sci-physics/sassena: Version bump. Fix #454146

Package-Manager: portage-2.2.23

4 files changed, 136 insertions, 51 deletions

diff --git a/sci-physics/sassena/files/sassena-1.4.1-libs.patch b/sci-physics/sassena/files/sassena-1.4.1-libs.patch
deleted file mode 100644
index cded9f7d40db..000000000000
--- a/sci-physics/sassena/files/sassena-1.4.1-libs.patch
+++ /dev/null
@@ -1,51 +0,0 @@
-diff -urN sassena-v1.4.1/cmake/CMakeLists.txt.executables sassena-v1.4.1.patched/cmake/CMakeLists.txt.executables
---- sassena-v1.4.1/cmake/CMakeLists.txt.executables	2012-02-03 04:43:33.000000000 +0400
-+++ sassena-v1.4.1.patched/cmake/CMakeLists.txt.executables	2012-03-21 18:07:13.000000000 +0400
-@@ -61,6 +61,20 @@
- INSTALL(TARGETS s_maketnx RUNTIME DESTINATION bin)
- INSTALL(TARGETS s_stage RUNTIME DESTINATION bin)
- 
-+IF(NOT STATIC)
-+INSTALL(TARGETS sass_controlio LIBRARY DESTINATION ${LIB_INSTALL_DIR})
-+INSTALL(TARGETS sass_decomposition LIBRARY DESTINATION ${LIB_INSTALL_DIR})
-+INSTALL(TARGETS sass_log LIBRARY DESTINATION ${LIB_INSTALL_DIR})
-+INSTALL(TARGETS sass_math LIBRARY DESTINATION ${LIB_INSTALL_DIR})
-+INSTALL(TARGETS sass_mpi LIBRARY DESTINATION ${LIB_INSTALL_DIR})
-+INSTALL(TARGETS sass_report LIBRARY DESTINATION ${LIB_INSTALL_DIR})
-+INSTALL(TARGETS sass_sample LIBRARY DESTINATION ${LIB_INSTALL_DIR})
-+INSTALL(TARGETS sass_scatter_devices LIBRARY DESTINATION ${LIB_INSTALL_DIR})
-+INSTALL(TARGETS sass_services LIBRARY DESTINATION ${LIB_INSTALL_DIR})
-+INSTALL(TARGETS sass_stager LIBRARY DESTINATION ${LIB_INSTALL_DIR})
-+INSTALL(TARGETS sass_vendor_xdrfile LIBRARY DESTINATION ${LIB_INSTALL_DIR})
-+ENDIF(NOT STATIC)
-+
- TARGET_LINK_LIBRARIES (unit_broadcast 
- 	sass_log
- 	sass_report
-@@ -69,4 +83,4 @@
- 	${BOOST_LIBRARIES}
- )
- 
--INSTALL(TARGETS unit_broadcast RUNTIME DESTINATION bin)
-\ В конце файла нет новой строки
-+INSTALL(TARGETS unit_broadcast RUNTIME DESTINATION bin)
-diff -urN sassena-v1.4.1/cmake/CMakeLists.txt.shared sassena-v1.4.1.patched/cmake/CMakeLists.txt.shared
---- sassena-v1.4.1/cmake/CMakeLists.txt.shared	2012-02-03 04:43:33.000000000 +0400
-+++ sassena-v1.4.1.patched/cmake/CMakeLists.txt.shared	2012-03-21 18:10:30.000000000 +0400
-@@ -4,6 +4,8 @@
- 
- SET(INTERNAL_LIBRARY_TYPE SHARED)
- 
-+SET(LIB_INSTALL_DIR  ${CMAKE_INSTALL_PREFIX}/lib)
-+
- IF(CMAKE_HOST_APPLE)
- SET(CMAKE_EXE_LINKER_FLAGS "-fPIC ${CMAKE_EXE_LINKER_FLAGS}")
- ELSE(CMAKE_HOST_APPLE)
-@@ -15,4 +17,4 @@
- INCLUDE(${CMAKE_PROJECT_PATH}/CMakeLists.txt.intern)
- INCLUDE(${CMAKE_PROJECT_PATH}/CMakeLists.txt.executables)
- 
--INCLUDE(${CMAKE_PROJECT_PATH}/CMakeLists.txt.packages)
-\ В конце файла нет новой строки
-+INCLUDE(${CMAKE_PROJECT_PATH}/CMakeLists.txt.packages)
-diff -urN sassena-v1.4.1/CMakeLists.txt sassena-v1.4.1.patched/CMakeLists.txt
diff --git a/sci-physics/sassena/files/sassena-1.4.2_cmake-remove-missing.patch b/sci-physics/sassena/files/sassena-1.4.2_cmake-remove-missing.patch
new file mode 100644
index 000000000000..7131d3514526
--- /dev/null
+++ b/sci-physics/sassena/files/sassena-1.4.2_cmake-remove-missing.patch
@@ -0,0 +1,33 @@
+diff -ru sassena-1.4.2_org/cmake/CMakeLists.txt.executables sassena-1.4.2/cmake/CMakeLists.txt.executables
+--- sassena-1.4.2_org/cmake/CMakeLists.txt.executables	2014-07-29 11:02:12.652053749 +0200
++++ sassena-1.4.2/cmake/CMakeLists.txt.executables	2014-07-29 11:04:57.831042602 +0200
+@@ -18,18 +18,12 @@
+     tests/unit_broadcast.cpp
+ )
+ 
+-ADD_EXECUTABLE(unit_parameters 
+-	src/common.cpp
+-    tests/unit_parameters.cpp
+-)
+-
+ 
+ IF(STATIC)
+ SET_TARGET_PROPERTIES(sassena PROPERTIES LINK_SEARCH_END_STATIC 1)
+ SET_TARGET_PROPERTIES(s_stage PROPERTIES LINK_SEARCH_END_STATIC 1)
+ SET_TARGET_PROPERTIES(s_maketnx PROPERTIES LINK_SEARCH_END_STATIC 1)
+ SET_TARGET_PROPERTIES(unit_broadcast PROPERTIES LINK_SEARCH_END_STATIC 1)
+-SET_TARGET_PROPERTIES(unit_parameters PROPERTIES LINK_SEARCH_END_STATIC 1)
+ ENDIF(STATIC)
+ 
+ TARGET_LINK_LIBRARIES (s_stage 
+@@ -89,10 +83,4 @@
+ 	${BOOST_LIBRARIES}
+ )
+ 
+-TARGET_LINK_LIBRARIES (unit_parameters 
+-	sass_log
+-	sass_controlio
+-	${BOOST_LIBRARIES}
+-)
+-
+ INSTALL(TARGETS unit_broadcast RUNTIME DESTINATION bin)
diff --git a/sci-physics/sassena/files/sassena-1.4.2_link_boost_thread.patch b/sci-physics/sassena/files/sassena-1.4.2_link_boost_thread.patch
new file mode 100644
index 000000000000..424ca381a511
--- /dev/null
+++ b/sci-physics/sassena/files/sassena-1.4.2_link_boost_thread.patch
@@ -0,0 +1,92 @@
+diff -ru sassena-1.4.2_org/src/main/sassena.cpp sassena-1.4.2/src/main/sassena.cpp
+--- sassena-1.4.2_org/src/main/sassena.cpp	2014-07-29 11:02:12.650053749 +0200
++++ sassena-1.4.2/src/main/sassena.cpp	2014-07-29 12:52:56.978605357 +0200
+@@ -62,6 +62,7 @@
+ #include <boost/serialization/complex.hpp>
+ #include <boost/serialization/map.hpp>
+ #include <boost/serialization/vector.hpp>
++#include <boost/thread/thread.hpp>
+ 
+ // other headers
+ #include "exceptions/exceptions.hpp"
+Nur in sassena-1.4.2/src/main: .sassena.cpp.swp.
+diff -ru sassena-1.4.2_org/src/main/s_stage.cpp sassena-1.4.2/src/main/s_stage.cpp
+--- sassena-1.4.2_org/src/main/s_stage.cpp	2014-07-29 11:02:12.650053749 +0200
++++ sassena-1.4.2/src/main/s_stage.cpp	2014-07-29 12:51:22.257611749 +0200
+@@ -33,6 +33,7 @@
+ #include <boost/serialization/complex.hpp>
+ #include <boost/serialization/map.hpp>
+ #include <boost/serialization/vector.hpp>
++#include <boost/thread/thread.hpp>
+ 
+ // other headers
+ #include "exceptions/exceptions.hpp"
+diff -ru sassena-1.4.2_org/src/scatter_devices/abstract_scatter_device.cpp sassena-1.4.2/src/scatter_devices/abstract_scatter_device.cpp
+--- sassena-1.4.2_org/src/scatter_devices/abstract_scatter_device.cpp	2014-07-29 11:02:12.650053749 +0200
++++ sassena-1.4.2/src/scatter_devices/abstract_scatter_device.cpp	2014-07-29 13:02:20.824567306 +0200
+@@ -18,6 +18,7 @@
+ #include <boost/accumulators/accumulators.hpp>
+ #include <boost/accumulators/statistics.hpp>
+ #include <boost/lexical_cast.hpp>
++#include <boost/thread/thread.hpp>
+ 
+ // other headers
+ #include "exceptions/exceptions.hpp"
+Nur in sassena-1.4.2/src/scatter_devices: .abstract_scatter_device.cpp.swp.
+diff -ru sassena-1.4.2_org/src/scatter_devices/all_vectors_scatter_device.cpp sassena-1.4.2/src/scatter_devices/all_vectors_scatter_device.cpp
+--- sassena-1.4.2_org/src/scatter_devices/all_vectors_scatter_device.cpp	2014-07-29 11:02:12.649053750 +0200
++++ sassena-1.4.2/src/scatter_devices/all_vectors_scatter_device.cpp	2014-07-29 13:04:04.907560282 +0200
+@@ -18,6 +18,7 @@
+ #include <boost/accumulators/accumulators.hpp>
+ #include <boost/accumulators/statistics.hpp>
+ #include <boost/lexical_cast.hpp>
++#include <boost/thread/thread.hpp>
+ 
+ // other headers
+ #include "math/coor3d.hpp"
+Nur in sassena-1.4.2/src/scatter_devices: .all_vectors_scatter_device.cpp.swp.
+diff -ru sassena-1.4.2_org/src/scatter_devices/multipole_scatter_device.cpp sassena-1.4.2/src/scatter_devices/multipole_scatter_device.cpp
+--- sassena-1.4.2_org/src/scatter_devices/multipole_scatter_device.cpp	2014-07-29 11:02:12.649053750 +0200
++++ sassena-1.4.2/src/scatter_devices/multipole_scatter_device.cpp	2014-07-29 13:01:16.038571678 +0200
+@@ -19,6 +19,7 @@
+ #include <boost/accumulators/statistics.hpp>
+ #include <boost/lexical_cast.hpp>
+ #include <boost/math/special_functions.hpp>
++#include <boost/thread/thread.hpp>
+ 
+ // other headers
+ #include "math/coor3d.hpp"
+diff -ru sassena-1.4.2_org/src/scatter_devices/self_vectors_scatter_device.cpp sassena-1.4.2/src/scatter_devices/self_vectors_scatter_device.cpp
+--- sassena-1.4.2_org/src/scatter_devices/self_vectors_scatter_device.cpp	2014-07-29 11:02:12.650053749 +0200
++++ sassena-1.4.2/src/scatter_devices/self_vectors_scatter_device.cpp	2014-07-29 13:01:45.753569673 +0200
+@@ -18,6 +18,7 @@
+ #include <boost/accumulators/accumulators.hpp>
+ #include <boost/accumulators/statistics.hpp>
+ #include <boost/lexical_cast.hpp>
++#include <boost/thread/thread.hpp>
+ 
+ // other headers
+ #include "math/coor3d.hpp"
+diff -ru sassena-1.4.2_org/src/services/file_writer_service.cpp sassena-1.4.2/src/services/file_writer_service.cpp
+--- sassena-1.4.2_org/src/services/file_writer_service.cpp	2014-07-29 11:02:12.650053749 +0200
++++ sassena-1.4.2/src/services/file_writer_service.cpp	2014-07-29 13:08:07.448543914 +0200
+@@ -13,6 +13,7 @@
+ 
+ #include <boost/lexical_cast.hpp>
+ #include <boost/filesystem.hpp>
++#include <boost/thread/thread.hpp>
+ #include <log.hpp>
+ #include <control.hpp>
+ #include <math/smath.hpp>
+Nur in sassena-1.4.2/src/services: .file_writer_service.cpp.swp.
+diff -ru sassena-1.4.2_org/src/services/monitor_service.cpp sassena-1.4.2/src/services/monitor_service.cpp
+--- sassena-1.4.2_org/src/services/monitor_service.cpp	2014-07-29 11:02:12.650053749 +0200
++++ sassena-1.4.2/src/services/monitor_service.cpp	2014-07-29 13:07:06.617548019 +0200
+@@ -13,6 +13,7 @@
+ #include <boost/lexical_cast.hpp>
+ #include <boost/filesystem.hpp>
+ #include <boost/random/uniform_int.hpp>
++#include <boost/thread/thread.hpp>
+ #include <log.hpp>
+ #include <control.hpp>
+ #include <report/timer.hpp>
diff --git a/sci-physics/sassena/files/sassena-1.4.2_uint32_t.patch b/sci-physics/sassena/files/sassena-1.4.2_uint32_t.patch
new file mode 100644
index 000000000000..ecb6e845a6b1
--- /dev/null
+++ b/sci-physics/sassena/files/sassena-1.4.2_uint32_t.patch
@@ -0,0 +1,11 @@
+diff -ru sassena-1.4.2_org/src/sample/frames.cpp sassena-1.4.2/src/sample/frames.cpp
+--- sassena-1.4.2_org/src/sample/frames.cpp	2014-07-29 11:02:12.651053749 +0200
++++ sassena-1.4.2/src/sample/frames.cpp	2014-07-29 11:11:39.229015514 +0200
+@@ -298,6 +298,7 @@
+ 	dcdfile.seekg(marker,ios_base::cur);
+ 	dcdfile.read((char*) &marker,sizeof(int32_t));
+ 
++    using boost::uint32_t;
+ 	uint32_t noa;
+ 	dcdfile.read((char*) &marker,sizeof(int32_t));
+ 	dcdfile.read((char*) &noa,sizeof(uint32_t));