[med-svn] [Git][med-team/sra-sdk][master] 2 commits: use_debian_packaged_re2.patch: Fully fix test/sharq/CMakeLists.txt.

Aaron M. Ucko (@ucko) gitlab at salsa.debian.org
Fri Aug 26 05:30:26 BST 2022 


Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk


Commits:
eeea4e29 by Aaron M. Ucko at 2022-08-26T00:25:37-04:00
use_debian_packaged_re2.patch: Fully fix test/sharq/CMakeLists.txt.

Comment out an inappropriate add_dependencies call.

- - - - -
76e79357 by Aaron M. Ucko at 2022-08-26T00:28:26-04:00
Add more patches for remaining build issues.

Add fix_javadoc_build.patch, link_magic_dynamically.patch,
link_vdb_dynamically.patch, and use_debian_packaged_compression_libs.patch.

- - - - -


7 changed files:

- debian/changelog
- + debian/patches/fix_javadoc_build.patch
- + debian/patches/link_magic_dynamically.patch
- + debian/patches/link_vdb_dynamically.patch
- debian/patches/series
- + debian/patches/use_debian_packaged_compression_libs.patch
- debian/patches/use_debian_packaged_re2.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,10 +1,18 @@
 sra-sdk (3.0.0+dfsg-1) UNRELEASED; urgency=medium
 
+  [ Andreas Tille ]
   * New upstream version
   * Standards-Version: 4.6.1 (routine-update)
   * Build-Depends: default-jdk, flex, bison
 
- -- Andreas Tille <tille at debian.org>  Wed, 27 Jul 2022 13:36:32 +0200
+  [ Aaron M. Ucko ]
+  * debian/patches/use_debian_packaged_re2.patch: Comment out an
+    inappropriate add_dependencies call in test/sharq/CMakeLists.txt.
+  * Add more patches for remaining build issues: fix_javadoc_build.patch,
+    link_magic_dynamically.patch, link_vdb_dynamically.patch, and
+    use_debian_packaged_compression_libs.patch.
+
+ -- Aaron M. Ucko <ucko at debian.org>  Fri, 26 Aug 2022 00:28:25 -0400
 
 sra-sdk (2.11.3+dfsg-1) unstable; urgency=medium
 


=====================================
debian/patches/fix_javadoc_build.patch
=====================================
@@ -0,0 +1,13 @@
+Index: b/ngs/ngs-java/CMakeLists.txt
+===================================================================
+--- a/ngs/ngs-java/CMakeLists.txt
++++ b/ngs/ngs-java/CMakeLists.txt
+@@ -133,7 +133,7 @@ if ( Java_FOUND )
+                 ngs-doc-jar ALL COMMAND
+                 bash -c "${Java_JAR_EXECUTABLE} -cfv ${CMAKE_JAR_OUTPUT_DIRECTORY}/ngs-doc.jar ."
+                 DEPENDS ngs-doc_javadoc
+-                WORKING_DIRECTORY "${TARGDIR}/obj/ngs/ngs-java/javadoc/ngs-doc"
++                WORKING_DIRECTORY "${TARGDIR}/ngs/ngs-java/javadoc/ngs-doc"
+             )
+             install( FILES ${CMAKE_JAR_OUTPUT_DIRECTORY}/ngs-doc.jar DESTINATION ${CMAKE_INSTALL_PREFIX}/jar/ )
+ 


=====================================
debian/patches/link_magic_dynamically.patch
=====================================
@@ -0,0 +1,13 @@
+Index: b/tools/copycat/CMakeLists.txt
+===================================================================
+--- a/tools/copycat/CMakeLists.txt
++++ b/tools/copycat/CMakeLists.txt
+@@ -37,7 +37,7 @@ if( ${OS} STREQUAL "linux" )
+         ccsubchunk
+         ccfile
+     )
+-    target_link_libraries( copycat ${COMMON_LINK_LIBRARIES} ${COMMON_LIBS_READ} ${NCBI_VDB_LIBDIR}/libkff.${STLX} ${NCBI_VDB_LIBDIR}/libmagic.${STLX} )
++    target_link_libraries( copycat ${COMMON_LINK_LIBRARIES} ${COMMON_LIBS_READ} ${NCBI_VDB_LIBDIR}/libkff.${STLX} ${NCBI_VDB_LIBDIR}/libmagic.${SHLX} )
+     MakeLinksExe( copycat false )
+ 
+     # copy/install the magic file


=====================================
debian/patches/link_vdb_dynamically.patch
=====================================
@@ -0,0 +1,22 @@
+Index: b/build/env.cmake
+===================================================================
+--- a/build/env.cmake
++++ b/build/env.cmake
+@@ -544,13 +544,13 @@ endfunction()
+ 
+ if( NOT SINGLE_CONFIG )
+     set( COMMON_LINK_LIBRARIES kapp load tk-version )
+-    set( COMMON_LIBS_READ  $<$<CONFIG:Debug>:${NCBI_VDB_LIBDIR_DEBUG}>$<$<CONFIG:Release>:${NCBI_VDB_LIBDIR_RELEASE}>/${LIBPFX}ncbi-vdb.${STLX} )
+-    set( COMMON_LIBS_WRITE $<$<CONFIG:Debug>:${NCBI_VDB_LIBDIR_DEBUG}>$<$<CONFIG:Release>:${NCBI_VDB_LIBDIR_RELEASE}>/${LIBPFX}ncbi-wvdb.${STLX} )
++    set( COMMON_LIBS_READ  $<$<CONFIG:Debug>:${NCBI_VDB_LIBDIR_DEBUG}>$<$<CONFIG:Release>:${NCBI_VDB_LIBDIR_RELEASE}>/${LIBPFX}ncbi-vdb.${SHLX} )
++    set( COMMON_LIBS_WRITE $<$<CONFIG:Debug>:${NCBI_VDB_LIBDIR_DEBUG}>$<$<CONFIG:Release>:${NCBI_VDB_LIBDIR_RELEASE}>/${LIBPFX}ncbi-wvdb.${SHLX} )
+ else()
+     # single-config generators need full path to ncbi-vdb libraries in order to handle the dependency correctly
+     set( COMMON_LINK_LIBRARIES ${NCBI_VDB_LIBDIR}/libkapp.${STLX} ${NCBI_VDB_LIBDIR}/libload.${STLX} tk-version )
+-    set( COMMON_LIBS_READ   ${NCBI_VDB_LIBDIR}/libncbi-vdb.${STLX} pthread dl m )
+-    set( COMMON_LIBS_WRITE  ${NCBI_VDB_LIBDIR}/libncbi-wvdb.${STLX} pthread dl m )
++    set( COMMON_LIBS_READ   ${NCBI_VDB_LIBDIR}/libncbi-vdb.${SHLX} pthread dl m )
++    set( COMMON_LIBS_WRITE  ${NCBI_VDB_LIBDIR}/libncbi-wvdb.${SHLX} pthread dl m )
+ endif()
+ 
+ if( WIN32 )


=====================================
debian/patches/series
=====================================
@@ -25,4 +25,8 @@ skip_test_using_lots_of_memory.patch
 allow_multi_help.patch
 run_unversioned_tools.patch
 find_ncbi-vdb-interfaces.patch
+link_vdb_dynamically.patch
 use_debian_packaged_re2.patch
+use_debian_packaged_compression_libs.patch
+link_magic_dynamically.patch
+fix_javadoc_build.patch


=====================================
debian/patches/use_debian_packaged_compression_libs.patch
=====================================
@@ -0,0 +1,34 @@
+Index: b/tools/bam-loader/CMakeLists.txt
+===================================================================
+--- a/tools/bam-loader/CMakeLists.txt
++++ b/tools/bam-loader/CMakeLists.txt
+@@ -32,7 +32,7 @@ add_executable( samview
+ 	sam
+ 	samview
+ )
+-target_link_libraries( samview ${COMMON_LINK_LIBRARIES} ${COMMON_LIBS_READ} )
++target_link_libraries( samview ${COMMON_LINK_LIBRARIES} ${COMMON_LIBS_READ} -lz )
+ MakeLinksExe( samview false )
+ 
+ # External
+@@ -48,6 +48,6 @@ if( NOT WIN32)
+ 		mem-bank
+ 		low-match-count
+ 	)
+-	target_link_libraries( bam-load ${COMMON_LINK_LIBRARIES}  ${COMMON_LIBS_WRITE} )
++	target_link_libraries( bam-load ${COMMON_LINK_LIBRARIES}  ${COMMON_LIBS_WRITE} -lz )
+ 	MakeLinksExe( bam-load false )
+ endif()
+Index: b/tools/sra-sort/CMakeLists.txt
+===================================================================
+--- a/tools/sra-sort/CMakeLists.txt
++++ b/tools/sra-sort/CMakeLists.txt
+@@ -27,7 +27,7 @@ add_compile_definitions( __mod__="tools/
+ # Internal
+ if( NOT WIN32 )
+ 	add_executable( dump-blob-boundaries dump-blob-boundaries )
+-	target_link_libraries( dump-blob-boundaries ${COMMON_LINK_LIBRARIES} ${COMMON_LIBS_READ} )
++	target_link_libraries( dump-blob-boundaries ${COMMON_LINK_LIBRARIES} ${COMMON_LIBS_READ} -lbz2 -llzma )
+ 	MakeLinksExe( dump-blob-boundaries false )
+ endif()
+ 


=====================================
debian/patches/use_debian_packaged_re2.patch
=====================================
@@ -1,3 +1,5 @@
+Index: b/tools/sharq/CMakeLists.txt
+===================================================================
 --- a/tools/sharq/CMakeLists.txt
 +++ b/tools/sharq/CMakeLists.txt
 @@ -58,27 +58,27 @@ set(LOCAL_INCDIR ${LOCAL_BUILD_DIR}/incl
@@ -65,9 +67,11 @@
 -endif()
 \ No newline at end of file
 +endif()
+Index: b/test/sharq/CMakeLists.txt
+===================================================================
 --- a/test/sharq/CMakeLists.txt
 +++ b/test/sharq/CMakeLists.txt
-@@ -37,26 +37,7 @@ if ( ZLIB_FOUND AND BZip2_FOUND AND Thre
+@@ -37,28 +37,9 @@ if ( ZLIB_FOUND AND BZip2_FOUND AND Thre
      set(LOCAL_INCDIR ${LOCAL_BUILD_DIR}/include)
      set(LOCAL_LIBDIR ${LOCAL_BUILD_DIR}/lib)
  
@@ -93,8 +97,11 @@
 -    set(RE2_STATIC_LIBRARIES -L${LOCAL_LIBDIR} -lre2 )
 +    set(RE2_STATIC_LIBRARIES -lre2 )
      add_executable(test-sharq-parser test-sharq-parser.cpp )
-     add_dependencies(test-sharq-parser RE2_)
+-    add_dependencies(test-sharq-parser RE2_)
++    # add_dependencies(test-sharq-parser RE2_)
      target_include_directories(test-sharq-parser PUBLIC ${LOCAL_INCDIR} ../../tools/sharq)
+     if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
+         set(CXX_FILESYSTEM_LIBRARIES "stdc++fs")
 @@ -131,4 +112,4 @@ if ( ZLIB_FOUND AND BZip2_FOUND AND Thre
  
  endif()



View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/2c722cc63d7b99195c4727c8e613461bb7ec7340...76e793579bf953d031b6a2820361624c40262d2e

-- 
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/2c722cc63d7b99195c4727c8e613461bb7ec7340...76e793579bf953d031b6a2820361624c40262d2e
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