[med-svn] [Git][med-team/seqwish][master] Patch to cmake for freshly packaged dependencies

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / seqwish


Commits:
4f676cc6 by Andreas Tille at 2020-11-10T21:53:40+01:00
Patch to cmake for freshly packaged dependencies

- - - - -


2 changed files:

- debian/control
- debian/patches/use_debian_packaged_libs.patch


Changes:

=====================================
debian/control
=====================================
@@ -7,6 +7,7 @@ Build-Depends: debhelper-compat (= 12),
                cmake,
                libsdsl-dev,
                libargs-dev,
+               libatomic-queue-dev,
                libbbhash-dev,
                libflathashmap-dev,
                libgzstream-dev,


=====================================
debian/patches/use_debian_packaged_libs.patch
=====================================
@@ -8,7 +8,7 @@
  # sdsl-lite (full build using its cmake config)
  ExternalProject_Add(sdsl-lite
    SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/sdsl-lite"
-@@ -36,6 +37,11 @@ set(sdsl-lite_INCLUDE "${INSTALL_DIR}/sr
+@@ -36,7 +37,14 @@ set(sdsl-lite_INCLUDE "${INSTALL_DIR}/sr
  set(sdsl-lite-divsufsort_INCLUDE "${INSTALL_DIR}/src/sdsl-lite-build/external/libdivsufsort/include")
  set(sdsl-lite_LIB "${INSTALL_DIR}/src/sdsl-lite-build/lib")
  set(sdsl-lite-divsufsort_LIB "${INSTALL_DIR}/src/sdsl-lite-build/external/libdivsufsort/lib")
@@ -17,46 +17,92 @@
 +message("=================================")
 +# FIXME: Not yet tested
 +# add_custom_target(libsdsl)
++endif()
  
++if(!DEBIAN_BUILD)
  # taywee's C++ args library, header only
  ExternalProject_Add(tayweeargs
-@@ -52,6 +58,7 @@ ExternalProject_Add(gzipreader
+   SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/args"
+@@ -44,7 +52,14 @@ ExternalProject_Add(tayweeargs
+   INSTALL_COMMAND "")
+ ExternalProject_Get_property(tayweeargs SOURCE_DIR)
+ set(tayweeargs_INCLUDE "${SOURCE_DIR}")
++else()
++message("Use Debian packaged libargs")
++message("===========================")
++# FIXME: Not yet tested
++# add_custom_target(libars)
++endif()
+ 
++if(!DEBIAN_BUILD)
+ # gzip file reader, header only
+ ExternalProject_Add(gzipreader
+   SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/gzip_reader"
+@@ -52,7 +67,14 @@ ExternalProject_Add(gzipreader
    INSTALL_COMMAND "")
  ExternalProject_Get_property(gzipreader SOURCE_DIR)
  set(gzipreader_INCLUDE "${SOURCE_DIR}")
++else()
++message("Use Debian packaged libgzipreader")
++message("=================================")
++# FIXME: Not yet tested
++# add_custom_target(libgzipreader)
 +endif()
  
++if(!DEBIAN_BUILD)
  # mmmulti (memory mapped multimap, multiset, and interval tree)
  ExternalProject_Add(mmmulti
-@@ -63,6 +70,7 @@ ExternalProject_Add(mmmulti
+   SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/mmmulti"
+@@ -62,7 +84,14 @@ ExternalProject_Add(mmmulti
+   CONFIGURE_COMMAND "")
  ExternalProject_Get_property(mmmulti SOURCE_DIR)
  set(mmmulti_INCLUDE "${SOURCE_DIR}/src")
++else()
++message("Use Debian packaged libmmmulti")
++message("=================================")
++# FIXME: Not yet tested
++# add_custom_target(libmmmulti)
++endif()
  
 +if(!DEBIAN_BUILD)
  # iitii, like cgranges but with interpolation and memory mapping
  ExternalProject_Add(iitii
    SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/iitii"
-@@ -72,6 +80,7 @@ ExternalProject_Add(iitii
-   CONFIGURE_COMMAND "")
- ExternalProject_Get_property(iitii SOURCE_DIR)
- set(iitii_INCLUDE "${SOURCE_DIR}/src")
-+endif()
- 
- ExternalProject_Add(mmap_allocator
-   SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/mmap_allocator"
-@@ -81,6 +90,7 @@ ExternalProject_Get_property(mmap_alloca
+@@ -80,7 +109,14 @@ ExternalProject_Add(mmap_allocator
+ ExternalProject_Get_property(mmap_allocator INSTALL_DIR)
  set(mmap_allocator_INCLUDE "${INSTALL_DIR}/include/mmap_allocator")
  set(mmap_allocator_LIB "${INSTALL_DIR}/lib")
++else()
++message("Use Debian packaged libiitii (implicitly injecting mmap_allocator)")
++message("==================================================================")
++# FIXME: Not yet tested
++# add_custom_target(libiitii)
++endif()
  
 +if(!DEBIAN_BUILD)
  # In-place Parallel Super Scalar Samplesort (IPS⁴o), header only
  ExternalProject_Add(ips4o
    SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/ips4o"
-@@ -109,6 +119,7 @@ ExternalProject_Add(atomicbitvector
+@@ -109,7 +145,9 @@ ExternalProject_Add(atomicbitvector
    CONFIGURE_COMMAND "")
  ExternalProject_Get_property(atomicbitvector SOURCE_DIR)
  set(atomicbitvector_INCLUDE "${SOURCE_DIR}/include")
 +endif()
  
++if(!DEBIAN_BUILD)
  # atomic queue library
  ExternalProject_Add(atomicqueue
+   SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/atomic_queue"
+@@ -119,6 +157,12 @@ ExternalProject_Add(atomicqueue
+   CONFIGURE_COMMAND "")
+ ExternalProject_Get_property(atomicqueue SOURCE_DIR)
+ set(atomicqueue_INCLUDE "${SOURCE_DIR}")
++else()
++message("Use Debian packaged atomicqueue")
++message("==================================================================")
++# FIXME: Not yet tested
++# add_custom_target(libatomic-queue)
++endif()
+ 
+ # ska
+ ExternalProject_Add(ska



View it on GitLab: https://salsa.debian.org/med-team/seqwish/-/commit/4f676cc651314332bc19547078b0e377b92be784

-- 
View it on GitLab: https://salsa.debian.org/med-team/seqwish/-/commit/4f676cc651314332bc19547078b0e377b92be784
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