academic/avogadro: Updated for version 1.1.0.

Signed-off-by: Matteo Bernardini <ponce@slackbuilds.org>

6 files changed, 218 insertions, 101 deletions

diff --git a/academic/avogadro/avogadro.SlackBuild b/academic/avogadro/avogadro.SlackBuild
index 009b66ccd8b1..38ab7c26fb57 100644
--- a/academic/avogadro/avogadro.SlackBuild
+++ b/academic/avogadro/avogadro.SlackBuild
@@ -5,8 +5,8 @@
 # Written by Larry Hajali <larryhaja[at]gmail[dot]com>
 
 PRGNAM=avogadro
-VERSION=1.0.3
-BUILD=${BUILD:-2}
+VERSION=${VERSION:-1.1.0}
+BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
 if [ -z "$ARCH" ]; then
@@ -52,11 +52,7 @@ find . \
  -exec chmod 644 {} \;
 
 # Fix gcc-4.7.x build issues.
-patch -p1 < $CWD/patches/gcc-4.7.patch
-# Fix for newer boost.
-patch -p1 < $CWD/patches/boost-1.48.patch
-# Fix mkspecs directory.
-patch -p1 < $CWD/patches/avogadro-1.0.3-mkspecs-dir.patch
+patch -p1 < $CWD/gcc-4.7.patch
 
 # Fix manpage directory.
 sed -i 's|share/man|man|' doc/CMakeLists.txt
@@ -72,6 +68,7 @@ cd build
     -DCMAKE_SKIP_RPATH=YES \
     -DENABLE_GLSL:BOOL=ON \
     -DENABLE_UPDATE_CHECKER=OFF \
+    -DQT_MKSPECS_RELATIVE=lib${LIBDIRSUFFIX}/qt/mkspecs \
     -DCMAKE_BUILD_TYPE=Release ..
 
   make VERBOSE=1
@@ -85,7 +82,8 @@ find $PKG/usr/man -type f -exec gzip -9 {} \;
 
 mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
 cp -a \
-  AUTHORS ChangeLog COPYING INSTALL README avogadro/gl2ps/{COPYING*,*.txt} \
+  AUTHORS ChangeLog 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 912cae3c834f..3f2283b135d2 100644
--- a/academic/avogadro/avogadro.info
+++ b/academic/avogadro/avogadro.info
@@ -1,8 +1,8 @@
 PRGNAM="avogadro"
-VERSION="1.0.3"
+VERSION="1.1.0"
 HOMEPAGE="http://avogadro.openmolecules.net/wiki/Main_Page"
-DOWNLOAD="http://downloads.sourceforge.net/avogadro/avogadro-1.0.3.tar.bz2"
-MD5SUM="92c2702c1980f70fb6d87a1a58147911"
+DOWNLOAD="http://downloads.sourceforge.net/avogadro/avogadro-1.1.0.tar.bz2"
+MD5SUM="f4fbef5ffc69cc312b2316426c36a78d"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 REQUIRES="openbabel"
diff --git a/academic/avogadro/gcc-4.7.patch b/academic/avogadro/gcc-4.7.patch
new file mode 100644
index 000000000000..8c74fa562032
--- /dev/null
+++ b/academic/avogadro/gcc-4.7.patch
@@ -0,0 +1,209 @@
+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>
+ 
diff --git a/academic/avogadro/patches/avogadro-1.0.3-mkspecs-dir.patch b/academic/avogadro/patches/avogadro-1.0.3-mkspecs-dir.patch
deleted file mode 100644
index a1e9ec92bd30..000000000000
--- a/academic/avogadro/patches/avogadro-1.0.3-mkspecs-dir.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -ur avogadro-1.0.3/CMakeLists.txt avogadro-1.0.3-mkspecs-dir/CMakeLists.txt
---- avogadro-1.0.3/CMakeLists.txt	2011-04-25 07:29:58.000000000 +0200
-+++ avogadro-1.0.3-mkspecs-dir/CMakeLists.txt	2011-04-27 02:42:26.000000000 +0200
-@@ -491,7 +491,7 @@
- if(QT_MKSPECS_DIR AND INSTALL_QMAKE_PRF)
-     install(FILES
-       "${CMAKE_CURRENT_BINARY_DIR}/avogadro.prf"
--      DESTINATION "${CMAKE_INSTALL_PREFIX}/${QT_MKSPECS_RELATIVE}/features"
-+      DESTINATION "${QT_MKSPECS_DIR}/features"
-     )
- else(QT_MKSPECS_DIR AND INSTALL_QMAKE_PRF)
-   message(WARNING "Qt mkspecs directory not found. File 'avogadro.prf' will be installed to ${SHARE_INSTALL_PREFIX}/avogadro/qmake.")
diff --git a/academic/avogadro/patches/boost-1.48.patch b/academic/avogadro/patches/boost-1.48.patch
deleted file mode 100644
index 380af0c938c7..000000000000
--- a/academic/avogadro/patches/boost-1.48.patch
+++ /dev/null
@@ -1,56 +0,0 @@
-diff -Naur avogadro-1.0.3.orig/libavogadro/src/extensions/pythonterminal.h avogadro-1.0.3/libavogadro/src/extensions/pythonterminal.h
---- avogadro-1.0.3.orig/libavogadro/src/extensions/pythonterminal.h	2011-04-25 05:22:18.000000000 +0000
-+++ avogadro-1.0.3/libavogadro/src/extensions/pythonterminal.h	2012-07-12 02:35:19.324975289 +0000
-@@ -23,6 +23,10 @@
- #ifndef PYTHONTERMINAL_H
- #define PYTHONTERMINAL_H
- 
-+#ifdef Q_MOC_RUN
-+#define BOOST_TT_HAS_OPERATOR_HPP_INCLUDED
-+#endif
-+
- #include <avogadro/extension.h>
- #include <avogadro/primitive.h>
- #include <avogadro/glwidget.h>
-diff -Naur avogadro-1.0.3.orig/libavogadro/src/pythonengine_p.h avogadro-1.0.3/libavogadro/src/pythonengine_p.h
---- avogadro-1.0.3.orig/libavogadro/src/pythonengine_p.h	2011-04-25 05:22:18.000000000 +0000
-+++ avogadro-1.0.3/libavogadro/src/pythonengine_p.h	2012-07-12 02:32:39.429980751 +0000
-@@ -25,6 +25,10 @@
- #ifndef PYTHONENGINE_H
- #define PYTHONENGINE_H
- 
-+#ifdef Q_MOC_RUN
-+#define BOOST_TT_HAS_OPERATOR_HPP_INCLUDED
-+#endif
-+
- #include <avogadro/global.h>
- #include <avogadro/engine.h>
- #include <boost/python.hpp>
-diff -Naur avogadro-1.0.3.orig/libavogadro/src/pythonextension_p.h avogadro-1.0.3/libavogadro/src/pythonextension_p.h
---- avogadro-1.0.3.orig/libavogadro/src/pythonextension_p.h	2011-04-25 05:22:18.000000000 +0000
-+++ avogadro-1.0.3/libavogadro/src/pythonextension_p.h	2012-07-12 02:33:46.838978444 +0000
-@@ -26,6 +26,10 @@
- #ifndef PYTHONEXTENSION_H
- #define PYTHONEXTENSION_H
- 
-+#ifdef Q_MOC_RUN
-+#define BOOST_TT_HAS_OPERATOR_HPP_INCLUDED
-+#endif
-+
- #include <avogadro/extension.h>
- #include <avogadro/primitive.h>
- #include <avogadro/glwidget.h>
-diff -Naur avogadro-1.0.3.orig/libavogadro/src/pythontool_p.h avogadro-1.0.3/libavogadro/src/pythontool_p.h
---- avogadro-1.0.3.orig/libavogadro/src/pythontool_p.h	2011-04-25 05:22:18.000000000 +0000
-+++ avogadro-1.0.3/libavogadro/src/pythontool_p.h	2012-07-12 02:34:14.068977512 +0000
-@@ -25,6 +25,10 @@
- #ifndef PYTHONTOOL_H
- #define PYTHONTOOL_H
- 
-+#ifdef Q_MOC_RUN
-+#define BOOST_TT_HAS_OPERATOR_HPP_INCLUDED
-+#endif
-+
- #include <avogadro/global.h>
- #include <avogadro/tool.h>
- #include <boost/python.hpp>
diff --git a/academic/avogadro/patches/gcc-4.7.patch b/academic/avogadro/patches/gcc-4.7.patch
deleted file mode 100644
index ffa4cd9439b9..000000000000
--- a/academic/avogadro/patches/gcc-4.7.patch
+++ /dev/null
@@ -1,22 +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 {