[med-svn] [Git][med-team/pbbam][master] 5 commits: Remove unused trigger
Andreas Tille
gitlab at salsa.debian.org
Thu Sep 6 12:50:06 BST 2018
Andreas Tille pushed to branch master at Debian Med / pbbam
Commits:
a3993183 by Andreas Tille at 2018-09-06T11:44:21Z
Remove unused trigger
- - - - -
408e9f6f by Andreas Tille at 2018-09-06T11:45:22Z
Fix library package name
- - - - -
34e471f0 by Andreas Tille at 2018-09-06T11:49:15Z
Remove binary files from upstream source
- - - - -
e78087f6 by Andreas Tille at 2018-09-06T11:49:35Z
New upstream version 0.18.0+dfsg
- - - - -
7ee473fe by Andreas Tille at 2018-09-06T11:49:38Z
Update upstream source from tag 'upstream/0.18.0+dfsg'
Update to upstream version '0.18.0+dfsg'
with Debian dir 2e5135e2fa8afda8cbb560b3cb28fa1152db8e63
- - - - -
13 changed files:
- + cmake/FindHTSlib.cmake
- + cmake/PbbamTool.cmake
- + cmake/pbbam-ccache.cmake
- + cmake/pbbam-compilerflags.cmake
- + cmake/pbbam-dependencies.cmake
- + cmake/pbbam-libtype.cmake
- debian/changelog
- debian/control
- debian/copyright
- − debian/libpbbam0.18.0.triggers
- − tools/Darwin/clang-format
- − tools/Linux/clang-format
- − tools/win32/clang-format.exe
Changes:
=====================================
cmake/FindHTSlib.cmake
=====================================
@@ -0,0 +1,11 @@
+# Find HTSlib
+find_package(PkgConfig REQUIRED)
+pkg_check_modules(HTSlib REQUIRED htslib)
+
+# because CMake is trying to be extra clever,
+# it will not properly load libraries with
+# absolute paths in *_LIBRARIES
+set(HTSlib_LIBRARIES "${HTSlib_LDFLAGS}")
+
+message(STATUS " HTSlib include dirs: ${HTSlib_INCLUDE_DIRS}")
+message(STATUS " HTSlib libraries: ${HTSlib_LIBRARIES}")
=====================================
cmake/PbbamTool.cmake
=====================================
@@ -0,0 +1,23 @@
+include(CMakeParseArguments)
+
+function(create_pbbam_tool)
+
+ # parse args
+ set(oneValueArgs TARGET)
+ set(multiValueArgs SOURCES)
+ cmake_parse_arguments(create_pbbam_tool "" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+
+ # create executable
+ include_directories(
+ ${ToolsCommonDir} # shared tool code
+ ${GeneratedDir} # generated version headers
+ ${PacBioBAM_INCLUDE_DIRS} # pbbam/htslib includes
+ )
+ add_executable(${create_pbbam_tool_TARGET} ${create_pbbam_tool_SOURCES})
+ set_target_properties(
+ ${create_pbbam_tool_TARGET} PROPERTIES
+ RUNTIME_OUTPUT_DIRECTORY ${PacBioBAM_BinDir}
+ )
+ target_link_libraries(${create_pbbam_tool_TARGET} pbbam)
+
+endfunction(create_pbbam_tool)
=====================================
cmake/pbbam-ccache.cmake
=====================================
@@ -0,0 +1,8 @@
+
+if(PacBioBAM_use_ccache)
+ find_program(CCACHE_FOUND ccache)
+ if(CCACHE_FOUND)
+ set_property(GLOBAL PROPERTY RULE_LAUNCH_COMPILE ccache)
+ set_property(GLOBAL PROPERTY RULE_LAUNCH_LINK ccache)
+ endif()
+endif()
=====================================
cmake/pbbam-compilerflags.cmake
=====================================
@@ -0,0 +1,44 @@
+
+include(CheckCXXCompilerFlag)
+
+# C++11 check & enabling
+if (CMAKE_VERSION VERSION_LESS "3.1")
+ if ("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang")
+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") # clang
+ else()
+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") # gcc
+ endif()
+else() # 3.1+
+ set(CMAKE_CXX_STANDARD 14)
+ set(CMAKE_CXX_STANDARD_REQUIRED ON)
+endif()
+
+# shared CXX flags for src & tests
+if (MSVC)
+ set(PacBioBAM_CXX_FLAGS "/Wall")
+else()
+ set(PacBioBAM_CXX_FLAGS "-Wall")
+endif()
+
+# NOTE: -Wno-unused-local-typedefs used to quash clang warnings w/ Boost
+check_cxx_compiler_flag("-Wno-unused-local-typedefs" HAS_NO_UNUSED_LOCAL_TYPEDEFS)
+if(HAS_NO_UNUSED_LOCAL_TYPEDEFS)
+ set(PacBioBAM_CXX_FLAGS "${PacBioBAM_CXX_FLAGS} -Wno-unused-local-typedefs")
+endif()
+
+check_cxx_compiler_flag("-Wno-sign-compare" HAS_NO_SIGN_COMPARE)
+if(HAS_NO_SIGN_COMPARE)
+ set(PacBioBAM_CXX_FLAGS "${PacBioBAM_CXX_FLAGS} -Wno-sign-compare")
+endif()
+
+# Turn on windows-style filepath resolution.
+# We need to add this #define early (not just in the C# SWIG wrapper)
+if(WIN32)
+ add_definitions(-DPBBAM_WIN_FILEPATHS)
+endif()
+
+# For now, keep @rpath out of install names on OS X, as it causes SWIG
+# tests to fail.
+if(APPLE)
+ set(CMAKE_MACOSX_RPATH OFF)
+endif()
=====================================
cmake/pbbam-dependencies.cmake
=====================================
@@ -0,0 +1,32 @@
+
+# pthreads
+find_package(Threads REQUIRED)
+
+# boost
+if(NOT Boost_INCLUDE_DIRS)
+ find_package(Boost REQUIRED)
+endif()
+
+# Winsock for htslib on Windows
+if(WIN32)
+ set(SOCKET_LIBRARIES "ws2_32")
+endif()
+
+# zlib
+if (NOT ZLIB_INCLUDE_DIRS OR NOT ZLIB_LIBRARIES)
+ find_package(PkgConfig REQUIRED)
+ pkg_check_modules(ZLIB zlib)
+ set(ZLIB_LIBRARIES ${ZLIB_LDFLAGS})
+else()
+ set(ZLIB_LDFLAGS ${ZLIB_LIBRARIES})
+endif()
+
+# htslib
+if(NOT HTSLIB_INCLUDE_DIRS OR NOT HTSLIB_LIBRARIES)
+ find_package(HTSlib)
+ set(hts_INCLUDE_DIRS ${HTSlib_INCLUDE_DIRS})
+ set(hts_LIBRARIES ${HTSlib_LIBRARIES})
+else()
+ set(hts_INCLUDE_DIRS ${HTSLIB_INCLUDE_DIRS})
+ set(hts_LIBRARIES ${HTSLIB_LIBRARIES})
+endif()
=====================================
cmake/pbbam-libtype.cmake
=====================================
@@ -0,0 +1,21 @@
+
+# determine if we need a shared lib
+if(PacBioBAM_build_shared)
+ set(BUILD_SHARED_LIBS ON)
+ set(htslib_build_shared ON CACHE BOOL "force htslibConfig to export proper library name")
+ set(PB_LIB_MODE SHARED)
+ set(PB_LIB_SUFFIX ${CMAKE_SHARED_LIBRARY_SUFFIX})
+else()
+ set(BUILD_SHARED_LIBS OFF)
+ set(PB_LIB_MODE STATIC)
+ set(PB_LIB_SUFFIX ${CMAKE_STATIC_LIBRARY_SUFFIX})
+endif()
+
+if(WIN32)
+ # Limit the number of DLLs we will have to bundle
+ set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -static-libgcc -static-libstdc++")
+ set(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -static-libgcc -static-libstdc++")
+endif()
+
+
+
=====================================
debian/changelog
=====================================
@@ -9,6 +9,7 @@ pbbam (0.18.0+dfsg-1) UNRELEASED; urgency=medium
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
* Use d-shlibs
+ * Remove unneeded trigger
[ Fabian Kloetzl ]
* fix dependency check for meson
=====================================
debian/control
=====================================
@@ -27,7 +27,7 @@ Package: pbbamtools
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
- libpbbam (= ${binary:Version})
+ libpbbam0.18.0 (= ${binary:Version})
Recommends: samtools
Description: processing Pacific Biosciences binary alignment/map files
The BAM format is a binary, compressed, record-oriented container format
=====================================
debian/copyright
=====================================
@@ -3,6 +3,7 @@ Upstream-Name: pbbam
Upstream-Contact: Pacific Biosciences <devnet at pacificbiosciences.com>
Source: https://github.com/PacificBiosciences/pbbam
Files-Excluded: third-party
+ */clang-format*
Files: *
Copyright: 2014-2016 Pacific Biosciences of California, Inc. <devnet at pacificbiosciences.com>
=====================================
debian/libpbbam0.18.0.triggers deleted
=====================================
@@ -1 +0,0 @@
-activate-noawait ldconfig
=====================================
tools/Darwin/clang-format deleted
=====================================
Binary files a/tools/Darwin/clang-format and /dev/null differ
=====================================
tools/Linux/clang-format deleted
=====================================
Binary files a/tools/Linux/clang-format and /dev/null differ
=====================================
tools/win32/clang-format.exe deleted
=====================================
Binary files a/tools/win32/clang-format.exe and /dev/null differ
View it on GitLab: https://salsa.debian.org/med-team/pbbam/compare/5b37e0193bcc56e7bdb6d7b017559941968707e2...7ee473fe6b0d840b1fc3b4ccc7ce4a0713962dd3
--
View it on GitLab: https://salsa.debian.org/med-team/pbbam/compare/5b37e0193bcc56e7bdb6d7b017559941968707e2...7ee473fe6b0d840b1fc3b4ccc7ce4a0713962dd3
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