pythontool_p.h~ 2013-03-29 12:47:33.335569185 +0000 -+++ avogadro-1.1.0/libavogadro/src/pythontool_p.h 2013-03-29 12:47:50.732101147 +0000 -@@ -27,7 +27,9 @@ - - #include <avogadro/global.h> - #include <avogadro/tool.h> -+#ifndef Q_MOC_RUN - #include <boost/python.hpp> -+#endif - - #include <QObject> - #include <QAction> ---- avogadro-1.1.0/libavogadro/src/pythoninterpreter.h~ 2013-03-29 12:50:46.550738652 +0000 -+++ avogadro-1.1.0/libavogadro/src/pythoninterpreter.h 2013-03-29 12:51:00.853961341 +0000 -@@ -26,7 +26,9 @@ - #define PYTHONINTERPRETER_H - - #include <avogadro/global.h> -+#ifndef Q_MOC_RUN - #include <boost/python.hpp> -+#endif - #include <avogadro/primitive.h> - #include <QString> - ---- avogadro-1.1.0/libavogadro/src/pythonscript.h~ 2013-03-29 12:52:00.723488935 +0000 -+++ avogadro-1.1.0/libavogadro/src/pythonscript.h 2013-03-29 12:52:11.676745364 +0000 -@@ -27,7 +27,9 @@ - #define PYTHONSCRIPT_H - - #include <avogadro/global.h> -+#ifndef Q_MOC_RUN - #include <boost/python.hpp> -+#endif - - #include "pythonerror.h" - diff --git a/academic/avogadro/gcc-4.7.patch b/academic/avogadro/gcc-4.7.patch deleted file mode 100644 index 8c74fa562032..000000000000 --- a/academic/avogadro/gcc-4.7.patch +++ /dev/null @@ -1,209 +0,0 @@ -diff -Naur avogadro-1.0.3.orig/avogadro/src/mainwindow.h avogadro-1.0.3/avogadro/src/mainwindow.h ---- avogadro-1.0.3.orig/avogadro/src/mainwindow.h 2011-04-25 05:22:18.000000000 +0000 -+++ avogadro-1.0.3/avogadro/src/mainwindow.h 2012-07-11 13:57:36.624006453 +0000 -@@ -24,6 +24,7 @@ - #ifndef MAINWINDOW_H - #define MAINWINDOW_H - -+#include <cstddef> - #include <Eigen/Geometry> - #include "ui_mainwindow.h" - #include "flattabwidget.h" -diff -Naur avogadro-1.0.3.orig/libavogadro/src/tools/eyecandy.h avogadro-1.0.3/libavogadro/src/tools/eyecandy.h ---- avogadro-1.0.3.orig/libavogadro/src/tools/eyecandy.h 2011-04-25 05:22:18.000000000 +0000 -+++ avogadro-1.0.3/libavogadro/src/tools/eyecandy.h 2012-07-11 13:43:22.892050693 +0000 -@@ -25,6 +25,7 @@ - #ifndef EYECANDY_H - #define EYECANDY_H - -+#include <cstddef> - #include <Eigen/Core> - - namespace Avogadro { -diff -Naur avogadro-1.1.0.orig/libavogadro/src/extensions/crystallography/avospglib.h avogadro-1.1.0/libavogadro/src/extensions/crystallography/avospglib.h ---- avogadro-1.1.0.orig/libavogadro/src/extensions/crystallography/avospglib.h 2012-09-03 17:07:00.000000000 +0000 -+++ avogadro-1.1.0/libavogadro/src/extensions/crystallography/avospglib.h 2012-12-02 23:46:44.297457487 +0000 -@@ -18,6 +18,7 @@ - #ifndef AVOSPGLIB_H - #define AVOSPGLIB_H - -+#include <cstddef> - #include <Eigen/Core> - - #include <QtCore/QList> -diff -Naur avogadro-1.1.0.orig/libavogadro/src/extensions/qtaim/qtaimcriticalpointlocator.cpp avogadro-1.1.0/libavogadro/src/extensions/qtaim/qtaimcriticalpointlocator.cpp ---- avogadro-1.1.0.orig/libavogadro/src/extensions/qtaim/qtaimcriticalpointlocator.cpp 2012-09-03 17:07:00.000000000 +0000 -+++ avogadro-1.1.0/libavogadro/src/extensions/qtaim/qtaimcriticalpointlocator.cpp 2012-12-03 00:46:44.820773931 +0000 -@@ -28,6 +28,7 @@ - #include "qtaimlsodaintegrator.h" - #include "qtaimmathutilities.h" - -+#include <cstddef> - #include <Eigen/Core> - - #include <QList> -diff -Naur avogadro-1.1.0.orig/libavogadro/src/extensions/qtaim/qtaimlsodaintegrator.h avogadro-1.1.0/libavogadro/src/extensions/qtaim/qtaimlsodaintegrator.h ---- avogadro-1.1.0.orig/libavogadro/src/extensions/qtaim/qtaimlsodaintegrator.h 2012-09-03 17:07:00.000000000 +0000 -+++ avogadro-1.1.0/libavogadro/src/extensions/qtaim/qtaimlsodaintegrator.h 2012-12-03 00:32:41.095760808 +0000 -@@ -30,6 +30,7 @@ - #include <QVector3D> - #include <QPair> - -+#include <cstddef> - #include <Eigen/Core> - - #include "qtaimwavefunction.h" -diff -Naur avogadro-1.1.0.orig/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp avogadro-1.1.0/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp ---- avogadro-1.1.0.orig/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp 2012-09-03 17:07:00.000000000 +0000 -+++ avogadro-1.1.0/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp 2012-12-03 00:46:24.188773609 +0000 -@@ -23,6 +23,7 @@ - **********************************************************************/ - - #include <cmath> -+#include <cstddef> - #include <Eigen/QR> - - #include "qtaimmathutilities.h" -diff -Naur avogadro-1.1.0.orig/libavogadro/src/extensions/qtaim/qtaimmathutilities.h avogadro-1.1.0/libavogadro/src/extensions/qtaim/qtaimmathutilities.h ---- avogadro-1.1.0.orig/libavogadro/src/extensions/qtaim/qtaimmathutilities.h 2012-09-03 17:07:00.000000000 +0000 -+++ avogadro-1.1.0/libavogadro/src/extensions/qtaim/qtaimmathutilities.h 2012-12-03 00:32:01.134760196 +0000 -@@ -26,6 +26,7 @@ - - #include <QtGlobal> - -+#include <cstddef> - #include <Eigen/Core> - - using namespace Eigen; -diff -Naur avogadro-1.1.0.orig/libavogadro/src/extensions/qtaim/qtaimodeintegrator.h avogadro-1.1.0/libavogadro/src/extensions/qtaim/qtaimodeintegrator.h ---- avogadro-1.1.0.orig/libavogadro/src/extensions/qtaim/qtaimodeintegrator.h 2012-09-03 17:07:00.000000000 +0000 -+++ avogadro-1.1.0/libavogadro/src/extensions/qtaim/qtaimodeintegrator.h 2012-12-03 00:33:01.432761053 +0000 -@@ -30,6 +30,7 @@ - #include <QVector3D> - #include <QPair> - -+#include <cstddef> - #include <Eigen/Core> - - #include "qtaimwavefunction.h" -diff -Naur avogadro-1.1.0.orig/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.h avogadro-1.1.0/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.h ---- avogadro-1.1.0.orig/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.h 2012-09-03 17:07:00.000000000 +0000 -+++ avogadro-1.1.0/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.h 2012-12-03 00:33:28.571761559 +0000 -@@ -10,6 +10,7 @@ - - #include "qtaimwavefunction.h" - -+#include <cstddef> - #include <Eigen/Core> - - using namespace Eigen; -diff -Naur avogadro-1.1.0.orig/libavogadro/src/extensions/surfaces/openqube/atom.h avogadro-1.1.0/libavogadro/src/extensions/surfaces/openqube/atom.h ---- avogadro-1.1.0.orig/libavogadro/src/extensions/surfaces/openqube/atom.h 2012-09-03 17:07:00.000000000 +0000 -+++ avogadro-1.1.0/libavogadro/src/extensions/surfaces/openqube/atom.h 2012-12-02 23:57:35.872728048 +0000 -@@ -19,6 +19,7 @@ - - #include "molecule.h" - -+#include <cstddef> - #include <Eigen/Core> - - namespace OpenQube { -diff -Naur avogadro-1.1.0.orig/libavogadro/src/extensions/surfaces/openqube/cube.h avogadro-1.1.0/libavogadro/src/extensions/surfaces/openqube/cube.h ---- avogadro-1.1.0.orig/libavogadro/src/extensions/surfaces/openqube/cube.h 2012-09-03 17:07:00.000000000 +0000 -+++ avogadro-1.1.0/libavogadro/src/extensions/surfaces/openqube/cube.h 2012-12-03 00:16:50.638746161 +0000 -@@ -20,6 +20,7 @@ - #include "openqubeabi.h" - - #include <vector> -+#include <cstddef> - #include <Eigen/Core> - #include <QtCore/QString> - -diff -Naur avogadro-1.1.0.orig/libavogadro/src/extensions/surfaces/openqube/gamessukout.h avogadro-1.1.0/libavogadro/src/extensions/surfaces/openqube/gamessukout.h ---- avogadro-1.1.0.orig/libavogadro/src/extensions/surfaces/openqube/gamessukout.h 2012-09-03 17:07:00.000000000 +0000 -+++ avogadro-1.1.0/libavogadro/src/extensions/surfaces/openqube/gamessukout.h 2012-12-03 00:17:25.300746590 +0000 -@@ -19,6 +19,7 @@ - - #include "gaussianset.h" - -+#include <cstddef> - #include <Eigen/Core> - - #include <vector> -diff -Naur avogadro-1.1.0.orig/libavogadro/src/extensions/surfaces/openqube/gamessus.h avogadro-1.1.0/libavogadro/src/extensions/surfaces/openqube/gamessus.h ---- avogadro-1.1.0.orig/libavogadro/src/extensions/surfaces/openqube/gamessus.h 2012-09-03 17:07:00.000000000 +0000 -+++ avogadro-1.1.0/libavogadro/src/extensions/surfaces/openqube/gamessus.h 2012-12-03 00:17:40.584746828 +0000 -@@ -18,6 +18,7 @@ - #define GAMESSUS_H - - #include <QtCore/QIODevice> -+#include <cstddef> - #include <Eigen/Core> - #include <vector> - -diff -Naur avogadro-1.1.0.orig/libavogadro/src/extensions/surfaces/openqube/gaussianfchk.h avogadro-1.1.0/libavogadro/src/extensions/surfaces/openqube/gaussianfchk.h ---- avogadro-1.1.0.orig/libavogadro/src/extensions/surfaces/openqube/gaussianfchk.h 2012-09-03 17:07:00.000000000 +0000 -+++ avogadro-1.1.0/libavogadro/src/extensions/surfaces/openqube/gaussianfchk.h 2012-12-03 00:17:52.130747005 +0000 -@@ -18,6 +18,7 @@ - #define GAUSSIANFCHK_H - - #include <QtCore/QIODevice> -+#include <cstddef> - #include <Eigen/Core> - #include <vector> - -diff -Naur avogadro-1.1.0.orig/libavogadro/src/extensions/surfaces/openqube/gaussianset.h avogadro-1.1.0/libavogadro/src/extensions/surfaces/openqube/gaussianset.h ---- avogadro-1.1.0.orig/libavogadro/src/extensions/surfaces/openqube/gaussianset.h 2012-09-03 17:07:00.000000000 +0000 -+++ avogadro-1.1.0/libavogadro/src/extensions/surfaces/openqube/gaussianset.h 2012-12-03 00:18:04.072747212 +0000 -@@ -22,6 +22,7 @@ - - #include <QtCore/QFuture> - -+#include <cstddef> - #include <Eigen/Core> - #include <vector> - -diff -Naur avogadro-1.1.0.orig/libavogadro/src/extensions/surfaces/openqube/molden.h avogadro-1.1.0/libavogadro/src/extensions/surfaces/openqube/molden.h ---- avogadro-1.1.0.orig/libavogadro/src/extensions/surfaces/openqube/molden.h 2012-09-03 17:07:00.000000000 +0000 -+++ avogadro-1.1.0/libavogadro/src/extensions/surfaces/openqube/molden.h 2012-12-03 00:18:23.164747493 +0000 -@@ -17,6 +17,7 @@ - #ifndef MOLDEN_H - #define MOLDEN_H - -+#include <cstddef> - #include <Eigen/Core> - #include <vector> - -diff -Naur avogadro-1.1.0.orig/libavogadro/src/extensions/surfaces/openqube/molecule.h avogadro-1.1.0/libavogadro/src/extensions/surfaces/openqube/molecule.h ---- avogadro-1.1.0.orig/libavogadro/src/extensions/surfaces/openqube/molecule.h 2012-09-03 17:07:00.000000000 +0000 -+++ avogadro-1.1.0/libavogadro/src/extensions/surfaces/openqube/molecule.h 2012-12-03 00:08:10.094737989 +0000 -@@ -22,6 +22,7 @@ - #include "atom.h" - - #include <vector> -+#include <cstddef> - #include <Eigen/Core> - - namespace OpenQube { -diff -Naur avogadro-1.1.0.orig/libavogadro/src/extensions/surfaces/openqube/mopacaux.h avogadro-1.1.0/libavogadro/src/extensions/surfaces/openqube/mopacaux.h ---- avogadro-1.1.0.orig/libavogadro/src/extensions/surfaces/openqube/mopacaux.h 2012-09-03 17:07:00.000000000 +0000 -+++ avogadro-1.1.0/libavogadro/src/extensions/surfaces/openqube/mopacaux.h 2012-12-03 00:18:48.113747871 +0000 -@@ -18,6 +18,7 @@ - #define MOPACAUX_H - - #include <QtCore/QTextStream> -+#include <cstddef> - #include <Eigen/Core> - #include <vector> - -diff -Naur avogadro-1.1.0.orig/libavogadro/src/extensions/surfaces/openqube/slaterset.h avogadro-1.1.0/libavogadro/src/extensions/surfaces/openqube/slaterset.h ---- avogadro-1.1.0.orig/libavogadro/src/extensions/surfaces/openqube/slaterset.h 2012-09-03 17:07:00.000000000 +0000 -+++ avogadro-1.1.0/libavogadro/src/extensions/surfaces/openqube/slaterset.h 2012-12-03 00:19:11.592748237 +0000 -@@ -21,6 +21,7 @@ - - #include <QtCore/QFuture> - -+#include <cstddef> - #include <Eigen/Core> - #include <vector> - |