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commit f964536dc168320362f26eddd0777814bf09c235 Author: Kevin Murray <[email protected]> Date: Thu Sep 24 17:26:07 2015 +1000 gbp pq import/export to refresh package queue --- .../0001-ignore-thirdparty-and-fix-jsoncpp.patch | 33 +++++++++------- .../patches/0002-support-out-of-source-build.patch | 18 ++++++--- ...om-ExportHeader-function-use-install-inst.patch | 45 +++++++++++++--------- ...ls-statically-with-libbamtools-utils-as-w.patch | 22 ----------- ...bamtools-to-lib.-Installing-libraries-to-.patch | 14 +++++-- debian/patches/0006-Doxygen-reproducibility | 15 +++++--- debian/patches/series | 1 - 7 files changed, 79 insertions(+), 69 deletions(-) diff --git a/debian/patches/0001-ignore-thirdparty-and-fix-jsoncpp.patch b/debian/patches/0001-ignore-thirdparty-and-fix-jsoncpp.patch index abfbc76..321e91d 100644 --- a/debian/patches/0001-ignore-thirdparty-and-fix-jsoncpp.patch +++ b/debian/patches/0001-ignore-thirdparty-and-fix-jsoncpp.patch @@ -3,10 +3,13 @@ Date: Wed, 7 Nov 2012 18:44:06 -0700 Subject: ignore-thirdparty-and-fix-jsoncpp --- - src/CMakeLists.txt | 2 +- - src/toolkit/bamtools_filter.cpp | 2 +- - 2 files changed, 238 insertions(+), 2 deletions(-) + src/CMakeLists.txt | 2 +- + src/toolkit/CMakeLists.txt | 1 - + 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 @@ @@ -18,6 +21,20 @@ Subject: ignore-thirdparty-and-fix-jsoncpp 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 @@ + # set include path + include_directories( ${BamTools_SOURCE_DIR}/src/api + ${BamTools_SOURCE_DIR}/src/utils +- ${BamTools_SOURCE_DIR}/src/third_party + ) + + # 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 @@ @@ -29,13 +46,3 @@ Subject: ignore-thirdparty-and-fix-jsoncpp using namespace Json; #include <cstdio> ---- a/src/toolkit/CMakeLists.txt -+++ b/src/toolkit/CMakeLists.txt -@@ -8,7 +8,6 @@ - # set include path - include_directories( ${BamTools_SOURCE_DIR}/src/api - ${BamTools_SOURCE_DIR}/src/utils -- ${BamTools_SOURCE_DIR}/src/third_party - ) - - # compile main bamtools application diff --git a/debian/patches/0002-support-out-of-source-build.patch b/debian/patches/0002-support-out-of-source-build.patch index 9a0c9b9..e5d1eb0 100644 --- a/debian/patches/0002-support-out-of-source-build.patch +++ b/debian/patches/0002-support-out-of-source-build.patch @@ -3,14 +3,16 @@ Date: Fri, 21 Sep 2012 11:16:28 -0400 Subject: support out-of-source build --- - CMakeLists.txt | 5 +++-- - src/ExportHeader.cmake | 2 +- - src/toolkit/CMakeLists.txt | 2 +- + CMakeLists.txt | 5 +++-- + src/ExportHeader.cmake | 2 +- + src/toolkit/CMakeLists.txt | 2 +- 3 files changed, 5 insertions(+), 4 deletions(-) +diff --git a/CMakeLists.txt b/CMakeLists.txt +index dade1e3..c4f5ab7 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt -@@ -35,8 +35,8 @@ set( BamTools_VERSION_MINOR 3 ) +@@ -35,8 +35,8 @@ set( BamTools_VERSION_MINOR 4 ) set( BamTools_VERSION_BUILD 0 ) # set our library and executable destination dirs @@ -29,9 +31,11 @@ Subject: support out-of-source build # list subdirectories to build in add_subdirectory( src ) +diff --git a/src/ExportHeader.cmake b/src/ExportHeader.cmake +index ec62573..ddfe410 100644 --- a/src/ExportHeader.cmake +++ b/src/ExportHeader.cmake -@@ -18,7 +18,7 @@ function( ExportHeader MODULE FILE DEST +@@ -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}/${FILE}" @@ -40,9 +44,11 @@ Subject: support out-of-source build # make sure files are properly 'installed' install( FILES "${FILE}" DESTINATION "include/bamtools/${DEST}" ) +diff --git a/src/toolkit/CMakeLists.txt b/src/toolkit/CMakeLists.txt +index d074870..e6a2da9 100644 --- a/src/toolkit/CMakeLists.txt +++ b/src/toolkit/CMakeLists.txt -@@ -34,7 +34,7 @@ set_target_properties( bamtools_cmd PROP +@@ -34,7 +34,7 @@ set_target_properties( bamtools_cmd PROPERTIES 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 60c8188..a465e85 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 @@ -3,13 +3,15 @@ Date: Fri, 19 Oct 2012 11:35:52 -0400 Subject: remove custom ExportHeader function, use install instead --- - src/CMakeLists.txt | 5 +---- - src/ExportHeader.cmake | 27 ------------------------ - src/api/CMakeLists.txt | 49 ++++++++++++++++++++++---------------------- - src/toolkit/CMakeLists.txt | 3 +++ - 4 files changed, 28 insertions(+), 56 deletions(-) + src/CMakeLists.txt | 5 +---- + src/ExportHeader.cmake | 27 --------------------------- + src/api/CMakeLists.txt | 42 +++++++++++++++++++----------------------- + src/toolkit/CMakeLists.txt | 3 +++ + 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 ) @@ -21,6 +23,9 @@ Subject: remove custom ExportHeader function, use install instead -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 @@ @@ -51,21 +56,11 @@ 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 ) +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 $ +@@ -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") @@ -112,3 +107,17 @@ Subject: remove custom ExportHeader function, use install instead -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 ) + + # define libraries to link + target_link_libraries( bamtools_cmd BamTools BamTools-utils jsoncpp ) diff --git a/debian/patches/0004-Link-bamtools-statically-with-libbamtools-utils-as-w.patch b/debian/patches/0004-Link-bamtools-statically-with-libbamtools-utils-as-w.patch deleted file mode 100644 index cd35a58..0000000 --- a/debian/patches/0004-Link-bamtools-statically-with-libbamtools-utils-as-w.patch +++ /dev/null @@ -1,22 +0,0 @@ -From: "Michael R. Crusoe" <[email protected]> -Date: Wed, 7 Nov 2012 19:07:43 -0700 -Subject: Link bamtools statically with libbamtools-utils as we aren't - distributing it seperately - ---- - src/utils/CMakeLists.txt | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/src/utils/CMakeLists.txt b/src/utils/CMakeLists.txt -index 2d91ca3..b38859c 100644 ---- a/src/utils/CMakeLists.txt -+++ b/src/utils/CMakeLists.txt -@@ -13,7 +13,7 @@ add_definitions( -DBAMTOOLS_UTILS_LIBRARY ) # (for proper exporting of library s - 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 SHARED -+add_library( BamTools-utils STATIC - bamtools_fasta.cpp - bamtools_options.cpp - bamtools_pileup_engine.cpp 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 c63c60a..1a35403 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 @@ -1,12 +1,18 @@ 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. +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 91ce1a2..b6fa538 100644 --- a/src/api/CMakeLists.txt +++ b/src/api/CMakeLists.txt -@@ -54,8 +54,8 @@ target_link_libraries( BamTools $ +@@ -54,8 +54,8 @@ target_link_libraries( BamTools ${APILibs} ) target_link_libraries( BamTools-static ${APILibs} ) # set library install destinations diff --git a/debian/patches/0006-Doxygen-reproducibility b/debian/patches/0006-Doxygen-reproducibility index 58229dd..d6710c8 100644 --- a/debian/patches/0006-Doxygen-reproducibility +++ b/debian/patches/0006-Doxygen-reproducibility @@ -1,11 +1,16 @@ -Description: Turns off timestamps in documentation generated by Doxygen -Author: Michael R. Crusoe <[email protected]> -Forwarded: no -Last-Update: 2015-02-21 +From: Debian Med Packaging Team <[email protected]> +Date: Thu, 24 Sep 2015 17:25:24 +1000 +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 @@ +@@ -853,7 +853,7 @@ HTML_STYLESHEET = # page will contain the date and time when the page was generated. Setting # this to NO can help when comparing the output of multiple runs. diff --git a/debian/patches/series b/debian/patches/series index f3a85fb..32d122c 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,6 +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 0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch 0006-Doxygen-reproducibility -- 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
