reinit the tree, so we can have metadata

9 files changed, 261 insertions, 0 deletions

diff --git a/sci-chemistry/avogadro/files/1.0.1-gl2ps.patch b/sci-chemistry/avogadro/files/1.0.1-gl2ps.patch
new file mode 100644
index 000000000000..d8a0c0f758e1
--- /dev/null
+++ b/sci-chemistry/avogadro/files/1.0.1-gl2ps.patch
@@ -0,0 +1,39 @@
+diff --git a/avogadro/src/CMakeLists.txt b/avogadro/src/CMakeLists.txt
+index 75b6dfb..d87ac2c 100644
+--- a/avogadro/src/CMakeLists.txt
++++ b/avogadro/src/CMakeLists.txt
+@@ -45,7 +45,7 @@ endif(ENABLE_UPDATE_CHECKER)
+ FILE(GLOB projectDelegates_SRCS "projectdelegates/*.cpp")
+ set(avogadro_SRCS ${avogadro_SRCS} ${projectDelegates_SRCS})
+ # Add GL2PS to the executable
+-set(avogadro_SRCS ${avogadro_SRCS} "../gl2ps/gl2ps.c")
++#set(avogadro_SRCS ${avogadro_SRCS} "../gl2ps/gl2ps.c")
+ 
+ if( WIN32 )
+   set(avogadro_SRCS ${avogadro_SRCS} windows/avogadro.rc)
+diff --git a/avogadro/src/mainwindow.cpp b/avogadro/src/mainwindow.cpp
+index 66785fd..2933953 100644
+--- a/avogadro/src/mainwindow.cpp
++++ b/avogadro/src/mainwindow.cpp
+@@ -51,7 +51,7 @@
+ //#endif
+ 
+ // Include the GL2PS header
+-#include "../gl2ps/gl2ps.h"
++#include <gl2ps.h>
+ 
+ #include <avogadro/pluginmanager.h>
+ 
+diff --git a/libavogadro/src/CMakeLists.txt b/libavogadro/src/CMakeLists.txt
+index cce8ece..cc084fb 100644
+--- a/libavogadro/src/CMakeLists.txt
++++ b/libavogadro/src/CMakeLists.txt
+@@ -152,7 +152,7 @@ endforeach(headerFile ${libavogadro_HDRS})
+ add_library(avogadro SHARED ${libavogadro_SRCS} ${libavogadro_QM} ${pythontool_RC_SRCS})
+ set_target_properties(avogadro
+   PROPERTIES VERSION ${Avogadro_VERSION_FULL} SOVERSION 1 )
+-target_link_libraries(avogadro ${AVO_LINK_LIBRARIES})
++target_link_libraries(avogadro ${AVO_LINK_LIBRARIES} gl2ps)
+ 
+ install(TARGETS avogadro DESTINATION ${LIB_INSTALL_DIR})
+ install(FILES ${libavogadro_HDRS}
diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.0-textrel.patch b/sci-chemistry/avogadro/files/avogadro-1.1.0-textrel.patch
new file mode 100644
index 000000000000..6d4536ef7c9b
--- /dev/null
+++ b/sci-chemistry/avogadro/files/avogadro-1.1.0-textrel.patch
@@ -0,0 +1,29 @@
+ libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt | 2 +-
+ libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt   | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt b/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt
+index fb88316..2ddcfdf 100644
+--- a/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt
++++ b/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt
+@@ -20,6 +20,6 @@ add_library(spglib STATIC ${spglib_SRCS})
+ set_target_properties(spglib PROPERTIES COMPILE_FLAGS "-w")
+ 
+ # Set -fPIC on x86_64
+-if("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "x86_64")
++if("${CMAKE_SYSTEM_PROCESSOR}" MATCHES "^(i.86|x86|x86_64|ppc|ppc64)$")
+   set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC"  )
+ endif()
+diff --git a/libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt b/libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt
+index 0cd0c3e..9e89daf 100644
+--- a/libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt
++++ b/libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt
+@@ -19,7 +19,7 @@ add_library(tubegen STATIC ${tubegen_SRCS})
+ set_target_properties(tubegen PROPERTIES COMPILE_FLAGS "-w")
+ 
+ # Set -fPIC on x86_64
+-if("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "x86_64")
++if("${CMAKE_SYSTEM_PROCESSOR}" MATCHES "^(i.86|x86|x86_64|ppc|ppc64)$")
+   set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC"  )
+   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC"  )
+ endif()
diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.0-xlibs.patch b/sci-chemistry/avogadro/files/avogadro-1.1.0-xlibs.patch
new file mode 100644
index 000000000000..74a5889ec8ae
--- /dev/null
+++ b/sci-chemistry/avogadro/files/avogadro-1.1.0-xlibs.patch
@@ -0,0 +1,16 @@
+ * Info: Using [gentoo] (https://bugs.gentoo.org/xmlrpc.cgi)
+ * Info: Getting attachment 403034
+ * Info: Viewing attachment: "X11.patch"
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 60ec98f..03443a7 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -225,6 +225,7 @@ set(I18N_LANGUAGE "" CACHE STRING "Build i18n only for selected language")
+ 
+ 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_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/sci-chemistry/avogadro/files/avogadro-1.1.1-boost-join-moc.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-boost-join-moc.patch
new file mode 100644
index 000000000000..a464fdac42ca
--- /dev/null
+++ b/sci-chemistry/avogadro/files/avogadro-1.1.1-boost-join-moc.patch
@@ -0,0 +1,78 @@
+Add include guards to all boost includes, as qt's moc trips
+over nested BOOST_JOIN macros:
+* usr/include/boost/type_traits/detail/has_binary_operator.hp:50: Parse error at "BOOST_JOIN"
+* libavogadro/src/CMakeFiles/avogadro.dir/build.make:217: recipe for target 'libavogadro/src/moc_pythonengine_p.cxx' failed
+See also: https://bugs.gentoo.org/show_bug.cgi?id=578896
+
+--- avogadro-1.1.1/libavogadro/src/pythonengine_p.h
++++ avogadro-1.1.1/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 {
+ 
+--- avogadro-1.1.1/libavogadro/src/pythonextension_p.h
++++ avogadro-1.1.1/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>
+--- avogadro-1.1.1/libavogadro/src/pythoninterpreter.h
++++ avogadro-1.1.1/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>
+ 
+--- avogadro-1.1.1/libavogadro/src/pythonscript.h
++++ avogadro-1.1.1/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"
+ 
+--- avogadro-1.1.1/libavogadro/src/pythonthread_p.h
++++ avogadro-1.1.1/libavogadro/src/pythonthread_p.h
+@@ -26,7 +26,9 @@
+ #define PYTHONTHREAD_H
+ 
+ #include <avogadro/global.h>
++#ifndef Q_MOC_RUN
+ #include <boost/python.hpp>
++#endif
+ 
+ namespace Avogadro {
+ 
+--- avogadro-1.1.1/libavogadro/src/pythontool_p.h
++++ avogadro-1.1.1/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>
diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.1-eigen3.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-eigen3.patch
new file mode 100644
index 000000000000..dc07d6974e12
--- /dev/null
+++ b/sci-chemistry/avogadro/files/avogadro-1.1.1-eigen3.patch
@@ -0,0 +1,51 @@
+--- 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/sci-chemistry/avogadro/files/avogadro-1.1.1-mkspecs-dir.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-mkspecs-dir.patch
new file mode 100644
index 000000000000..45c616422efe
--- /dev/null
+++ b/sci-chemistry/avogadro/files/avogadro-1.1.1-mkspecs-dir.patch
@@ -0,0 +1,12 @@
+diff -up avogadro-1.1.1/CMakeLists.txt.mkspecs-dir avogadro-1.1.1/CMakeLists.txt
+--- avogadro-1.1.1/CMakeLists.txt.mkspecs-dir	2014-01-24 23:43:01.618510517 -0600
++++ avogadro-1.1.1/CMakeLists.txt	2014-01-24 23:44:03.236844746 -0600
+@@ -547,7 +547,7 @@ 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"
+     )
+ #  endif ("${QT_MKSPECS_DIR}" MATCHES ^$"${CMAKE_INSTALL_PREFIX}/")
+ else()
diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.1-no-strip.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-no-strip.patch
new file mode 100644
index 000000000000..490dd58907df
--- /dev/null
+++ b/sci-chemistry/avogadro/files/avogadro-1.1.1-no-strip.patch
@@ -0,0 +1,12 @@
+diff -up avogadro-1.1.1/CMakeLists.txt.no-strip avogadro-1.1.1/CMakeLists.txt
+--- avogadro-1.1.1/CMakeLists.txt.no-strip	2014-01-24 23:14:44.473840038 -0600
++++ avogadro-1.1.1/CMakeLists.txt	2014-01-24 23:15:46.869166459 -0600
+@@ -114,7 +114,7 @@ if (CMAKE_COMPILER_IS_GNUCXX)
+   endif()
+   # Set up additional build flags for particular build types. These will be added to CMAKE_CXX_FLAGS,
+   # they will not replace them.
+-  set(CMAKE_CXX_FLAGS_RELEASE "-O2 -DNDEBUG -DQT_NO_DEBUG_OUTPUT -Wl,-s")
++  set(CMAKE_CXX_FLAGS_RELEASE "-O2 -DNDEBUG -DQT_NO_DEBUG_OUTPUT")
+   set(CMAKE_CXX_FLAGS_RELWITHDEBINFO
+     "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} ${CMAKE_CXX_FLAGS_WARN}")
+   set(CMAKE_CXX_FLAGS_DEBUG   "-g3 -fno-inline ${CMAKE_CXX_FLAGS_WARN}")
diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.1-openbabel.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-openbabel.patch
new file mode 100644
index 000000000000..4bdc6b2e780e
--- /dev/null
+++ b/sci-chemistry/avogadro/files/avogadro-1.1.1-openbabel.patch
@@ -0,0 +1,16 @@
+ libavogadro/src/python/CMakeLists.txt | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/libavogadro/src/python/CMakeLists.txt b/libavogadro/src/python/CMakeLists.txt
+index efb518a..1a3d91a 100644
+--- a/libavogadro/src/python/CMakeLists.txt
++++ b/libavogadro/src/python/CMakeLists.txt
+@@ -21,7 +21,7 @@ if (WIN32)
+   target_link_libraries(python-module avogadro ${PYTHON_LIBRARIES})
+ else()
+   target_link_libraries(python-module stdc++ avogadro
+-    ${QT_LIBRARIES} ${PYTHON_LIBRARIES} ${Boost_LIBRARIES})
++    ${QT_LIBRARIES} ${PYTHON_LIBRARIES} ${Boost_LIBRARIES} ${OPENBABEL2_LIBRARIES})
+ endif()
+ 
+ # Let's try to use this instead:
diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.1-pkgconfig_eigen.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-pkgconfig_eigen.patch
new file mode 100644
index 000000000000..93dbe2ff4ecc
--- /dev/null
+++ b/sci-chemistry/avogadro/files/avogadro-1.1.1-pkgconfig_eigen.patch
@@ -0,0 +1,8 @@
+diff -up avogadro-1.1.1/avogadro.pc.in.eigen avogadro-1.1.1/avogadro.pc.in
+--- avogadro-1.1.1/avogadro.pc.in.eigen	2013-12-06 09:50:04.000000000 -0600
++++ avogadro-1.1.1/avogadro.pc.in	2014-01-25 00:37:45.732007852 -0600
+@@ -9,3 +9,4 @@ Description: Avogadro libraries
+ Version: @Avogadro_VERSION_FULL@
+ Libs: -L${libdir} -lavogadro
+ Cflags: -I${pkgincludedir}
++Requires.private: eigen3