From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-chemistry/avogadro/files/1.0.1-gl2ps.patch | 39 +++++++++++ .../avogadro/files/avogadro-1.1.0-textrel.patch | 29 ++++++++ .../avogadro/files/avogadro-1.1.0-xlibs.patch | 16 +++++ .../files/avogadro-1.1.1-boost-join-moc.patch | 78 ++++++++++++++++++++++ .../avogadro/files/avogadro-1.1.1-eigen3.patch | 51 ++++++++++++++ .../files/avogadro-1.1.1-mkspecs-dir.patch | 12 ++++ .../avogadro/files/avogadro-1.1.1-no-strip.patch | 12 ++++ .../avogadro/files/avogadro-1.1.1-openbabel.patch | 16 +++++ .../files/avogadro-1.1.1-pkgconfig_eigen.patch | 8 +++ 9 files changed, 261 insertions(+) create mode 100644 sci-chemistry/avogadro/files/1.0.1-gl2ps.patch create mode 100644 sci-chemistry/avogadro/files/avogadro-1.1.0-textrel.patch create mode 100644 sci-chemistry/avogadro/files/avogadro-1.1.0-xlibs.patch create mode 100644 sci-chemistry/avogadro/files/avogadro-1.1.1-boost-join-moc.patch create mode 100644 sci-chemistry/avogadro/files/avogadro-1.1.1-eigen3.patch create mode 100644 sci-chemistry/avogadro/files/avogadro-1.1.1-mkspecs-dir.patch create mode 100644 sci-chemistry/avogadro/files/avogadro-1.1.1-no-strip.patch create mode 100644 sci-chemistry/avogadro/files/avogadro-1.1.1-openbabel.patch create mode 100644 sci-chemistry/avogadro/files/avogadro-1.1.1-pkgconfig_eigen.patch (limited to 'sci-chemistry/avogadro/files') 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 + + #include + +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 + #include ++#ifndef Q_MOC_RUN + #include ++#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 + #include + #include ++#ifndef Q_MOC_RUN + #include ++#endif + + #include + #include +--- avogadro-1.1.1/libavogadro/src/pythoninterpreter.h ++++ avogadro-1.1.1/libavogadro/src/pythoninterpreter.h +@@ -26,7 +26,9 @@ + #define PYTHONINTERPRETER_H + + #include ++#ifndef Q_MOC_RUN + #include ++#endif + #include + #include + +--- avogadro-1.1.1/libavogadro/src/pythonscript.h ++++ avogadro-1.1.1/libavogadro/src/pythonscript.h +@@ -27,7 +27,9 @@ + #define PYTHONSCRIPT_H + + #include ++#ifndef Q_MOC_RUN + #include ++#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 ++#ifndef Q_MOC_RUN + #include ++#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 + #include ++#ifndef Q_MOC_RUN + #include ++#endif + + #include + #include 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 -- cgit v1.2.3