[med-svn] [Git][med-team/pufferfish][master] No need to add step dependencies for built libraries.

[Andrius Merkys (@merkys)]

Andrius Merkys pushed to branch master at Debian Med / pufferfish


Commits:
b554f21b by Andrius Merkys at 2022-03-24T13:01:57-04:00
No need to add step dependencies for built libraries.

- - - - -


1 changed file:

- debian/patches/use-debian-libs


Changes:

=====================================
debian/patches/use-debian-libs
=====================================
@@ -1,6 +1,6 @@
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -130,7 +130,7 @@ set(WARN_ALL_THINGS "-fdiagnostics-color
+@@ -130,7 +130,7 @@
  #set(WARN_ALL_THINGS "-fdiagnostics-color=always -Wall -Wcast-align -Wcast-qual -Wconversion -Wctor-dtor-privacy -Wdisabled-optimization -Wdouble-promotion -Wduplicated-branches -Wduplicated-cond -Wextra -Wformat=2 -Winit-self -Wlogical-op -Wmissing-declarations -Wmissing-include-dirs -Wno-sign-conversion -Wnoexcept -Wnull-dereference -Wold-style-cast -Woverloaded-virtual -Wpedantic -Wredundant-decls -Wrestrict -Wshadow -Wstrict-aliasing=1 -Wstrict-null-sentinel -Wstrict-overflow=5 -Wswitch-default -Wundef -Wno-unknown-pragmas -Wuseless-cast") 
  
  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.
-@@ -363,24 +363,7 @@ endif()
+@@ -363,43 +363,17 @@
  message("TBB_LIBRARIES = ${TBB_LIBRARIES}")
  
  
@@ -31,11 +31,18 @@
 -                  cp -r json <INSTALL_DIR>/include &&
 -                  cp -r htslib <INSTALL_DIR>/include
 -)
+-
+-if(NOT LIBLZMA_FOUND)
+-  ExternalProject_Add_StepDependencies(libseqlib build liblzma)
+-endif()
+-
+-if(NOT BZIP2_FOUND)
+-  ExternalProject_Add_StepDependencies(libseqlib build bz2)
+-endif()
 +pkg_check_modules(libseqlib IMPORTED_TARGET libseqlib)
  
- if(NOT LIBLZMA_FOUND)
-   ExternalProject_Add_StepDependencies(libseqlib build liblzma)
-@@ -395,11 +378,10 @@ endif()
+ 
+ 
  
  
  ExternalProject_Add(libSetCover
@@ -50,7 +57,7 @@
          SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/setcover
 --- a/src/CMakeLists.txt
 +++ b/src/CMakeLists.txt
-@@ -163,7 +163,6 @@ target_include_directories(cedar PRIVATE
+@@ -163,7 +163,6 @@
  )
  target_compile_options(cedar PUBLIC "$<$<CONFIG:DEBUG>:${PUFF_DEBUG_FLAGS}>")
  target_compile_options(cedar PUBLIC "$<$<CONFIG:RELEASE>:${PUFF_RELEASE_FLAGS}>")
@@ -58,7 +65,7 @@
  add_dependencies(cedar libSetCover)
  
  add_executable(filtersam testing/SAMFilter.cpp)
-@@ -173,7 +172,6 @@ target_include_directories(filtersam PRI
+@@ -173,7 +172,6 @@
      )
  target_compile_options(filtersam PUBLIC "$<$<CONFIG:DEBUG>:${PUFF_DEBUG_FLAGS}>")
  target_compile_options(filtersam PUBLIC "$<$<CONFIG:RELEASE>:${PUFF_RELEASE_FLAGS}>")
@@ -66,7 +73,7 @@
  
  #get_target_property(dirs filtersam INCLUDE_DIRECTORIES)
  #foreach(dir ${dirs})
-@@ -200,6 +198,6 @@ target_link_libraries(bcalm_pufferize Th
+@@ -200,6 +198,6 @@
  target_link_libraries(edgedensity Threads::Threads z puffer ${ASAN_LIB})
  target_link_libraries(edgedensity2 Threads::Threads z puffer ${ASAN_LIB})
  #target_link_libraries(krakmap Threads::Threads puffer ${ASAN_LIB})



View it on GitLab: https://salsa.debian.org/med-team/pufferfish/-/commit/b554f21b704a685aa0e607e89d12c3f90bebaf30

-- 
View it on GitLab: https://salsa.debian.org/med-team/pufferfish/-/commit/b554f21b704a685aa0e607e89d12c3f90bebaf30
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