[med-svn] [salmon] 04/04: Remove salmon_core lib & unused libraires w/ patch
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sat Jan 30 17:06:18 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository salmon.
commit b6bd2dd3eb9a3384e1e67ee8546813719fcf4a97
Author: Kevin Murray <spam at kdmurray.id.au>
Date: Sat Jan 30 18:09:48 2016 +0200
Remove salmon_core lib & unused libraires w/ patch
---
...007-Remove-unnecessarily-linked-libraries.patch | 44 ++++++++
debian/patches/0008-Remove-salmon_core-lib.patch | 42 ++++++++
...emove-FIND_PACKAGE-for-liblzma-and-libbz2.patch | 114 +++++++++++++++++++++
debian/patches/series | 3 +
4 files changed, 203 insertions(+)
diff --git a/debian/patches/0007-Remove-unnecessarily-linked-libraries.patch b/debian/patches/0007-Remove-unnecessarily-linked-libraries.patch
new file mode 100644
index 0000000..f29f1a9
--- /dev/null
+++ b/debian/patches/0007-Remove-unnecessarily-linked-libraries.patch
@@ -0,0 +1,44 @@
+From: Kevin Murray <spam at kdmurray.id.au>
+Date: Sat, 30 Jan 2016 18:06:06 +0200
+Subject: Remove unnecessarily linked libraries
+
+---
+ CMakeLists.txt | 2 +-
+ src/CMakeLists.txt | 6 +-----
+ 2 files changed, 2 insertions(+), 6 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 378eb83..bd6393b 100755
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -226,7 +226,7 @@ endif()
+ # Set the latest version and look for what we need
+ ##
+ set(Boost_ADDITIONAL_VERSIONS "1.53" "1.53.0" "1.54" "1.55" "1.56" "1.57.0" "1.58")
+-find_package(Boost 1.53.0 COMPONENTS iostreams filesystem system thread timer chrono program_options serialization)
++find_package(Boost 1.53.0 COMPONENTS filesystem system thread program_options)
+ message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}")
+ message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}")
+ message("Boost_FOUND = ${Boost_FOUND}")
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index 3f300c8..df31909 100755
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -112,16 +112,12 @@ target_link_libraries(salmon
+ libjellyfish-2.0.so
+ /usr/lib/libbwa.a
+ m
+- ${LIBLZMA_LIBRARIES}
+- ${BZIP2_LIBRARIES}
+- ${TBB_LIBRARIES}
++ tbb
+ ${LIBSALMON_LINKER_FLAGS}
+ ${NON_APPLECLANG_LIBS}
+ ${FAST_MALLOC_LIB}
+ )
+
+-add_dependencies(salmon libbwa)
+-
+ ##
+ # This ensures that the salmon executable should work with or without `make install`
+ ##
diff --git a/debian/patches/0008-Remove-salmon_core-lib.patch b/debian/patches/0008-Remove-salmon_core-lib.patch
new file mode 100644
index 0000000..6eed4e6
--- /dev/null
+++ b/debian/patches/0008-Remove-salmon_core-lib.patch
@@ -0,0 +1,42 @@
+From: Kevin Murray <spam at kdmurray.id.au>
+Date: Sat, 30 Jan 2016 18:06:52 +0200
+Subject: Remove salmon_core lib
+
+---
+ src/CMakeLists.txt | 8 ++------
+ 1 file changed, 2 insertions(+), 6 deletions(-)
+
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index df31909..346d507 100755
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -73,11 +73,8 @@ endif()
+
+ set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
+
+-# Build the Salmon library
+-add_library(salmon_core ${SALMON_LIB_SRCS} )
+-
+ # Build the salmon executable
+-add_executable(salmon ${SALMON_MAIN_SRCS} ${SALMON_ALIGN_SRCS})
++add_executable(salmon ${SALMON_LIB_SRCS} ${SALMON_MAIN_SRCS} ${SALMON_ALIGN_SRCS})
+
+ #add_executable(salmon-read ${SALMON_READ_SRCS})
+ #set_target_properties(salmon-read PROPERTIES COMPILE_FLAGS "${CMAKE_CXX_FLAGS} -DHAVE_LIBPTHREAD -D_PBGZF_USE -fopenmp"
+@@ -103,7 +100,6 @@ endif()
+
+ # Link the executable
+ target_link_libraries(salmon
+- salmon_core
+ gff
+ ${PTHREAD_LIB}
+ ${Boost_LIBRARIES}
+@@ -158,7 +154,7 @@ endif()
+ # install(FILES ${Boost_LIBRARIES}
+ # DESTINATION ${INSTALL_LIB_DIR})
+
+-install(TARGETS salmon salmon_core
++install(TARGETS salmon
+ RUNTIME DESTINATION bin
+ LIBRARY DESTINATION lib
+ ARCHIVE DESTINATION lib
diff --git a/debian/patches/0009-Remove-FIND_PACKAGE-for-liblzma-and-libbz2.patch b/debian/patches/0009-Remove-FIND_PACKAGE-for-liblzma-and-libbz2.patch
new file mode 100644
index 0000000..9c0a473
--- /dev/null
+++ b/debian/patches/0009-Remove-FIND_PACKAGE-for-liblzma-and-libbz2.patch
@@ -0,0 +1,114 @@
+From: Kevin Murray <spam at kdmurray.id.au>
+Date: Sat, 30 Jan 2016 18:33:36 +0200
+Subject: Remove FIND_PACKAGE for liblzma and libbz2
+
+As these seem not to be required.
+---
+ CMakeLists.txt | 94 +++++++++++++++++++++++++++++-----------------------------
+ 1 file changed, 47 insertions(+), 47 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index bd6393b..0f320f1 100755
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -174,53 +174,53 @@ if (NOT ZLIB_FOUND)
+ message (FATAL_ERROR "zlib must be installed before configuration & building can proceed")
+ endif()
+
+-find_package (LibLZMA)
+-if (NOT LIBLZMA_FOUND)
+- message ("Will attempt to fetch and build liblzma")
+- message ("=======================================")
+-ExternalProject_Add(liblzma
+- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+- URL http://tukaani.org/xz/xz-5.2.0.tar.gz
+- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.0
+- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+- BUILD_IN_SOURCE TRUE
+- CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.0/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
+- BUILD_COMMAND make
+- INSTALL_COMMAND make install
+-)
+-# Tell cmake that the external project generated a library so we can
+-# add dependencies here instead of later
+-set (LIBLZMA_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/liblzma.a)
+-set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib")
+-set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include")
+-else()
+- message("Found liblzma library: ${LIBLZMA_LIBRARIES}")
+- message("===========================================")
+-endif()
+-
+-find_package (BZip2)
+-if (NOT BZIP2_FOUND)
+- message ("Will attempt to fetch and build libbz2")
+- message ("=======================================")
+-ExternalProject_Add(libbz2
+- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+- URL http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz
+- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bzip2-1.0.6
+- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+- BUILD_IN_SOURCE TRUE
+- CONFIGURE_COMMAND ""
+- BUILD_COMMAND make CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
+- INSTALL_COMMAND make install PREFIX=<INSTALL_DIR>
+-)
+-# Tell cmake that the external project generated a library so we can
+-# add dependencies here instead of later
+-set (BZIP2_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/libbz2.a)
+-set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib -I${GAT_SOURCE_DIR}/external/install/include")
+-set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include")
+-else()
+- message("Found libbz2 library: ${BZIP2_LIBRARIES}")
+- message("===========================================")
+-endif()
++# find_package (LibLZMA)
++# if (NOT LIBLZMA_FOUND)
++# message ("Will attempt to fetch and build liblzma")
++# message ("=======================================")
++# ExternalProject_Add(liblzma
++# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
++# URL http://tukaani.org/xz/xz-5.2.0.tar.gz
++# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.0
++# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
++# BUILD_IN_SOURCE TRUE
++# CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.0/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
++# BUILD_COMMAND make
++# INSTALL_COMMAND make install
++# )
++# # Tell cmake that the external project generated a library so we can
++# # add dependencies here instead of later
++# set (LIBLZMA_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/liblzma.a)
++# set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib")
++# set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include")
++# else()
++# message("Found liblzma library: ${LIBLZMA_LIBRARIES}")
++# message("===========================================")
++# endif()
++
++# find_package (BZip2)
++# if (NOT BZIP2_FOUND)
++# message ("Will attempt to fetch and build libbz2")
++# message ("=======================================")
++# ExternalProject_Add(libbz2
++# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
++# URL http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz
++# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bzip2-1.0.6
++# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
++# BUILD_IN_SOURCE TRUE
++# CONFIGURE_COMMAND ""
++# BUILD_COMMAND make CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
++# INSTALL_COMMAND make install PREFIX=<INSTALL_DIR>
++# )
++# # Tell cmake that the external project generated a library so we can
++# # add dependencies here instead of later
++# set (BZIP2_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/libbz2.a)
++# set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib -I${GAT_SOURCE_DIR}/external/install/include")
++# set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include")
++# else()
++# message("Found libbz2 library: ${BZIP2_LIBRARIES}")
++# message("===========================================")
++# endif()
+
+ ##
+ # Set the latest version and look for what we need
diff --git a/debian/patches/series b/debian/patches/series
index 36557a7..22910fd 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -5,3 +5,6 @@ drop-mathjax
cmake-typo-fixes
disable-version-check
use-system-pkg-config-tbb
+0007-Remove-unnecessarily-linked-libraries.patch
+0008-Remove-salmon_core-lib.patch
+0009-Remove-FIND_PACKAGE-for-liblzma-and-libbz2.patch
--
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