[med-svn] [Git][med-team/pufferfish][master] Do not link with setcover, it is already linked with SetCover.

[Andrius Merkys (@merkys)]

Andrius Merkys pushed to branch master at Debian Med / pufferfish


Commits:
c5eae7dd by Andrius Merkys at 2022-09-29T03:00:12-04:00
Do not link with setcover, it is already linked with SetCover.

- - - - -


1 changed file:

- debian/patches/use-debian-libs


Changes:

=====================================
debian/patches/use-debian-libs
=====================================
@@ -1,6 +1,6 @@
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -136,7 +136,7 @@ set(WARN_ALL_THINGS "-fdiagnostics-color
+@@ -136,7 +136,7 @@
  
  
  set(OPT_FLAGS "-DHAVE_SIMDE;-D__STDC_FORMAT_MACROS;-DSTX_NO_STD_STRING_VIEW;-O3;-fPIC;-DNDEBUG;-funroll-loops;-ftree-vectorize;-fno-strict-aliasing")
@@ -9,7 +9,7 @@
  
  ##
  # OSX is strange (some might say, stupid in this regard).  Deal with it's quirkines here.
-@@ -395,6 +395,7 @@ if(TBB_RECONFIGURE)
+@@ -395,6 +395,7 @@
  endif()
  message("TBB_LIBRARIES = ${TBB_LIBRARIES}")
  
@@ -17,7 +17,7 @@
  ExternalProject_Add(libseqlib
  GIT_REPOSITORY https://github.com/COMBINE-lab/SeqLib.git
  GIT_TAG        master
-@@ -425,7 +426,11 @@ endif()
+@@ -425,7 +426,11 @@
  if(NOT BZIP2_FOUND)
    ExternalProject_Add_StepDependencies(libseqlib build bz2)
  endif()
@@ -29,7 +29,7 @@
  ExternalProject_Add(libsetcover
          GIT_REPOSITORY https://github.com/martin-steinegger/setcover.git
          GIT_TAG        master
-@@ -448,6 +453,7 @@ ExternalProject_Add(libsetcover
+@@ -448,6 +453,7 @@
  if(FETCHED_TBB)
  add_dependencies(libsetcover libtbb)
  endif()
@@ -37,7 +37,7 @@
  
  endif() # end of NOT BUILD_PUFF_FOR_SALMON
  
-@@ -455,8 +461,10 @@ set(LIB_FLAGS "-L ${CMAKE_CURRENT_SOURCE
+@@ -455,8 +461,10 @@
  set(PUFF_RELEASE_FLAGS "${DEFINE_FLAGS};${KSW_FLAGS};${PF_CPP_FLAGS};${OPT_FLAGS}")
  set(PUFF_DEBUG_FLAGS "${DEFINE_FLAGS};${KSW_FLAGS};${PF_CPP_FLAGS};${DEBUG_FLAGS}")
  
@@ -50,7 +50,7 @@
  add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/external/asyncplusplus)
 --- a/src/CMakeLists.txt
 +++ b/src/CMakeLists.txt
-@@ -123,9 +123,9 @@ endif()
+@@ -123,9 +123,9 @@
  
  add_dependencies(pufferfish puffer)
  add_dependencies(pufferfish ksw2pp) 
@@ -63,7 +63,7 @@
  
  if(TBB_RECONFIGURE OR TBB_TARGET_EXISTED)
    target_link_libraries(pufferfish 
-@@ -169,7 +169,7 @@ target_include_directories(filtersam PRI
+@@ -169,7 +169,7 @@
      )
  target_compile_options(filtersam PUBLIC "$<$<CONFIG:DEBUG>:${PUFF_DEBUG_FLAGS}>")
  target_compile_options(filtersam PUBLIC "$<$<CONFIG:RELEASE>:${PUFF_RELEASE_FLAGS}>")
@@ -72,18 +72,16 @@
  #add_dependencies(filtersam puffer)
  
  
-@@ -186,8 +186,8 @@ target_include_directories(cedar PRIVATE
+@@ -186,8 +186,6 @@
  target_compile_options(cedar PUBLIC "$<$<CONFIG:DEBUG>:${PUFF_DEBUG_FLAGS}>")
  target_compile_options(cedar PUBLIC "$<$<CONFIG:RELEASE>:${PUFF_RELEASE_FLAGS}>")
  target_link_libraries(cedar Async++ Threads::Threads seqlib hts puffer bz2 lzma z SetCover ${ASAN_LIB})
 -add_dependencies(cedar libseqlib)
 -add_dependencies(cedar libsetcover)
-+target_link_libraries(cedar seqlib)
-+target_link_libraries(cedar setcover)
  #add_dependencies(ceder Async++)
  #add_dependencies(ceder seqlib)
  
-@@ -219,7 +219,7 @@ target_link_libraries(bcalm_pufferize Th
+@@ -219,7 +217,7 @@
  #target_link_libraries(edgedensity Threads::Threads z puffer ${ASAN_LIB})
  #target_link_libraries(edgedensity2 Threads::Threads z puffer ${ASAN_LIB})
  target_link_libraries(filtersam Threads::Threads seqlib hts puffer bz2 lzma z ${ASAN_LIB})



View it on GitLab: https://salsa.debian.org/med-team/pufferfish/-/commit/c5eae7dd86a307812802f98f37893cae0ca134f8

-- 
View it on GitLab: https://salsa.debian.org/med-team/pufferfish/-/commit/c5eae7dd86a307812802f98f37893cae0ca134f8
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/20220929/8c985e1c/attachment-0001.htm>