|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
--- CMakeLists.txt.fix_libpaths 2018-09-18 23:33:59.000000000 +0200
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
+++ CMakeLists.txt 2019-02-03 19:25:01.064012276 +0100
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
@@ -73,10 +73,7 @@
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
source/lib/SFMT/SFMT.h
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
source/Smoldyn/smoldyn.h
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
source/Smoldyn/smoldynfuncs.h
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
- source/vcell/SimpleMesh.h
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
- source/vcell/SimpleValueProvider.h
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
source/NextSubVolume/nsvc.h
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
- source/vtk/vtkwrapper.h
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
)
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
set(SRC_FILES
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
@@ -130,7 +127,7 @@
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
set_source_files_properties(${SRC_FILES} PROPERTIES LANGUAGE CXX )
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
set_source_files_properties(${MAIN_FILES} PROPERTIES LANGUAGE CXX )
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
-include_directories(source/lib source/Smoldyn source/vcell source/NextSubVolume source/vtk ${CMAKE_BINARY_DIR})
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
+include_directories(source/lib source/Smoldyn source/NextSubVolume source/vtk ${CMAKE_BINARY_DIR})
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
@@ -141,8 +138,8 @@
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
endif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
if(CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANGXX)
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
- set(CMAKE_CXX_FLAGS_DEBUG "-O0 -g -Wall -Wno-deprecated-declarations")
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
- set(CMAKE_CXX_FLAGS_RELEASE "-O2 -Wall -Wno-deprecated-declarations -DNDEBUG")
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
+ set(CMAKE_CXX_FLAGS_DEBUG "-O0 -g -Wall -I/usr/include")
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
+ set(CMAKE_CXX_FLAGS_RELEASE "-O2 -Wall -DNDEBUG -I/usr/include")
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
endif(CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANGXX)
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
if(NOT CMAKE_BUILD_TYPE)
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
@@ -193,7 +190,7 @@
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
set(BNG2_PATH "/usr/local/bin/BioNetGen/BNG2.pl")
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
else()
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
set(NIX_BUILD 1)
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
- set(BNG2_PATH "/usr/local/bin/BioNetGen/BNG2.pl")
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
+ set(BNG2_PATH "${PERL_VENDORLIB}/BioNetGen/BNG2.pl")
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
endif()
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
@@ -348,7 +345,8 @@
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
find_path(ZLIB_INCLUDE_DIRS zlib.h)
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
find_library(ZLIB_LIBRARIES libz.a)
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
else()
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
- include(FindZlib)
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
+ find_path(ZLIB_INCLUDE_DIRS zlib.h PATHS ${INCLUDE_INSTALL_DIR})
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
+ find_library(ZLIB_LIBRARIES libz.so PATHS ${CMAKE_INSTALL_LIBDIR})
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
endif()
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
if(ZLIB_INCLUDE_DIRS AND ZLIB_LIBRARIES)
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
@@ -406,7 +404,7 @@
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
list(APPEND SRC_FILES source/vtk/vtkwrapper.cpp)
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
list(APPEND HEADER_FILES source/vtk/vtkwrapper.h)
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
- add_definitions("-Wno-deprecated")
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
+ add_definitions(" ")
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
list(APPEND DEP_LIBS ${VTK_LIBRARIES})
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
endif(OPTION_VTK)
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
@@ -430,7 +428,7 @@
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
endif()
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
- set(Boost_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/source/NextSubVolume/boost_include)
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
+ set(Boost_INCLUDE_DIR ${INCLUDE_INSTALL_DIR}/boost)
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
include_directories(SYSTEM ${Boost_INCLUDE_DIR})
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
list(APPEND SRC_FILES
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
@@ -457,7 +455,7 @@
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
source/NextSubVolume/nsvc.h
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
)
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
- add_definitions("-Wno-deprecated")
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
+ add_definitions(" ")
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
endif(OPTION_NSV)
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
####### Option: Build with PDE ##########
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
@@ -489,9 +487,9 @@
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
endif()
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
if(OPTION_TARGET_LIBSMOLDYN)
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
- install(TARGETS smoldyn_shared LIBRARY DESTINATION lib)
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
- install(TARGETS smoldyn_static ARCHIVE DESTINATION lib)
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
- install(FILES source/Smoldyn/libsmoldyn.h source/Smoldyn/smoldyn.h ${CMAKE_CURRENT_BINARY_DIR}/smoldynconfigure.h DESTINATION include)
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
+ install(TARGETS smoldyn_shared LIBRARY DESTINATION lib${LIB_SUFFIX}/smoldyn)
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
+ install(TARGETS smoldyn_static ARCHIVE DESTINATION lib${LIB_SUFFIX}/smoldyn)
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
+ install(FILES source/Smoldyn/libsmoldyn.h source/Smoldyn/smoldyn.h ${CMAKE_CURRENT_BINARY_DIR}/smoldynconfigure.h DESTINATION include/smoldyn)
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
endif(OPTION_TARGET_LIBSMOLDYN)
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
|
|
![](https://seccdn.libravatar.org/avatar/4481e8330de14058f1af1adb772e33c170b636165fc56b573b4087bad5f81439?s=16&d=retro) |
00ff2c8 |
endif(NOT OPTION_MINGW)
|