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authorAvatar Heiko Becker <heirecka@exherbo.org> 2016-06-10 15:46:17 +0200
committerAvatar Heiko Becker <heirecka@exherbo.org> 2016-11-06 12:13:50 +0100
commit77e6c08d393f1c5c97918d9148740f49fa71f76a (patch)
tree3d86000ebc61842910681c15a26c81036548d6b6
parent71a7bc90cfd6d7f406195bf6200d1cae0656a763 (diff)
downloadscientific-77e6c08d393f1c5c97918d9148740f49fa71f76a.tar.gz
scientific-77e6c08d393f1c5c97918d9148740f49fa71f76a.tar.xz
avogadro: Version bump to 1.2.0
-rw-r--r--packages/sci-chemistry/avogadro/avogadro-1.2.0.exheres-0 (renamed from packages/sci-chemistry/avogadro/avogadro-1.1.1.exheres-0)23
-rw-r--r--packages/sci-chemistry/avogadro/files/avogadro-Fix-build-with-boost-1.53.patch88
-rw-r--r--packages/sci-chemistry/avogadro/files/avogadro-Fix-build-with-gcc6.patch34
-rw-r--r--packages/sci-chemistry/avogadro/files/avogadro-Fix-detection-of-gcc6-s-version-number.patch27
-rw-r--r--packages/sci-chemistry/avogadro/files/avogadro-cmake-3.2.patch16
-rw-r--r--packages/sci-chemistry/avogadro/files/avogadro-cmake-Use-SHARE_INSTALL_PREFIX-instead-of-share.patch72
6 files changed, 145 insertions, 115 deletions
diff --git a/packages/sci-chemistry/avogadro/avogadro-1.1.1.exheres-0 b/packages/sci-chemistry/avogadro/avogadro-1.2.0.exheres-0
index 37b042a..1912a89 100644
--- a/packages/sci-chemistry/avogadro/avogadro-1.1.1.exheres-0
+++ b/packages/sci-chemistry/avogadro/avogadro-1.2.0.exheres-0
@@ -1,7 +1,8 @@
# Copyright 2010 Bo ├śrsted Andresen
# Distributed under the terms of the GNU General Public License v2
-require sourceforge cmake [ api=2 cmake_minimum_version='2.8.9' ]
+require sourceforge [ suffix=tar.gz ]
+require cmake [ api=2 cmake_minimum_version='2.8.9' ]
SUMMARY="Advanced molecular editor"
DESCRIPTION="
@@ -9,7 +10,7 @@ Advanced molecular editor designed for cross-platform use in computational chemi
modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a
powerful plugin architecture.
"
-HOMEPAGE="http://avogadro.openmolecules.net/ ${HOMEPAGE}"
+HOMEPAGE="http://avogadro.cc/ ${HOMEPAGE}"
LICENCES="GPL-2"
SLOT="0"
@@ -23,7 +24,8 @@ DEPENDENCIES="
build+run:
media-libs/glew
sci-chemistry/openbabel[>=2.3.0]
- sci-libs/eigen:2[>=2.0.3]
+ sci-libs/eigen:3
+ sys-libs/zlib
x11-dri/glu
x11-dri/mesa
x11-libs/libICE
@@ -41,19 +43,18 @@ DEPENDENCIES="
# 5 of 5 tests need a running X server
RESTRICT="test"
-UPSTREAM_RELEASE_NOTES="http://avogadro.openmolecules.net/wiki/Avogadro_${PV}"
+# No release notes for 1.2.0 yet
+#UPSTREAM_RELEASE_NOTES="http://avogadro.openmolecules.net/wiki/Avogadro_${PV}"
-DEFAULT_SRC_PREPARE_PATCHES=(
- "${FILES}"/${PN}-Fix-build-with-boost-1.53.patch
- "${FILES}"/${PN}-cmake-3.2.patch
+DEFAULT_SRC_PREPARE_PATCHES+=(
+ "${FILES}"/${PN}-Fix-detection-of-gcc6-s-version-number.patch
+ "${FILES}"/${PN}-Fix-build-with-gcc6.patch
+ "${FILES}"/${PN}-cmake-Use-SHARE_INSTALL_PREFIX-instead-of-share.patch
)
CMAKE_SRC_CONFIGURE_PARAMS=(
- # Not every part seems to work with eigen:3
- -DCMAKE_DISABLE_FIND_PACKAGE_Eigen3:BOOL=TRUE
-DENABLE_GLSL:BOOL=TRUE
- -DQT_MKSPECS_DIR=/usr/share/qt4/mkspecs
- -DQT_MKSPECS_RELATIVE=share/qt4/mkspecs
+ -DSHARE_INSTALL_PREFIX:PATH=/usr/share
)
CMAKE_SRC_CONFIGURE_OPTION_DISABLE_FINDS=( 'doc Doxygen' )
CMAKE_SRC_CONFIGURE_OPTION_ENABLES=( PYTHON )
diff --git a/packages/sci-chemistry/avogadro/files/avogadro-Fix-build-with-boost-1.53.patch b/packages/sci-chemistry/avogadro/files/avogadro-Fix-build-with-boost-1.53.patch
deleted file mode 100644
index 1e81955..0000000
--- a/packages/sci-chemistry/avogadro/files/avogadro-Fix-build-with-boost-1.53.patch
+++ /dev/null
@@ -1,88 +0,0 @@
-Upstream: Proposed on https://github.com/cryos/avogadro/pull/5/commits
-
-From eaea17f2d7b2bce1f1ecd615d0ba08061dfd10df Mon Sep 17 00:00:00 2001
-From: Andrea Scarpino <andrea@archlinux.org>
-Date: Fri, 29 Mar 2013 18:57:34 +0059
-Subject: [PATCH] Fix build with boost 1.53
-
----
- libavogadro/src/pythonengine_p.h | 2 ++
- libavogadro/src/pythonextension_p.h | 2 ++
- libavogadro/src/pythoninterpreter.h | 2 ++
- libavogadro/src/pythonscript.h | 2 ++
- libavogadro/src/pythontool_p.h | 2 ++
- 5 files changed, 10 insertions(+)
-
-diff --git a/libavogadro/src/pythonengine_p.h b/libavogadro/src/pythonengine_p.h
-index 951b31e..8e404ba 100644
---- a/libavogadro/src/pythonengine_p.h
-+++ b/libavogadro/src/pythonengine_p.h
-@@ -27,7 +27,9 @@
-
- #include <avogadro/global.h>
- #include <avogadro/engine.h>
-+#ifndef Q_MOC_RUN
- #include <boost/python.hpp>
-+#endif
-
- namespace Avogadro {
-
-diff --git a/libavogadro/src/pythonextension_p.h b/libavogadro/src/pythonextension_p.h
-index d8fdae4..ebe6831 100644
---- a/libavogadro/src/pythonextension_p.h
-+++ b/libavogadro/src/pythonextension_p.h
-@@ -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>
-diff --git a/libavogadro/src/pythoninterpreter.h b/libavogadro/src/pythoninterpreter.h
-index cb54a00..08af8ea 100644
---- a/libavogadro/src/pythoninterpreter.h
-+++ b/libavogadro/src/pythoninterpreter.h
-@@ -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>
-
-diff --git a/libavogadro/src/pythonscript.h b/libavogadro/src/pythonscript.h
-index 9b35b24..13b8aa5 100644
---- a/libavogadro/src/pythonscript.h
-+++ b/libavogadro/src/pythonscript.h
-@@ -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/libavogadro/src/pythontool_p.h b/libavogadro/src/pythontool_p.h
-index 43471c7..12fc201 100644
---- a/libavogadro/src/pythontool_p.h
-+++ b/libavogadro/src/pythontool_p.h
-@@ -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>
---
-2.3.0
-
diff --git a/packages/sci-chemistry/avogadro/files/avogadro-Fix-build-with-gcc6.patch b/packages/sci-chemistry/avogadro/files/avogadro-Fix-build-with-gcc6.patch
new file mode 100644
index 0000000..7e2a1f3
--- /dev/null
+++ b/packages/sci-chemistry/avogadro/files/avogadro-Fix-build-with-gcc6.patch
@@ -0,0 +1,34 @@
+Upstream: under review, https://github.com/cryos/avogadro/pull/845
+
+From d9d38e71f6e3afd232b0e422d03159e48084c9a6 Mon Sep 17 00:00:00 2001
+From: Heiko Becker <heirecka@exherbo.org>
+Date: Tue, 5 Jul 2016 00:22:27 +0200
+Subject: [PATCH] Fix build with gcc6
+
+---
+ libavogadro/src/extensions/symmetry/libmsym/src/orbital.c | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/libavogadro/src/extensions/symmetry/libmsym/src/orbital.c b/libavogadro/src/extensions/symmetry/libmsym/src/orbital.c
+index 143b4de..0bad4ad 100644
+--- a/libavogadro/src/extensions/symmetry/libmsym/src/orbital.c
++++ b/libavogadro/src/extensions/symmetry/libmsym/src/orbital.c
+@@ -67,13 +67,13 @@ msym_error_t orbitalFromQuantumNumbers(int n, int l, int m, msym_orbital_t *o){
+ }
+ case 2 : {
+ //o->v = dpolynomial[m+l];
+- char *d = (signbit(m) == 1 ? "-" : "+");
++ char *d = (signbit((float)m) == 1 ? "-" : "+");
+ snprintf(o->name, sizeof(o->name), "%dd%d%s",n,abs(m),d);
+ break;
+ }
+ default : {
+ char t = 'f' - 3 + l;
+- char *d = (signbit(m) == 1 ? "-" : "+");
++ char *d = (signbit((float)m) == 1 ? "-" : "+");
+ snprintf(o->name, sizeof(o->name), "%d%c%d%s",n,t,abs(m),d);
+ }
+ }
+--
+2.9.0
+
diff --git a/packages/sci-chemistry/avogadro/files/avogadro-Fix-detection-of-gcc6-s-version-number.patch b/packages/sci-chemistry/avogadro/files/avogadro-Fix-detection-of-gcc6-s-version-number.patch
new file mode 100644
index 0000000..09d0cbe
--- /dev/null
+++ b/packages/sci-chemistry/avogadro/files/avogadro-Fix-detection-of-gcc6-s-version-number.patch
@@ -0,0 +1,27 @@
+Upstream: under review, https://github.com/cryos/avogadro/pull/845
+
+From 0b0aab49f92c49c6e64b9e9f7e998cdcbabfac72 Mon Sep 17 00:00:00 2001
+From: Heiko Becker <heirecka@exherbo.org>
+Date: Tue, 5 Jul 2016 00:10:26 +0200
+Subject: [PATCH] Fix detection of gcc6's version number
+
+---
+ CMakeLists.txt | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 1cbeb8f..8d29587 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -69,7 +69,7 @@ if (CMAKE_COMPILER_IS_GNUCXX)
+ # Now check if we can use visibility to selectively export symbols
+ # Get the GCC version - from KDE4 cmake files
+ exec_program(${CMAKE_C_COMPILER} ARGS --version OUTPUT_VARIABLE _gcc_version_info)
+- string (REGEX MATCH "[345]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}")
++ string (REGEX MATCH "[3-9]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}")
+ # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the
+ # patch level, handle this here:
+ if (NOT _gcc_version)
+--
+2.9.0
+
diff --git a/packages/sci-chemistry/avogadro/files/avogadro-cmake-3.2.patch b/packages/sci-chemistry/avogadro/files/avogadro-cmake-3.2.patch
deleted file mode 100644
index 796b27c..0000000
--- a/packages/sci-chemistry/avogadro/files/avogadro-cmake-3.2.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-Source: submitted on http://sourceforge.net/p/avogadro/bugs/746/
-Upstream: see above
-Reason: Fix build with cmake-3.2
-
-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/packages/sci-chemistry/avogadro/files/avogadro-cmake-Use-SHARE_INSTALL_PREFIX-instead-of-share.patch b/packages/sci-chemistry/avogadro/files/avogadro-cmake-Use-SHARE_INSTALL_PREFIX-instead-of-share.patch
new file mode 100644
index 0000000..753ec9d
--- /dev/null
+++ b/packages/sci-chemistry/avogadro/files/avogadro-cmake-Use-SHARE_INSTALL_PREFIX-instead-of-share.patch
@@ -0,0 +1,72 @@
+Upstream: under review, https://github.com/cryos/avogadro/pull/846
+
+From 5f58a62e6ba5b260f070ecc6c57fc75abf02b20e Mon Sep 17 00:00:00 2001
+From: Heiko Becker <heirecka@exherbo.org>
+Date: Thu, 27 Oct 2016 09:45:27 +0200
+Subject: [PATCH] [cmake] Use ${SHARE_INSTALL_PREFIX} instead of share
+
+---
+ doc/CMakeLists.txt | 2 +-
+ libavogadro/src/engines/CMakeLists.txt | 2 +-
+ libavogadro/src/extensions/CMakeLists.txt | 4 ++--
+ libavogadro/src/tools/CMakeLists.txt | 2 +-
+ 4 files changed, 5 insertions(+), 5 deletions(-)
+
+diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt
+index 0863e61..e89d7bd 100644
+--- a/doc/CMakeLists.txt
++++ b/doc/CMakeLists.txt
+@@ -55,5 +55,5 @@ endif( DOCBOOK2PDF_EXECUTABLE AND DOCBOOK2HTML_EXECUTABLE )
+ # Manpages
+ if(UNIX)
+ file(GLOB man_1 *.1)
+- install(FILES ${man_1} DESTINATION share/man/man1)
++ install(FILES ${man_1} DESTINATION ${SHARE_INSTALL_PREFIX}/man/man1)
+ endif(UNIX)
+diff --git a/libavogadro/src/engines/CMakeLists.txt b/libavogadro/src/engines/CMakeLists.txt
+index b29268e..e13c355 100644
+--- a/libavogadro/src/engines/CMakeLists.txt
++++ b/libavogadro/src/engines/CMakeLists.txt
+@@ -68,5 +68,5 @@ avogadro_plugin(qtaimengine qtaimengine.cpp qtaimsettingswidget.ui)
+
+ if(ALL_PYTHON_FOUND)
+ file(GLOB python_SCRIPTS "python/*.py")
+- install(FILES ${python_SCRIPTS} DESTINATION share/libavogadro/engineScripts)
++ install(FILES ${python_SCRIPTS} DESTINATION ${SHARE_INSTALL_PREFIX}/libavogadro/engineScripts)
+ endif()
+diff --git a/libavogadro/src/extensions/CMakeLists.txt b/libavogadro/src/extensions/CMakeLists.txt
+index 5ed225d..b5506d4 100644
+--- a/libavogadro/src/extensions/CMakeLists.txt
++++ b/libavogadro/src/extensions/CMakeLists.txt
+@@ -76,7 +76,7 @@ if(ENABLE_PYTHON AND ALL_PYTHON_FOUND)
+ target_link_libraries(pythonterminal ${PYTHON_LIBRARIES})
+
+ file(GLOB python_SCRIPTS "python/*.py")
+- install(FILES ${python_SCRIPTS} DESTINATION share/libavogadro/extensionScripts)
++ install(FILES ${python_SCRIPTS} DESTINATION ${SHARE_INSTALL_PREFIX}/libavogadro/extensionScripts)
+ endif()
+
+ ### Animation
+@@ -110,7 +110,7 @@ if(GLEW_FOUND)
+ file(GLOB shader_FRAG "shaders/*.frag")
+ file(GLOB shader_PARAMS "shaders/*.params")
+ install(FILES ${shader_VERT} ${shader_FRAG} ${shader_PARAMS}
+- DESTINATION share/libavogadro/shaders)
++ DESTINATION ${SHARE_INSTALL_PREFIX}/libavogadro/shaders)
+ endif()
+
+ ### super cells
+diff --git a/libavogadro/src/tools/CMakeLists.txt b/libavogadro/src/tools/CMakeLists.txt
+index 58e2669..5f8b890 100644
+--- a/libavogadro/src/tools/CMakeLists.txt
++++ b/libavogadro/src/tools/CMakeLists.txt
+@@ -64,5 +64,5 @@ avogadro_plugin(aligntool aligntool.cpp aligntool.qrc)
+
+ if(ALL_PYTHON_FOUND)
+ file(GLOB python_SCRIPTS "python/*.py")
+- install(FILES ${python_SCRIPTS} DESTINATION share/libavogadro/toolScripts)
++ install(FILES ${python_SCRIPTS} DESTINATION ${SHARE_INSTALL_PREFIX}/libavogadro/toolScripts)
+ endif()
+--
+2.10.1
+