This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository bamtools.
commit f76c001173c812b2e184e41f6ca0f7824a2cc95f Author: Andreas Tille <[email protected]> Date: Tue Feb 6 11:17:58 2018 +0100 New upstream version, refresh patches --- debian/changelog | 6 ++ .../0001-ignore-thirdparty-and-fix-jsoncpp.patch | 8 +- .../patches/0002-support-out-of-source-build.patch | 35 +------ ...om-ExportHeader-function-use-install-inst.patch | 109 +++++++++------------ ...bamtools-to-lib.-Installing-libraries-to-.patch | 25 ----- debian/patches/0006-Doxygen-reproducibility | 2 - debian/patches/0007-Big_Endian.patch | 23 ----- debian/patches/0008_Cmake_Test.patch | 14 +-- debian/patches/doxygen-tweak | 47 +++++---- .../patches/non-deprecated-jsoncpp-function-names | 15 --- debian/patches/series | 5 +- debian/patches/spelling | 12 +-- 12 files changed, 89 insertions(+), 212 deletions(-) diff --git a/debian/changelog b/debian/changelog index 07a30ec..32916de 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +bamtools (2.5.1+dfsg-1) UNRELEASED; urgency=medium + + * New upstream version + + -- Andreas Tille <[email protected]> Tue, 06 Feb 2018 10:08:37 +0100 + bamtools (2.4.1+dfsg-2) unstable; urgency=medium * Team upload. diff --git a/debian/patches/0001-ignore-thirdparty-and-fix-jsoncpp.patch b/debian/patches/0001-ignore-thirdparty-and-fix-jsoncpp.patch index 321e91d..65b0d77 100644 --- a/debian/patches/0001-ignore-thirdparty-and-fix-jsoncpp.patch +++ b/debian/patches/0001-ignore-thirdparty-and-fix-jsoncpp.patch @@ -8,8 +8,6 @@ Subject: ignore-thirdparty-and-fix-jsoncpp src/toolkit/bamtools_filter.cpp | 2 +- 3 files changed, 2 insertions(+), 3 deletions(-) -diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt -index e359695..636bd62 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -6,7 +6,7 @@ @@ -21,8 +19,6 @@ index e359695..636bd62 100644 add_subdirectory( toolkit ) add_subdirectory( utils ) -diff --git a/src/toolkit/CMakeLists.txt b/src/toolkit/CMakeLists.txt -index c781148..d074870 100644 --- a/src/toolkit/CMakeLists.txt +++ b/src/toolkit/CMakeLists.txt @@ -8,7 +8,6 @@ @@ -33,15 +29,13 @@ index c781148..d074870 100644 ) # compile main bamtools application -diff --git a/src/toolkit/bamtools_filter.cpp b/src/toolkit/bamtools_filter.cpp -index 2f17242..521e7c2 100644 --- a/src/toolkit/bamtools_filter.cpp +++ b/src/toolkit/bamtools_filter.cpp @@ -16,7 +16,7 @@ #include <utils/bamtools_utilities.h> using namespace BamTools; --#include <jsoncpp/json.h> +-#include <json/json.h> +#include <jsoncpp/json/json.h> using namespace Json; diff --git a/debian/patches/0002-support-out-of-source-build.patch b/debian/patches/0002-support-out-of-source-build.patch index d93d2d3..e011a65 100644 --- a/debian/patches/0002-support-out-of-source-build.patch +++ b/debian/patches/0002-support-out-of-source-build.patch @@ -10,18 +10,7 @@ Forwarded: https://github.com/pezmaster31/bamtools/pull/117 --- a/CMakeLists.txt +++ b/CMakeLists.txt -@@ -35,8 +35,8 @@ 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" ) -+set( EXECUTABLE_OUTPUT_PATH "${CMAKE_BINARY_DIR}/bin" ) -+set( LIBRARY_OUTPUT_PATH "${CMAKE_BINARY_DIR}/lib" ) - - # define compiler flags for all code - set( CMAKE_BUILD_TYPE Release ) -@@ -61,6 +61,7 @@ endif() +@@ -94,6 +94,7 @@ endif() # add our includes root path include_directories( src ) @@ -29,25 +18,3 @@ Forwarded: https://github.com/pezmaster31/bamtools/pull/117 # list subdirectories to build in add_subdirectory( src ) ---- a/src/ExportHeader.cmake -+++ b/src/ExportHeader.cmake -@@ -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}/${FILE}" -- "${CMAKE_SOURCE_DIR}/include/${DEST}/${FILENAME}" ) -+ "${CMAKE_BINARY_DIR}/include/${DEST}/${FILENAME}" ) - - # make sure files are properly 'installed' - install( FILES "${FILE}" DESTINATION "include/bamtools/${DEST}" ) ---- a/src/toolkit/CMakeLists.txt -+++ b/src/toolkit/CMakeLists.txt -@@ -34,7 +34,7 @@ set_target_properties( bamtools_cmd PROP - 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( bamtools_version.h.in ${BamTools_BINARY_DIR}/include/bamtools_version.h ) - - # define libraries to link - target_link_libraries( bamtools_cmd BamTools BamTools-utils jsoncpp ) 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 a465e85..684ea0f 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 @@ -10,59 +10,11 @@ Subject: remove custom ExportHeader function, use install instead 4 files changed, 23 insertions(+), 54 deletions(-) delete mode 100644 src/ExportHeader.cmake -diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt -index 636bd62..3298ff9 100644 ---- a/src/CMakeLists.txt -+++ b/src/CMakeLists.txt -@@ -10,7 +10,4 @@ add_subdirectory( api ) - add_subdirectory( toolkit ) - add_subdirectory( utils ) - --# export shared headers --include( ExportHeader.cmake ) --set( SharedIncludeDir "shared" ) --ExportHeader( SharedHeaders shared/bamtools_global.h ${SharedIncludeDir} ) -+install( FILES shared/bamtools_global.h DESTINATION "include/bamtools/shared" COMPONENT Development ) -diff --git a/src/ExportHeader.cmake b/src/ExportHeader.cmake -deleted file mode 100644 -index ddfe410..0000000 ---- a/src/ExportHeader.cmake -+++ /dev/null -@@ -1,27 +0,0 @@ --# --# ExportHeader --# -- --function( ExportHeader MODULE FILE DEST ) -- -- # if haven't defined our custom 'build target' -- # not exactly a build target, but lets this command get -- # checked any time build step happens -- if( NOT TARGET ${MODULE} ) -- add_custom_target( ${MODULE} ALL COMMENT "Exporting ${MODULE}" ) -- endif( NOT TARGET ${MODULE} ) -- -- # get the filename (without path) -- get_filename_component( FILENAME "${FILE}" NAME ) -- -- # copy header to destination -- add_custom_command( TARGET ${MODULE} COMMAND -- ${CMAKE_COMMAND} -E copy_if_different -- "${CMAKE_CURRENT_SOURCE_DIR}/${FILE}" -- "${CMAKE_BINARY_DIR}/include/${DEST}/${FILENAME}" ) -- -- # make sure files are properly 'installed' -- install( FILES "${FILE}" DESTINATION "include/bamtools/${DEST}" ) -- --endfunction( ExportHeader ) -- -diff --git a/src/api/CMakeLists.txt b/src/api/CMakeLists.txt -index 32edcff..91ce1a2 100644 --- a/src/api/CMakeLists.txt +++ b/src/api/CMakeLists.txt -@@ -57,27 +57,23 @@ target_link_libraries( BamTools-static ${APILibs} ) - install( TARGETS BamTools LIBRARY DESTINATION "lib/bamtools" RUNTIME DESTINATION "bin") - install( TARGETS BamTools-static ARCHIVE DESTINATION "lib/bamtools") +@@ -51,27 +51,23 @@ install( TARGETS BamTools + LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}" + RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}" ) -# export API headers -include(../ExportHeader.cmake) @@ -107,17 +59,46 @@ index 32edcff..91ce1a2 100644 -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/src/toolkit/CMakeLists.txt b/src/toolkit/CMakeLists.txt -index e6a2da9..d4a221f 100644 ---- a/src/toolkit/CMakeLists.txt -+++ b/src/toolkit/CMakeLists.txt -@@ -35,6 +35,9 @@ set_target_properties( bamtools_cmd PROPERTIES - ) - # 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 ) +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -11,9 +11,7 @@ add_subdirectory( toolkit ) + add_subdirectory( utils ) - # define libraries to link - target_link_libraries( bamtools_cmd BamTools BamTools-utils jsoncpp ) + # export shared headers +-include( ExportHeader.cmake ) +-set( SharedIncludeDir "shared" ) +-ExportHeader( SharedHeaders shared/bamtools_global.h ${SharedIncludeDir} ) ++install( FILES shared/bamtools_global.h DESTINATION "include/bamtools/shared" COMPONENT Development ) + + # configure and install pkg-config file + configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/bamtools.pc.in ${CMAKE_CURRENT_BINARY_DIR}/bamtools-1.pc @ONLY ) +--- a/src/ExportHeader.cmake ++++ b/src/ExportHeader.cmake +@@ -1,27 +0,0 @@ +-# +-# ExportHeader +-# +- +-function( ExportHeader MODULE FILE DEST ) +- +- # if haven't defined our custom 'build target' +- # not exactly a build target, but lets this command get +- # checked any time build step happens +- if( NOT TARGET ${MODULE} ) +- add_custom_target( ${MODULE} ALL COMMENT "Exporting ${MODULE}" ) +- endif( NOT TARGET ${MODULE} ) +- +- # get the filename (without path) +- get_filename_component( FILENAME "${FILE}" NAME ) +- +- # copy header to destination +- add_custom_command( TARGET ${MODULE} COMMAND +- ${CMAKE_COMMAND} -E copy_if_different +- "${CMAKE_CURRENT_SOURCE_DIR}/${FILE}" +- "${CMAKE_CURRENT_BINARY_DIR}/include/${DEST}/${FILENAME}" ) +- +- # make sure files are properly 'installed' +- install( FILES "${FILE}" DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/bamtools/${DEST}" ) +- +-endfunction( ExportHeader ) +- 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 deleted file mode 100644 index ddd0575..0000000 --- a/debian/patches/0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch +++ /dev/null @@ -1,25 +0,0 @@ -From: "Michael R. Crusoe" <[email protected]> -Date: Wed, 7 Nov 2012 19:11:51 -0700 -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. -Forwarded: https://github.com/pezmaster31/bamtools/pull/82 ---- - 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 91ce1a2..b6fa538 100644 ---- a/src/api/CMakeLists.txt -+++ b/src/api/CMakeLists.txt -@@ -54,8 +54,8 @@ target_link_libraries( BamTools ${APILibs} ) - 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" 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/0006-Doxygen-reproducibility b/debian/patches/0006-Doxygen-reproducibility index d6710c8..9122f19 100644 --- a/debian/patches/0006-Doxygen-reproducibility +++ b/debian/patches/0006-Doxygen-reproducibility @@ -6,8 +6,6 @@ Subject: Doxygen-reproducibility docs/Doxyfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) -diff --git a/docs/Doxyfile b/docs/Doxyfile -index 7c21624..2a0f578 100644 --- a/docs/Doxyfile +++ b/docs/Doxyfile @@ -853,7 +853,7 @@ HTML_STYLESHEET = diff --git a/debian/patches/0007-Big_Endian.patch b/debian/patches/0007-Big_Endian.patch deleted file mode 100644 index 2a329ac..0000000 --- a/debian/patches/0007-Big_Endian.patch +++ /dev/null @@ -1,23 +0,0 @@ -Subject: read bam files on big endian systems -Author: Dominique Belhachemi <[email protected]> -Bug-Debian: https://bugs.debian.org/807979 -Forwarded: https://github.com/pezmaster31/bamtools/pull/119 - ---- a/src/api/BamAux.h -+++ b/src/api/BamAux.h -@@ -370,8 +370,15 @@ API_EXPORT inline signed int UnpackSigne - API_EXPORT inline signed short UnpackSignedShort(const char* buffer) { - union { signed short value; unsigned char valueBuffer[sizeof(signed short)]; } un; - un.value = 0; -+#if __BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__ - un.valueBuffer[0] = buffer[0]; - un.valueBuffer[1] = buffer[1]; -+#elif __BYTE_ORDER__ == __ORDER_BIG_ENDIAN__ -+ un.valueBuffer[0] = buffer[1]; -+ un.valueBuffer[1] = buffer[0]; -+#else -+ #error "Unsupported hardware" -+#endif - return un.value; - } - diff --git a/debian/patches/0008_Cmake_Test.patch b/debian/patches/0008_Cmake_Test.patch index fe542f1..5afda7b 100644 --- a/debian/patches/0008_Cmake_Test.patch +++ b/debian/patches/0008_Cmake_Test.patch @@ -4,16 +4,16 @@ Author: Dominique Belhachemi <[email protected]> --- a/CMakeLists.txt +++ b/CMakeLists.txt -@@ -8,6 +8,8 @@ - # set project name - project( BamTools ) +@@ -15,6 +15,8 @@ cmake_policy( SET CMP0048 NEW ) + # set project name and version + project( BamTools LANGUAGES CXX VERSION 2.5.1 ) +enable_testing() + - # Cmake requirements - cmake_minimum_required( VERSION 2.6.4 ) - -@@ -65,3 +67,11 @@ include_directories("${CMAKE_BINARY_DIR} + # 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 ) +@@ -98,3 +100,11 @@ include_directories("${CMAKE_BINARY_DIR} # list subdirectories to build in add_subdirectory( src ) diff --git a/debian/patches/doxygen-tweak b/debian/patches/doxygen-tweak index 452a144..b02f152 100644 --- a/debian/patches/doxygen-tweak +++ b/debian/patches/doxygen-tweak @@ -4,36 +4,33 @@ Forwarded: https://github.com/pezmaster31/bamtools/pull/120 --- a/src/api/BamAlignment.h +++ b/src/api/BamAlignment.h -@@ -143,12 +143,13 @@ class API_EXPORT BamAlignment { - bool SkipToNextTag(const char storageType, - char*& pTagData, - unsigned int& numBytesParsed) const; +@@ -149,12 +149,13 @@ private: + bool IsValidSize(const std::string& tag, const std::string& type) const; + void SetErrorString(const std::string& where, const std::string& what) const; + bool SkipToNextTag(const char storageType, char*& pTagData, unsigned int& numBytesParsed) const; - + //! \internal // internal data - private: + private: + struct BamAlignmentSupportData + { - struct BamAlignmentSupportData { -- -+ -+ //! \internal - // data members - std::string AllCharData; - uint32_t BlockLength; -@@ -156,7 +157,8 @@ class API_EXPORT BamAlignment { - uint32_t QueryNameLength; - uint32_t QuerySequenceLength; - bool HasCoreOnly; -- -+ -+ //! \internal - // constructor - BamAlignmentSupportData(void) - : BlockLength(0) -@@ -171,7 +173,6 @@ class API_EXPORT BamAlignment { - friend class Internal::BamWriterPrivate; ++ //! \internal + // data members + std::string AllCharData; + uint32_t BlockLength; +@@ -163,6 +164,7 @@ private: + uint32_t QuerySequenceLength; + bool HasCoreOnly; - mutable std::string ErrorString; // mutable to allow updates even in logically const methods ++ //! \internal + // constructor + BamAlignmentSupportData() + : BlockLength(0) +@@ -177,7 +179,6 @@ private: + friend class Internal::BamWriterPrivate; + + mutable std::string ErrorString; // mutable to allow updates even in logically const methods - //! \endinternal }; diff --git a/debian/patches/non-deprecated-jsoncpp-function-names b/debian/patches/non-deprecated-jsoncpp-function-names deleted file mode 100644 index 7b9b73f..0000000 --- a/debian/patches/non-deprecated-jsoncpp-function-names +++ /dev/null @@ -1,15 +0,0 @@ -From: Michael R. Crusoe <[email protected]> -Subject: Use the non-deprecated function name -Forwarded: https://github.com/pezmaster31/bamtools/pull/121 - ---- bamtools.orig/src/toolkit/bamtools_filter.cpp -+++ bamtools/src/toolkit/bamtools_filter.cpp -@@ -647,7 +647,7 @@ - if ( !reader.parse(document, root) ) { - // use built-in error reporting mechanism to alert user what was wrong with the script - cerr << "bamtools filter ERROR: failed to parse script - see error message(s) below" << endl -- << reader.getFormatedErrorMessages(); -+ << reader.getFormattedErrorMessages(); - return false; - } - diff --git a/debian/patches/series b/debian/patches/series index 74e2912..4ff6c90 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,11 +1,8 @@ doxygen-tweak 0001-ignore-thirdparty-and-fix-jsoncpp.patch -non-deprecated-jsoncpp-function-names 0002-support-out-of-source-build.patch 0003-remove-custom-ExportHeader-function-use-install-inst.patch -0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch 0006-Doxygen-reproducibility -0007-Big_Endian.patch 0008_Cmake_Test.patch spelling -fix_soversion.patch +# fix_soversion.patch diff --git a/debian/patches/spelling b/debian/patches/spelling index d3a0ae8..8fc861c 100644 --- a/debian/patches/spelling +++ b/debian/patches/spelling @@ -4,12 +4,12 @@ Forwarded: https://github.com/pezmaster31/bamtools/pull/122 --- a/src/toolkit/bamtools_resolve.cpp +++ b/src/toolkit/bamtools_resolve.cpp -@@ -868,7 +868,7 @@ bool ResolveTool::ResolveToolPrivate::Ch - +@@ -928,7 +928,7 @@ bool ResolveTool::ResolveToolPrivate::Ch // make sure required stats file supplied - if ( !m_settings->HasStatsFile ) -- errors.push_back("Ouptut stats filename required for -makeStats mode. Please specify one using -stats option."); -+ errors.push_back("Output stats filename required for -makeStats mode. Please specify one using -stats option."); + if (!m_settings->HasStatsFile) + errors.push_back( +- "Ouptut stats filename required for -makeStats mode. Please specify one using " ++ "Output stats filename required for -makeStats mode. Please specify one using " + "-stats option."); // check for UseStats options - if ( m_settings->HasForceMarkReadGroups ) -- 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
