[med-svn] [bamtools] 03/05: New upstream version, refresh patches
Andreas Tille
tille at debian.org
Tue Feb 6 10:31:51 UTC 2018
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 <tille at debian.org>
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 <tille at debian.org> 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" <michael.crusoe at gmail.com>
-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 <domibel at debian.org>
-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 <domibel at debian.org>
--- 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 <crusoe at ucdavis.edu>
-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
More information about the debian-med-commit
mailing list