[med-svn] [Git][med-team/bamtools][master] 2 commits: Fix shared + static library building
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Fri Sep 17 15:44:42 BST 2021
Michael R. Crusoe pushed to branch master at Debian Med / bamtools
Commits:
3cc5008f by Michael R. Crusoe at 2021-09-17T16:39:41+02:00
Fix shared + static library building
- - - - -
f368869f by Michael R. Crusoe at 2021-09-17T16:43:49+02:00
routine-update: Ready to upload to unstable
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/patches/series
- debian/patches/shared_and_static.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,10 +1,10 @@
-bamtools (2.5.2+dfsg-1) UNRELEASED; urgency=medium
+bamtools (2.5.2+dfsg-1) unstable; urgency=medium
* New upstream version, fixes FTBFS with gcc-11. Closes: #983981
* Standards-Version: 4.6.0 (routine-update)
- * refresh patches
+ * refresh patches including reworking the shared & static library patch
- -- Michael R. Crusoe <crusoe at debian.org> Fri, 17 Sep 2021 15:17:35 +0200
+ -- Michael R. Crusoe <crusoe at debian.org> Fri, 17 Sep 2021 16:43:49 +0200
bamtools (2.5.1+dfsg-9) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -56,11 +56,12 @@ Package: libbamtools-dev
Architecture: any
Multi-Arch: same
Section: libdevel
-Depends: libbamtools2.5.1 (= ${binary:Version}),
- ${misc:Depends}
+Depends: libbamtools2.5.2 (= ${binary:Version}),
+ ${misc:Depends},
+ ${devlibs:Depends}
Suggests: libbamtools-doc (= ${binary:Version})
-Breaks: libbamtools2.4.0 (<< 2.5.1+dfsg-2~)
-Replaces: libbamtools2.4.0 (<< 2.5.1+dfsg-2~)
+Breaks: libbamtools2.5.1
+Replaces: libbamtools2.5.1
Description: C++ API for manipulating BAM (genome alignment) files
BamTools facilitates research analysis and data management using BAM
files. It copes with the enormous amount of data produced by current
@@ -73,7 +74,7 @@ Description: C++ API for manipulating BAM (genome alignment) files
.
This is the developers API package.
-Package: libbamtools2.5.1
+Package: libbamtools2.5.2
Architecture: any
Multi-Arch: same
Section: libs
=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
0001-ignore-thirdparty-and-fix-jsoncpp.patch
+shared_and_static.patch
=====================================
debian/patches/shared_and_static.patch
=====================================
@@ -2,31 +2,116 @@ Description: Build additional static lib
Author: Andreas Tille <tille at debian.org>
Last-Update: Wed, 27 May 2020 09:59:29 +0200
---- a/src/api/CMakeLists.txt
-+++ b/src/api/CMakeLists.txt
-@@ -38,18 +38,24 @@ if( WIN32 )
- endif()
+--- bamtools.orig/src/CMakeLists.txt
++++ bamtools/src/CMakeLists.txt
+@@ -33,7 +33,7 @@
# create main BamTools API library
--add_library( BamTools ${BamToolsAPISources} )
-+add_library( BamTools SHARED ${BamToolsAPISources} )
-+add_library( BamTools_static STATIC ${BamToolsAPISources} )
+ add_library(
+- BamTools
++ BamTools SHARED
+
+ api/BamAlignment.cpp
+ api/BamMultiReader.cpp
+@@ -73,6 +73,48 @@
+ api/internal/sam/SamHeaderValidator_p.cpp
+ api/internal/utils/BamException_p.cpp
+ )
++add_library(
++ BamTools_static STATIC
++
++ api/BamAlignment.cpp
++ api/BamMultiReader.cpp
++ api/BamReader.cpp
++ api/BamWriter.cpp
++ api/SamHeader.cpp
++ api/SamProgram.cpp
++ api/SamProgramChain.cpp
++ api/SamReadGroup.cpp
++ api/SamReadGroupDictionary.cpp
++ api/SamSequence.cpp
++ api/SamSequenceDictionary.cpp
++ api/internal/bam/BamHeader_p.cpp
++ api/internal/bam/BamMultiReader_p.cpp
++ api/internal/bam/BamRandomAccessController_p.cpp
++ api/internal/bam/BamReader_p.cpp
++ api/internal/bam/BamWriter_p.cpp
++ api/internal/index/BamIndexFactory_p.cpp
++ api/internal/index/BamStandardIndex_p.cpp
++ api/internal/index/BamToolsIndex_p.cpp
++ api/internal/io/BamDeviceFactory_p.cpp
++ api/internal/io/BamFile_p.cpp
++ api/internal/io/BamFtp_p.cpp
++ api/internal/io/BamHttp_p.cpp
++ api/internal/io/BamPipe_p.cpp
++ api/internal/io/BgzfStream_p.cpp
++ api/internal/io/ByteArray_p.cpp
++ api/internal/io/HostAddress_p.cpp
++ api/internal/io/HostInfo_p.cpp
++ api/internal/io/HttpHeader_p.cpp
++ api/internal/io/ILocalIODevice_p.cpp
++ api/internal/io/RollingBuffer_p.cpp
++ api/internal/io/TcpSocketEngine_p.cpp
++ api/internal/io/TcpSocket_p.cpp
++ api/internal/sam/SamFormatParser_p.cpp
++ api/internal/sam/SamFormatPrinter_p.cpp
++ api/internal/sam/SamHeaderValidator_p.cpp
++ api/internal/utils/BamException_p.cpp
++)
++
+
# The SONAME is bumped on every version increment
# as Bamtools does not yet guarantee a stable ABI
- set_target_properties( BamTools PROPERTIES
- SOVERSION "${BamTools_VERSION}"
- OUTPUT_NAME "bamtools" )
-+set_target_properties( BamTools_static PROPERTIES
-+ OUTPUT_NAME "bamtools" )
- target_include_directories( BamTools PRIVATE "${ZLIB_INCLUDE_DIRS}" )
- target_link_libraries( BamTools PRIVATE "${ZLIB_LIBRARIES}" "${WIN32_LIBRARIES}" )
- install( TARGETS BamTools
- ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}"
- LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}"
- RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}" )
-+install( TARGETS BamTools_static
-+ ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}"
-+ LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}" )
+@@ -83,6 +125,12 @@
+ CXX_STANDARD 11
+ CXX_STANDARD_REQUIRED ON
+ CXX_EXTENSIONS OFF)
++set_target_properties(
++ BamTools_static PROPERTIES
++ OUTPUT_NAME bamtools
++ CXX_STANDARD 11
++ CXX_STANDARD_REQUIRED ON
++ CXX_EXTENSIONS OFF)
+ target_include_directories(
+ BamTools PRIVATE
+ ${ZLIB_INCLUDE_DIRS}
+@@ -91,6 +139,15 @@
+ target_link_libraries(
+ BamTools PRIVATE
+ ${ZLIB_LIBRARIES})
++target_include_directories(
++ BamTools_static PRIVATE
++ ${ZLIB_INCLUDE_DIRS}
++ ${CMAKE_CURRENT_SOURCE_DIR}
++ ${CMAKE_CURRENT_BINARY_DIR})
++target_link_libraries(
++ BamTools_static PRIVATE
++ ${ZLIB_LIBRARIES})
++
+
+ if(WIN32)
+ target_link_libraries(
+@@ -103,6 +160,9 @@
+ target_sources(
+ BamTools PRIVATE
+ api/internal/io/TcpSocketEngine_unix_p.cpp)
++ target_sources(
++ BamTools_static PRIVATE
++ api/internal/io/TcpSocketEngine_unix_p.cpp)
+ endif()
+
+ if(EnableNodeJS)
+@@ -195,6 +255,13 @@
+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
- install( FILES api_global.h DESTINATION "include/bamtools/api" COMPONENT Development )
- install( FILES BamAlgorithms.h DESTINATION "include/bamtools/api" COMPONENT Development )
+ install(
++ TARGETS BamTools_static
++ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
++ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
++ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
++
++
++install(
+ TARGETS bamtools_cmd
+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
View it on GitLab: https://salsa.debian.org/med-team/bamtools/-/compare/aca8e44548feb580ff00db8d3dd37c7e27d8969e...f368869f1f7f8ee34635fdcf6e4c3c005e33379c
--
View it on GitLab: https://salsa.debian.org/med-team/bamtools/-/compare/aca8e44548feb580ff00db8d3dd37c7e27d8969e...f368869f1f7f8ee34635fdcf6e4c3c005e33379c
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20210917/2ba24c29/attachment-0001.htm>
More information about the debian-med-commit
mailing list