This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch debian in repository bamtools.
commit 87e9ad2f73f924fd30938165d08b1177f0372478 Author: Andreas Tille <[email protected]> Date: Wed Apr 2 15:25:36 2014 +0200 Adapt patches to new upstream version --- .../patches/0002-support-out-of-source-build.patch | 10 ++--- ...om-ExportHeader-function-use-install-inst.patch | 46 +++++++++------------- ...bamtools-to-lib.-Installing-libraries-to-.patch | 28 +++++-------- debian/patches/series | 2 +- 4 files changed, 34 insertions(+), 52 deletions(-) diff --git a/debian/patches/0002-support-out-of-source-build.patch b/debian/patches/0002-support-out-of-source-build.patch index 9dcd1c6..9a0c9b9 100644 --- a/debian/patches/0002-support-out-of-source-build.patch +++ b/debian/patches/0002-support-out-of-source-build.patch @@ -10,8 +10,8 @@ Subject: support out-of-source build --- a/CMakeLists.txt +++ b/CMakeLists.txt -@@ -35,8 +35,8 @@ - set( BamTools_VERSION_BUILD 3 ) +@@ -35,8 +35,8 @@ set( BamTools_VERSION_MINOR 3 ) + set( BamTools_VERSION_BUILD 0 ) # set our library and executable destination dirs -set( EXECUTABLE_OUTPUT_PATH "${CMAKE_SOURCE_DIR}/bin" ) @@ -21,7 +21,7 @@ Subject: support out-of-source build # define compiler flags for all code set( CMAKE_BUILD_TYPE Release ) -@@ -60,6 +60,7 @@ +@@ -60,6 +60,7 @@ endif() # add our includes root path include_directories( src ) @@ -31,7 +31,7 @@ Subject: support out-of-source build add_subdirectory( src ) --- a/src/ExportHeader.cmake +++ b/src/ExportHeader.cmake -@@ -18,7 +18,7 @@ +@@ -18,7 +18,7 @@ function( ExportHeader MODULE FILE DEST add_custom_command( TARGET ${MODULE} COMMAND ${CMAKE_COMMAND} -E copy_if_different "${CMAKE_CURRENT_SOURCE_DIR}/${FILE}" @@ -42,7 +42,7 @@ Subject: support out-of-source build install( FILES "${FILE}" DESTINATION "include/bamtools/${DEST}" ) --- a/src/toolkit/CMakeLists.txt +++ b/src/toolkit/CMakeLists.txt -@@ -34,7 +34,7 @@ +@@ -34,7 +34,7 @@ set_target_properties( bamtools_cmd PROP OUTPUT_NAME "bamtools" ) # make version info available in application diff --git a/debian/patches/0003-remove-custom-ExportHeader-function-use-install-inst.patch b/debian/patches/0003-remove-custom-ExportHeader-function-use-install-inst.patch index b2aea53..60c8188 100644 --- a/debian/patches/0003-remove-custom-ExportHeader-function-use-install-inst.patch +++ b/debian/patches/0003-remove-custom-ExportHeader-function-use-install-inst.patch @@ -12,7 +12,7 @@ Subject: remove custom ExportHeader function, use install instead --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt -@@ -10,7 +10,4 @@ +@@ -10,7 +10,4 @@ add_subdirectory( api ) add_subdirectory( toolkit ) add_subdirectory( utils ) @@ -51,17 +51,23 @@ Subject: remove custom ExportHeader function, use install instead - -endfunction( ExportHeader ) - +--- a/src/toolkit/CMakeLists.txt ++++ b/src/toolkit/CMakeLists.txt +@@ -35,6 +35,9 @@ set_target_properties( bamtools_cmd PROP + ) + # make version info available in application + configure_file( bamtools_version.h.in ${BamTools_BINARY_DIR}/include/bamtools_version.h ) ++install( FILES ${BamTools_BINARY_DIR}/include/bamtools_version.h ++ DESTINATION "include/bamtools" ++ COMPONENT Development ) + + # define libraries to link + target_link_libraries( bamtools_cmd BamTools BamTools-utils jsoncpp ) --- a/src/api/CMakeLists.txt +++ b/src/api/CMakeLists.txt -@@ -54,30 +54,29 @@ - target_link_libraries( BamTools-static ${APILibs} ) - - # set library install destinations --install( TARGETS BamTools LIBRARY DESTINATION "lib/bamtools" RUNTIME DESTINATION "bin") --install( TARGETS BamTools-static ARCHIVE DESTINATION "lib/bamtools") -+install( TARGETS BamTools -+ LIBRARY DESTINATION "lib/bamtools" -+ RUNTIME DESTINATION "bin") +@@ -57,27 +57,23 @@ target_link_libraries( BamTools-static $ + install( TARGETS BamTools LIBRARY DESTINATION "lib/bamtools" RUNTIME DESTINATION "bin") + install( TARGETS BamTools-static ARCHIVE DESTINATION "lib/bamtools") -# export API headers -include(../ExportHeader.cmake) @@ -84,11 +90,6 @@ Subject: remove custom ExportHeader function, use install instead -ExportHeader(APIHeaders SamReadGroupDictionary.h ${ApiIncludeDir}) -ExportHeader(APIHeaders SamSequence.h ${ApiIncludeDir}) -ExportHeader(APIHeaders SamSequenceDictionary.h ${ApiIncludeDir}) -+install( TARGETS BamTools-static -+ ARCHIVE DESTINATION "lib/bamtools") - --set( AlgorithmsIncludeDir "api/algorithms" ) --ExportHeader( AlgorithmsHeaders algorithms/Sort.h ${AlgorithmsIncludeDir} ) +install( FILES api_global.h DESTINATION "include/bamtools/api" COMPONENT Development ) +install( FILES BamAlgorithms.h DESTINATION "include/bamtools/api" COMPONENT Development ) +install( FILES BamAlignment.h DESTINATION "include/bamtools/api" COMPONENT Development ) @@ -107,16 +108,7 @@ Subject: remove custom ExportHeader function, use install instead +install( FILES SamReadGroupDictionary.h DESTINATION "include/bamtools/api" COMPONENT Development ) +install( FILES SamSequence.h DESTINATION "include/bamtools/api" COMPONENT Development ) +install( FILES SamSequenceDictionary.h DESTINATION "include/bamtools/api" COMPONENT Development ) -+install( FILES algorithms/Sort.h DESTINATION "include/bamtools/api/algorithms" COMPONENT Development ) ---- a/src/toolkit/CMakeLists.txt -+++ b/src/toolkit/CMakeLists.txt -@@ -35,6 +35,9 @@ - ) - # make version info available in application - configure_file( bamtools_version.h.in ${BamTools_BINARY_DIR}/include/bamtools_version.h ) -+install( FILES ${BamTools_BINARY_DIR}/include/bamtools_version.h -+ DESTINATION "include/bamtools" -+ COMPONENT Development ) - # define libraries to link - target_link_libraries( bamtools_cmd BamTools BamTools-utils jsoncpp ) +-set( AlgorithmsIncludeDir "api/algorithms" ) +-ExportHeader( AlgorithmsHeaders algorithms/Sort.h ${AlgorithmsIncludeDir} ) ++install( FILES algorithms/Sort.h DESTINATION "include/bamtools/api/algorithms" COMPONENT Development ) diff --git a/debian/patches/0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch b/debian/patches/0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch index a9b76f0..c63c60a 100644 --- a/debian/patches/0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch +++ b/debian/patches/0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch @@ -1,29 +1,19 @@ From: "Michael R. Crusoe" <[email protected]> Date: Wed, 7 Nov 2012 19:11:51 -0700 -Subject: =?UTF-8?q?Install=20libbamtools=20to=20/lib.=20Installing=20librari?= - =?UTF-8?q?es=20to=20/lib/bamtools=20requires=20setting=0ALD=5FLIBRARY=5FPAT?= - =?UTF-8?q?H=20or=20the=20executable's=20rpath.=20Installing=20libraries=20t?= - =?UTF-8?q?o=0A/lib=20is=20cleaner.?= +Subject: Install libbamtools to /usr/lib. Installing libraries to + /usr/lib/bamtools requires setting LD_LIBRARY_PATH or the + executable's rpath. Installing libraries to /usr/lib is cleaner. ---- - src/api/CMakeLists.txt | 4 ++-- - 1 file changed, 2 insertions(+), 2 deletions(-) - -diff --git a/src/api/CMakeLists.txt b/src/api/CMakeLists.txt -index 8234e78..b1b372a 100644 --- a/src/api/CMakeLists.txt +++ b/src/api/CMakeLists.txt -@@ -55,11 +55,11 @@ target_link_libraries( BamTools-static ${APILibs} ) +@@ -54,8 +54,8 @@ target_link_libraries( BamTools $ + target_link_libraries( BamTools-static ${APILibs} ) # set library install destinations - install( TARGETS BamTools -- LIBRARY DESTINATION "lib/bamtools" -+ LIBRARY DESTINATION "lib" - RUNTIME DESTINATION "bin") - - install( TARGETS BamTools-static -- ARCHIVE DESTINATION "lib/bamtools") -+ ARCHIVE DESTINATION "lib") +-install( TARGETS BamTools LIBRARY DESTINATION "lib/bamtools" RUNTIME DESTINATION "bin") +-install( TARGETS BamTools-static ARCHIVE DESTINATION "lib/bamtools") ++install( TARGETS BamTools LIBRARY DESTINATION "lib" RUNTIME DESTINATION "bin") ++install( TARGETS BamTools-static ARCHIVE DESTINATION "lib") install( FILES api_global.h DESTINATION "include/bamtools/api" COMPONENT Development ) install( FILES BamAlgorithms.h DESTINATION "include/bamtools/api" COMPONENT Development ) diff --git a/debian/patches/series b/debian/patches/series index d623b9a..794a5a2 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,5 +1,5 @@ 0001-ignore-thirdparty-and-fix-jsoncpp.patch 0002-support-out-of-source-build.patch 0003-remove-custom-ExportHeader-function-use-install-inst.patch -0004-Link-bamtools-statically-with-libbamtools-utils-as-w.patch +# 0004-Link-bamtools-statically-with-libbamtools-utils-as-w.patch 0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bamtools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
