academic/avogadro: Updated for version 1.2.0

Signed-off-by: Larry Hajali <larryhaja[at]gmail[dot]com>

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 dc07d6974e..0000000000
--- 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 0000000000..c819b08502
--- /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 0000000000..818b2e434b
--- /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 1c6a38d4ca..0000000000
--- 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 070bf3f192..481347fe3c 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 2faa4a6baa..226b33bef0 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 fd8685974c..0000000000
--- 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 8c74fa5620..0000000000
--- 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>
-