path: root/sci-biology/bamtools/files/bamtools-2.4.1-fix-build-system.patch

* Unbundle jsoncpp
* Remove forcing C++98
* Remove forcing CMAKE_BUILD_TYPE
* Remove -fPIC globally
* Fix LFS macro definitions
* Make building static library optional
* Use GNUInstallDirs conventions
* Install .pc file
See also: https://bugs.gentoo.org/show_bug.cgi?id=550144

Taken from https://github.com/pezmaster31/bamtools/pull/139

--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -9,7 +9,14 @@
 project( BamTools )
 
 # Cmake requirements
-cmake_minimum_required( VERSION 2.6.4 )
+cmake_minimum_required( VERSION 3.0 )
+
+# on macOS, MACOSX_RPATH is enabled by default on more recent versions
+# of CMake. Disable this behaviour, and let user enable it if need be.
+cmake_policy( SET CMP0042 OLD )
+
+# Adhere to GNU filesystem layout conventions
+include( GNUInstallDirs )
 
 # Force the build directory to be different from source directory
 macro( ENSURE_OUT_OF_SOURCE_BUILD MSG )
@@ -34,18 +41,21 @@
 set( BamTools_VERSION_MINOR 4 )
 set( BamTools_VERSION_BUILD 1 )
 
-# set our library and executable destination dirs
-set( EXECUTABLE_OUTPUT_PATH "${CMAKE_SOURCE_DIR}/bin" )
-set( LIBRARY_OUTPUT_PATH    "${CMAKE_SOURCE_DIR}/lib" )
-
 # define compiler flags for all code
-set( CMAKE_BUILD_TYPE Release )
-set( CMAKE_CXX_FLAGS_RELEASE "-std=c++98 ${CMAKE_CXX_FLAGS_RELEASE}" )
-add_definitions( -Wall -D_FILE_OFFSET_BITS=64 )
+add_definitions( -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE )
+add_compile_options( -Wall )
 
 # -----------------------------------------------
 # handle platform-/environment-specific defines
 
+# Make building the static library optional
+option( BUILD_STATIC "Build static libbamtools archive" OFF )
+if( BUILD_STATIC )
+    set( BAMTOOLS_CMD_LDFLAGS BamTools-static )
+else()
+    set( BAMTOOLS_CMD_LDFLAGS BamTools )
+endif()
+
 # If planning to run in Node.js environment, run:
 # cmake -DEnableNodeJS=true
 if( EnableNodeJS )
@@ -57,6 +67,11 @@
     add_definitions( -DSUN_OS )
 endif()
 
+# find system JsonCpp
+find_package( PkgConfig )
+pkg_search_module( JSONCPP jsoncpp>=1 )
+
+
 # -------------------------------------------
 
 # add our includes root path
--- a/src/api/CMakeLists.txt
+++ b/src/api/CMakeLists.txt
@@ -10,7 +10,6 @@
 
 # add compiler definitions 
 add_definitions( -DBAMTOOLS_API_LIBRARY ) # (for proper exporting of library symbols)
-add_definitions( -fPIC ) # (attempt to force PIC compiling on CentOS, not being set on shared libs by CMake)
 
 # fetch all internal source files
 add_subdirectory( internal )
@@ -31,18 +30,6 @@
         ${InternalSources}
 )
 
-# create main BamTools API shared library
-add_library( BamTools SHARED ${BamToolsAPISources} )
-set_target_properties( BamTools PROPERTIES
-                       SOVERSION "2.4.1"
-                       OUTPUT_NAME "bamtools" )
-
-# create main BamTools API static library
-add_library( BamTools-static STATIC ${BamToolsAPISources} )
-set_target_properties( BamTools-static PROPERTIES 
-                       OUTPUT_NAME "bamtools" 
-                       PREFIX "lib" )
-
 # link libraries automatically with zlib (and Winsock2, if applicable)
 if( WIN32 )
     set( APILibs z ws2_32 )
@@ -50,12 +37,23 @@
     set( APILibs z )
 endif()
 
-target_link_libraries( BamTools        ${APILibs} )
-target_link_libraries( BamTools-static ${APILibs} )
+# create main BamTools API shared library
+add_library( BamTools SHARED ${BamToolsAPISources} )
+set_target_properties( BamTools PROPERTIES
+                       SOVERSION "2.4.1"
+                       OUTPUT_NAME "bamtools" )
+target_link_libraries( BamTools ${APILibs} )
+install( TARGETS BamTools LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}" RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}" )
 
-# set library install destinations
-install( TARGETS BamTools        LIBRARY DESTINATION "lib/bamtools" RUNTIME DESTINATION "bin")
-install( TARGETS BamTools-static ARCHIVE DESTINATION "lib/bamtools")
+# create main BamTools API static library
+if( BUILD_STATIC )
+    add_library( BamTools-static STATIC ${BamToolsAPISources} )
+    set_target_properties( BamTools-static PROPERTIES
+                           OUTPUT_NAME "bamtools"
+                           PREFIX "lib" )
+    target_link_libraries( BamTools-static ${APILibs} )
+    install( TARGETS BamTools-static ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}" )
+endif()
 
 # export API headers
 include(../ExportHeader.cmake)
--- a/src/bamtools.pc.in
+++ b/src/bamtools.pc.in
@@ -0,0 +1,11 @@
+prefix=@CMAKE_INSTALL_PREFIX@
+exec_prefix=${prefix}
+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@
+includedir=${prefix}/@CMAKE_INSTALL_INCLUDEDIR@
+
+Name: BamTools
+Description: BamTools is a C++ library for reading and manipulating BAM files
+Version: @BamTools_VERSION_MAJOR@.@BamTools_VERSION_MINOR@.@BamTools_VERSION_BUILD@
+
+Libs: -L${libdir} -lbamtools
+Cflags: -I${includedir}
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -14,3 +14,7 @@
 include( ExportHeader.cmake )
 set( SharedIncludeDir "shared" )
 ExportHeader( SharedHeaders shared/bamtools_global.h ${SharedIncludeDir} )
+
+# configure and install pkg-config file
+configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/bamtools.pc.in ${CMAKE_CURRENT_BINARY_DIR}/bamtools-1.pc @ONLY )
+install( FILES ${CMAKE_CURRENT_BINARY_DIR}/bamtools-1.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig )
--- a/src/ExportHeader.cmake
+++ b/src/ExportHeader.cmake
@@ -18,10 +18,10 @@
     add_custom_command( TARGET ${MODULE} COMMAND
         ${CMAKE_COMMAND} -E copy_if_different
         "${CMAKE_CURRENT_SOURCE_DIR}/${FILE}"
-        "${CMAKE_SOURCE_DIR}/include/${DEST}/${FILENAME}" )
+        "${CMAKE_CURRENT_BINARY_DIR}/include/${DEST}/${FILENAME}" )
 
     # make sure files are properly 'installed'
-    install( FILES "${FILE}" DESTINATION "include/bamtools/${DEST}" )
+    install( FILES "${FILE}" DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/bamtools/${DEST}" )
 
 endfunction( ExportHeader )
 
--- a/src/third_party/CMakeLists.txt
+++ b/src/third_party/CMakeLists.txt
@@ -5,5 +5,3 @@
 # src/third-party/
 # ==========================
 
-# list third-party subdirectories to build in
-add_subdirectory( jsoncpp )
--- a/src/toolkit/CMakeLists.txt
+++ b/src/toolkit/CMakeLists.txt
@@ -35,10 +35,14 @@
                        OUTPUT_NAME "bamtools"
                      )
 # make version info available in application
-configure_file( bamtools_version.h.in ${BamTools_SOURCE_DIR}/src/toolkit/bamtools_version.h )
+configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/bamtools_version.h.in ${CMAKE_CURRENT_BINARY_DIR}/bamtools_version.h )
+include_directories( ${CMAKE_CURRENT_BINARY_DIR} )
+
+# set include paths for system JsonCpp
+target_include_directories( bamtools_cmd PRIVATE ${JSONCPP_INCLUDE_DIRS} )
 
 # define libraries to link
-target_link_libraries( bamtools_cmd BamTools BamTools-utils jsoncpp )
+target_link_libraries( bamtools_cmd BamTools-utils ${BAMTOOLS_CMD_LDFLAGS} ${JSONCPP_LDFLAGS} )
 
 # set application install destinations
-install( TARGETS bamtools_cmd DESTINATION "bin")
+install( TARGETS bamtools_cmd DESTINATION "${CMAKE_INSTALL_BINDIR}" )
--- a/src/utils/CMakeLists.txt
+++ b/src/utils/CMakeLists.txt
@@ -8,9 +8,8 @@
 # list include paths
 include_directories( ${BamTools_SOURCE_DIR}/src/api )
 
-# add compiler definitions 
+# add compiler definitions
 add_definitions( -DBAMTOOLS_UTILS_LIBRARY ) # (for proper exporting of library symbols)
-add_definitions( -fPIC ) # (attempt to force PIC compiling on CentOS, not being set on shared libs by CMake)
 
 # create BamTools utils library
 add_library( BamTools-utils STATIC