diff options
| author | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
|---|---|---|
| committer | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
| commit | 4f2d7949f03e1c198bc888f2d05f421d35c57e21 (patch) | |
| tree | ba5f07bf3f9d22d82e54a462313f5d244036c768 /sci-biology/express/files | |
reinit the tree, so we can have metadata
Diffstat (limited to 'sci-biology/express/files')
| -rw-r--r-- | sci-biology/express/files/express-1.5.1-buildsystem.patch | 55 | ||||
| -rw-r--r-- | sci-biology/express/files/express-1.5.1-gcc6.patch | 19 |
2 files changed, 74 insertions, 0 deletions
diff --git a/sci-biology/express/files/express-1.5.1-buildsystem.patch b/sci-biology/express/files/express-1.5.1-buildsystem.patch new file mode 100644 index 000000000000..fca5feadd111 --- /dev/null +++ b/sci-biology/express/files/express-1.5.1-buildsystem.patch @@ -0,0 +1,55 @@ + CMakeLists.txt | 8 +++----- + src/CMakeLists.txt | 4 ++-- + 2 files changed, 5 insertions(+), 7 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index c768e28..65d5633 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -6,14 +6,12 @@ set(${PROJECT_NAME}_VERSION_MAJOR 1) + set(${PROJECT_NAME}_VERSION_MINOR 5) + set(${PROJECT_NAME}_VERSION_PATCH 1) + +-set(CMAKE_CXX_FLAGS "-Wall") +- + set(CMAKE_CXX_FLAGS_DEBUG "-g ${CMAKE_CXX_FLAGS}") + set(CMAKE_CXX_FLAGS_RHDEBINFO "-O3 -g ${CMAKE_CXX_FLAGS}") + set(CMAKE_CXX_FLAGS_MINSIZEREL "-Os ${CMAKE_CXX_FLAGS}") + + set(CMAKE_BUILD_TYPE Release) +-set(Boost_USE_STATIC_LIBS ON) ++set(Boost_USE_STATIC_LIBS OFF) + + find_package(Boost 1.39 + COMPONENTS +@@ -33,10 +31,10 @@ endif(GPERFTOOLS_TCMALLOC_LIB) + + find_package(Protobuf) + if (PROTOBUF_FOUND) +- include_directories(${Boost_INCLUDE_DIRS} ${PROTOBUF_INCLUDE_DIR} "${CMAKE_CURRENT_SOURCE_DIR}/bamtools/include") ++ include_directories(${Boost_INCLUDE_DIRS} ${PROTOBUF_INCLUDE_DIR} ${BAMTOOLS_INCLUDE}) + set(PROTO_INT 1) + else (PROTOBUF_FOUND) +- include_directories(${Boost_INCLUDE_DIRS} "${CMAKE_CURRENT_SOURCE_DIR}/bamtools/include") ++ include_directories(${Boost_INCLUDE_DIRS} ${BAMTOOLS_INCLUDE}) + set(PROTO_INT 0) + endif(PROTOBUF_FOUND) + +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt +index 1cc0c01..8929d1f 100644 +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -16,11 +16,11 @@ endif (GPERFTOOLS_TCMALLOC) + if(WIN32) + set(LIBRARIES ${LIBRARIES} "${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.lib" "${CMAKE_CURRENT_SOURCE_DIR}/../win_build/zlibd.lib") + else(WIN32) +- set(LIBRARIES ${LIBRARIES} "${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.a" "pthread") ++ set(LIBRARIES ${LIBRARIES} "bamtools" "pthread") + endif(WIN32) + + if (PROTOBUF_FOUND) +- set(LIBRARIES ${LIBRARIES} "libprotobuf.a") ++ set(LIBRARIES ${LIBRARIES} "protobuf") + endif(PROTOBUF_FOUND) + + target_link_libraries(express ${LIBRARIES}) diff --git a/sci-biology/express/files/express-1.5.1-gcc6.patch b/sci-biology/express/files/express-1.5.1-gcc6.patch new file mode 100644 index 000000000000..8a608b97b056 --- /dev/null +++ b/sci-biology/express/files/express-1.5.1-gcc6.patch @@ -0,0 +1,19 @@ +Bug: https://bugs.gentoo.org/610692 + +--- a/src/targets.cpp ++++ b/src/targets.cpp +@@ -113,12 +113,12 @@ + + double ll = LOG_1; + double tot_mass = mass(with_pseudo); +- double tot_eff_len = cached_effective_length(lib.bias_table); ++ double tot_eff_len = cached_effective_length(static_cast<bool>(lib.bias_table)); + if (neighbors) { + foreach (const Target* neighbor, *neighbors) { + tot_mass = log_add(tot_mass, neighbor->mass(with_pseudo)); + tot_eff_len = log_add(tot_eff_len, +- neighbor->cached_effective_length(lib.bias_table)); ++ neighbor->cached_effective_length(static_cast<bool>(lib.bias_table))); + } + } + ll += tot_mass - tot_eff_len; |