diff options
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, 0 insertions, 74 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 deleted file mode 100644 index fca5feadd111..000000000000 --- a/sci-biology/express/files/express-1.5.1-buildsystem.patch +++ /dev/null @@ -1,55 +0,0 @@ - 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 deleted file mode 100644 index 8a608b97b056..000000000000 --- a/sci-biology/express/files/express-1.5.1-gcc6.patch +++ /dev/null @@ -1,19 +0,0 @@ -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; |