gentoo resync : 10.04.2018

4 files changed, 205 insertions, 34 deletions

diff --git a/sci-libs/avogadrolibs/files/avogadrolibs-0.8.0-underlinking.patch b/sci-libs/avogadrolibs/files/avogadrolibs-0.8.0-underlinking.patch
deleted file mode 100644
index b29f3afe7613..000000000000
--- a/sci-libs/avogadrolibs/files/avogadrolibs-0.8.0-underlinking.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-Fix underlinking problems in shared libraries.
-
---- avogadrolibs-0.8.0/avogadro/qtplugins/apbs/CMakeLists.txt
-+++ avogadrolibs-0.8.0/avogadro/qtplugins/apbs/CMakeLists.txt
-@@ -23,4 +23,4 @@
-   "${apbs_uis}"
- )
- 
--target_link_libraries(apbs LINK_PRIVATE AvogadroIO MoleQueueClient)
-+target_link_libraries(apbs LINK_PRIVATE AvogadroIO MoleQueueClient AvogadroMoleQueue)
---- avogadrolibs-0.8.0/avogadro/qtplugins/playertool/CMakeLists.txt
-+++ avogadrolibs-0.8.0/avogadro/qtplugins/playertool/CMakeLists.txt
-@@ -7,3 +7,5 @@
-   ""
-   playertool.qrc
- )
-+
-+target_link_libraries(PlayerTool LINK_PRIVATE Qt5OpenGL)
---- avogadrolibs-0.8.0/avogadro/qtplugins/povray/CMakeLists.txt
-+++ avogadrolibs-0.8.0/avogadro/qtplugins/povray/CMakeLists.txt
-@@ -8,3 +8,5 @@
-   "povray.cpp"
-   ""
- )
-+
-+target_link_libraries(POVRay LINK_PRIVATE AvogadroRendering)
---- avogadrolibs-0.8.0/avogadro/qtplugins/qtaim/CMakeLists.txt
-+++ avogadrolibs-0.8.0/avogadro/qtplugins/qtaim/CMakeLists.txt
-@@ -34,3 +34,5 @@
- 
- target_link_libraries(QTAIMScenePlugin
-   LINK_PRIVATE AvogadroRendering ${Qt5Concurrent_LIBRARIES})
-+target_link_libraries(QTAIMExtension
-+  LINK_PRIVATE ${Qt5Concurrent_LIBRARIES})
diff --git a/sci-libs/avogadrolibs/files/avogadrolibs-1.91.0_pre20180406-bundled-genxrdpattern.patch b/sci-libs/avogadrolibs/files/avogadrolibs-1.91.0_pre20180406-bundled-genxrdpattern.patch
new file mode 100644
index 000000000000..2072b8fa9b66
--- /dev/null
+++ b/sci-libs/avogadrolibs/files/avogadrolibs-1.91.0_pre20180406-bundled-genxrdpattern.patch
@@ -0,0 +1,44 @@
+From 0287e83eb8706f5237d66873cb6a1b3730891c07 Mon Sep 17 00:00:00 2001
+From: Andreas Sturmlechner <andreas.sturmlechner@gmail.com>
+Date: Sun, 8 Apr 2018 11:21:17 +0200
+Subject: [PATCH] Provide overrideable BUNDLED_GENXRDPATTERN location
+
+---
+ cmake/DownloadGenXrdPattern.cmake | 10 +++++++---
+ 1 file changed, 7 insertions(+), 3 deletions(-)
+
+diff --git a/cmake/DownloadGenXrdPattern.cmake b/cmake/DownloadGenXrdPattern.cmake
+index ab5c5f0..7d4ecb4 100644
+--- a/cmake/DownloadGenXrdPattern.cmake
++++ b/cmake/DownloadGenXrdPattern.cmake
+@@ -10,8 +10,12 @@ macro(DownloadGenXrdPattern)
+     set(GENXRDPATTERN_NAME "genXrdPattern")
+   endif(WIN32)
+ 
++  if(NOT BUNDLED_GENXRDPATTERN)
++    set(BUNDLED_GENXRDPATTERN "${CMAKE_CURRENT_BINARY_DIR}/bin/${GENXRDPATTERN_NAME}")
++  endif()
++
+   # If it already exists, don't download it again
+-  if(NOT EXISTS "${CMAKE_CURRENT_BINARY_DIR}/bin/${GENXRDPATTERN_NAME}")
++  if(NOT EXISTS "${BUNDLED_GENXRDPATTERN}")
+     set(GENXRDPATTERN_V "1.0-static")
+     # Linux
+     if(UNIX AND NOT APPLE)
+@@ -52,11 +56,11 @@ macro(DownloadGenXrdPattern)
+     # Now remove the temporary directory
+     file(REMOVE_RECURSE "${CMAKE_CURRENT_BINARY_DIR}/tmp")
+ 
+-  endif(NOT EXISTS "${CMAKE_CURRENT_BINARY_DIR}/bin/${GENXRDPATTERN_NAME}")
++  endif(NOT EXISTS "${BUNDLED_GENXRDPATTERN}")
+ 
+   set(GENXRDPATTERN_DESTINATION "bin")
+ 
+-  install(FILES "${CMAKE_CURRENT_BINARY_DIR}/bin/${GENXRDPATTERN_NAME}"
++  install(FILES "${BUNDLED_GENXRDPATTERN}"
+           DESTINATION "${GENXRDPATTERN_DESTINATION}"
+           PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE
+                       GROUP_READ GROUP_EXECUTE
+-- 
+2.17.0
+
diff --git a/sci-libs/avogadrolibs/files/avogadrolibs-1.91.0_pre20180406-unbundle-jsoncpp.patch b/sci-libs/avogadrolibs/files/avogadrolibs-1.91.0_pre20180406-unbundle-jsoncpp.patch
new file mode 100644
index 000000000000..3b5280cdc47e
--- /dev/null
+++ b/sci-libs/avogadrolibs/files/avogadrolibs-1.91.0_pre20180406-unbundle-jsoncpp.patch
@@ -0,0 +1,143 @@
+From 7e01a11dde25af75b21090fdaa2ca574ef703e53 Mon Sep 17 00:00:00 2001
+From: Andreas Sturmlechner <andreas.sturmlechner@gmail.com>
+Date: Sun, 8 Apr 2018 01:48:27 +0200
+Subject: [PATCH 1/2] Drop bogus jsoncpp.cpp include from spectra.cpp
+
+---
+ avogadro/qtplugins/spectra/spectra.cpp | 2 --
+ 1 file changed, 2 deletions(-)
+
+diff --git a/avogadro/qtplugins/spectra/spectra.cpp b/avogadro/qtplugins/spectra/spectra.cpp
+index 043b52e..aa9c641 100644
+--- a/avogadro/qtplugins/spectra/spectra.cpp
++++ b/avogadro/qtplugins/spectra/spectra.cpp
+@@ -26,8 +26,6 @@
+ #include <QtWidgets/QFileDialog>
+ #include <avogadro/qtgui/molecule.h>
+ 
+-#include <jsoncpp.cpp>
+-
+ namespace Avogadro {
+ namespace QtPlugins {
+ 
+-- 
+2.17.0
+
+
+From 52cd35662aa2094db77ab4002b7c44f3dab2802d Mon Sep 17 00:00:00 2001
+From: Andreas Sturmlechner <andreas.sturmlechner@gmail.com>
+Date: Sun, 8 Apr 2018 02:00:30 +0200
+Subject: [PATCH 2/2] Use pkgconfig to find system-jsoncpp
+
+---
+ CMakeLists.txt                                     | 5 ++++-
+ avogadro/io/CMakeLists.txt                         | 4 ++--
+ avogadro/qtplugins/importpqr/CMakeLists.txt        | 4 ++--
+ avogadro/qtplugins/plugindownloader/CMakeLists.txt | 4 ++--
+ avogadro/qtplugins/spectra/CMakeLists.txt          | 2 +-
+ avogadro/quantumio/CMakeLists.txt                  | 4 ++--
+ 6 files changed, 13 insertions(+), 10 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 7574fa0..7ce80b0 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -52,8 +52,11 @@ option(USE_PROTOCALL "Enable libraries that use ProtoCall" OFF)
+ option(USE_MOLEQUEUE "Enable the MoleQueue dependent functionality" ON)
+ option(USE_PYTHON "Use Python to wrap some of our API" OFF)
+ 
++find_package(PkgConfig REQUIRED)
++pkg_check_modules(JSONCPP jsoncpp)
++
+ add_subdirectory(utilities)
+-add_subdirectory(thirdparty)
++# add_subdirectory(thirdparty)
+ add_subdirectory(avogadro)
+ 
+ if(ENABLE_TESTING)
+diff --git a/avogadro/io/CMakeLists.txt b/avogadro/io/CMakeLists.txt
+index 1dd7967..10ddbb6 100644
+--- a/avogadro/io/CMakeLists.txt
++++ b/avogadro/io/CMakeLists.txt
+@@ -15,7 +15,7 @@ endif()
+ # compilers that support that notion.
+ include_directories(SYSTEM "${EIGEN3_INCLUDE_DIR}"
+   "${AvogadroLibs_SOURCE_DIR}/thirdparty/pugixml"
+-  "${AvogadroLibs_SOURCE_DIR}/thirdparty/jsoncpp")
++  "${JSONCPP_INCLUDE_DIRS}")
+ 
+ if(DEFINED AvogadroLibs_MEMORY_INCLUDE_DIRS)
+   # The smart pointer classes just require headers.
+@@ -51,7 +51,7 @@ endif()
+ 
+ avogadro_add_library(AvogadroIO ${HEADERS} ${SOURCES})
+ 
+-target_link_libraries(AvogadroIO LINK_PUBLIC AvogadroCore LINK_PRIVATE jsoncpp)
++target_link_libraries(AvogadroIO LINK_PUBLIC AvogadroCore LINK_PRIVATE ${JSONCPP_LIBRARIES})
+ if(USE_HDF5)
+   target_link_libraries(AvogadroIO LINK_PRIVATE ${HDF5_LIBRARIES})
+ endif()
+diff --git a/avogadro/qtplugins/importpqr/CMakeLists.txt b/avogadro/qtplugins/importpqr/CMakeLists.txt
+index ee27da9..365c51a 100644
+--- a/avogadro/qtplugins/importpqr/CMakeLists.txt
++++ b/avogadro/qtplugins/importpqr/CMakeLists.txt
+@@ -1,4 +1,4 @@
+-include_directories(SYSTEM "${AvogadroLibs_SOURCE_DIR}/thirdparty/jsoncpp")
++include_directories(SYSTEM ${JSONCPP_INCLUDE_DIRS})
+ 
+ # Extension
+ set(importpqr_srcs
+@@ -17,4 +17,4 @@ avogadro_plugin(ImportPQR
+   ""
+ )
+ 
+-target_link_libraries(ImportPQR LINK_PRIVATE ${Qt5Network_LIBRARIES} jsoncpp)
++target_link_libraries(ImportPQR LINK_PRIVATE ${Qt5Network_LIBRARIES} ${JSONCPP_LIBRARIES})
+diff --git a/avogadro/qtplugins/plugindownloader/CMakeLists.txt b/avogadro/qtplugins/plugindownloader/CMakeLists.txt
+index 4b07a53..ab4c661 100644
+--- a/avogadro/qtplugins/plugindownloader/CMakeLists.txt
++++ b/avogadro/qtplugins/plugindownloader/CMakeLists.txt
+@@ -1,4 +1,4 @@
+-include_directories(SYSTEM "${AvogadroLibs_SOURCE_DIR}/thirdparty/jsoncpp")
++include_directories(SYSTEM ${JSONCPP_INCLUDE_DIRS})
+ 
+ find_package(LibArchive REQUIRED)
+ include_directories(SYSTEM ${LIBARCHIVE_INCLUDE_DIRS})
+@@ -20,4 +20,4 @@ avogadro_plugin(PluginDownloader
+ )
+ 
+ target_link_libraries(PluginDownloader LINK_PRIVATE ${Qt5Network_LIBRARIES}
+-  ${LIBARCHIVE_LIBRARIES} jsoncpp)
++  ${LIBARCHIVE_LIBRARIES} ${JSONCPP_LIBRARIES})
+diff --git a/avogadro/qtplugins/spectra/CMakeLists.txt b/avogadro/qtplugins/spectra/CMakeLists.txt
+index a2216b8..09d8fc9 100644
+--- a/avogadro/qtplugins/spectra/CMakeLists.txt
++++ b/avogadro/qtplugins/spectra/CMakeLists.txt
+@@ -1,4 +1,4 @@
+-include_directories(SYSTEM "${AvogadroLibs_SOURCE_DIR}/thirdparty/jsoncpp")
++include_directories(SYSTEM ${JSONCPP_INCLUDE_DIRS})
+ 
+ set(plugin_srcs
+   vibrationdialog.cpp
+diff --git a/avogadro/quantumio/CMakeLists.txt b/avogadro/quantumio/CMakeLists.txt
+index 15073e8..35fc766 100644
+--- a/avogadro/quantumio/CMakeLists.txt
++++ b/avogadro/quantumio/CMakeLists.txt
+@@ -2,7 +2,7 @@ find_package(Eigen3 REQUIRED)
+ # Add as "system headers" to avoid warnings generated by them with
+ # compilers that support that notion.
+ include_directories(SYSTEM "${EIGEN3_INCLUDE_DIR}"
+-  "${AvogadroLibs_SOURCE_DIR}/thirdparty/jsoncpp")
++  ${JSONCPP_INCLUDE_DIRS})
+ 
+ include_directories(${CMAKE_CURRENT_BINARY_DIR})
+ 
+@@ -30,4 +30,4 @@ set(SOURCES
+ )
+ 
+ avogadro_add_library(AvogadroQuantumIO ${HEADERS} ${SOURCES})
+-target_link_libraries(AvogadroQuantumIO LINK_PUBLIC AvogadroIO LINK_PRIVATE jsoncpp)
++target_link_libraries(AvogadroQuantumIO LINK_PUBLIC AvogadroIO LINK_PRIVATE ${JSONCPP_LIBRARIES})
+-- 
+2.17.0
+
diff --git a/sci-libs/avogadrolibs/files/avogadrolibs-1.91.0_pre20180406-underlinking.patch b/sci-libs/avogadrolibs/files/avogadrolibs-1.91.0_pre20180406-underlinking.patch
new file mode 100644
index 000000000000..f6f39c9e6b7b
--- /dev/null
+++ b/sci-libs/avogadrolibs/files/avogadrolibs-1.91.0_pre20180406-underlinking.patch
@@ -0,0 +1,18 @@
+Fix underlinking problems in shared libraries.
+
+--- a/avogadro/qtplugins/playertool/CMakeLists.txt
++++ b/avogadro/qtplugins/playertool/CMakeLists.txt
+@@ -7,3 +7,5 @@
+   ""
+   playertool.qrc
+ )
++
++target_link_libraries(PlayerTool LINK_PRIVATE Qt5OpenGL)
+--- a/avogadro/qtplugins/qtaim/CMakeLists.txt
++++ b/avogadro/qtplugins/qtaim/CMakeLists.txt
+@@ -34,3 +34,5 @@
+ 
+ target_link_libraries(QTAIMScenePlugin
+   LINK_PRIVATE AvogadroRendering ${Qt5Concurrent_LIBRARIES})
++target_link_libraries(QTAIMExtension
++  LINK_PRIVATE ${Qt5Concurrent_LIBRARIES})