[med-svn] [Git][med-team/spoa][master] 3 commits: all issues resolved courtesy of upstream

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / spoa


Commits:
2f552202 by Michael R. Crusoe at 2021-01-07T15:34:18+01:00
all issues resolved courtesy of upstream

- - - - -
02ce893a by Michael R. Crusoe at 2021-01-07T15:47:47+01:00
routine-update: Remove trailing whitespace in debian/changelog

- - - - -
bed75419 by Michael R. Crusoe at 2021-01-07T15:49:23+01:00
routine-update: Ready to upload to unstable

- - - - -


3 changed files:

- debian/changelog
- debian/patches/shared_and_static.patch
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,4 +1,6 @@
-spoa (4.0.5+ds-1) UNRELEASED; urgency=medium
+spoa (4.0.5+ds-1) unstable; urgency=medium
+
+  * Team upload.
 
   [ Andreas Tille ]
   * New upstream version
@@ -10,15 +12,11 @@ spoa (4.0.5+ds-1) UNRELEASED; urgency=medium
   * build-dep on libcereal-dev and newer libbioparser-dev
   * Drop no_march_native.patch in favor of setting the option in debian/rules
   * debian/rules: test/data/sample.fastq is now gziped upstream
-  * Update symbols for new version 
-
-    TODO: devlibs error: There is no package matching
-    [libcpu_featureslibcpu_features.so-dev] and noone provides it, please
-    report bug to d-shlibs maintainer
-    Some issue with libcpu_features being linked dynamically instead of
-    statically?
+  * Update symbols for new version
+  * debian/patches/shared_and_static.patch: updated courtesy of upstream
+  * Remove trailing whitespace in debian/changelog (routine-update)
 
- -- Andreas Tille <tille at debian.org>  Wed, 23 Sep 2020 21:11:35 +0200
+ -- Michael R. Crusoe <crusoe at debian.org>  Thu, 07 Jan 2021 15:47:48 +0100
 
 spoa (3.4.0+ds-2) unstable; urgency=medium
 


=====================================
debian/patches/shared_and_static.patch
=====================================
@@ -9,38 +9,59 @@ Description: Build shared and static lib
  set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
  set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/bin)
 -set(BUILD_SHARED_LIBS OFF CACHE BOOL "Build all libraries as shared")
-+#set(BUILD_SHARED_LIBS OFF CACHE BOOL "Build all libraries as shared")
++# set(BUILD_SHARED_LIBS OFF CACHE BOOL "Build all libraries as shared")
  
  option(spoa_optimize_for_native "Build spoa with -march=native" ON)
  option(spoa_optimize_for_portability "Build spoa with -msse4.1" OFF)
-@@ -48,7 +48,13 @@
+@@ -48,7 +48,7 @@
    add_subdirectory(vendor/cereal EXCLUDE_FROM_ALL)
  endif ()
  
 -add_library(${PROJECT_NAME}
 +add_library(${PROJECT_NAME} SHARED
-+  src/alignment_engine.cpp
-+  src/graph.cpp
-+  src/sisd_alignment_engine.cpp
-+  src/dispatcher.cpp)
-+
-+add_library(${PROJECT_NAME}_static STATIC
    src/alignment_engine.cpp
    src/graph.cpp
    src/sisd_alignment_engine.cpp
-@@ -58,6 +64,11 @@
-   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/vendor/simde>
-   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/vendor/cpu_features/include>
+@@ -60,9 +60,22 @@
    $<INSTALL_INTERFACE:include>)
+ target_link_libraries(${PROJECT_NAME}
+   cereal)
+-if (BUILD_SHARED_LIBS)
++# if (BUILD_SHARED_LIBS)
+   set_property(TARGET ${PROJECT_NAME} PROPERTY SOVERSION "7.0.0")
+-endif ()
++# endif ()
++
++add_library(${PROJECT_NAME}_static STATIC
++  src/alignment_engine.cpp
++  src/graph.cpp
++  src/sisd_alignment_engine.cpp
++  src/dispatcher.cpp)
 +target_include_directories(${PROJECT_NAME}_static PUBLIC
 +  $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
 +  $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/vendor/simde>
 +  $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/vendor/cpu_features/include>
 +  $<INSTALL_INTERFACE:include>)
- target_link_libraries(${PROJECT_NAME}
-   cereal)
- if (BUILD_SHARED_LIBS)
-@@ -99,6 +110,8 @@
++target_link_libraries(${PROJECT_NAME}_static
++  cereal)
+ 
+ if (spoa_generate_dispatch)
+   if (NOT TARGET cpu_features)
+@@ -91,14 +104,22 @@
+     ${PROJECT_NAME}_avx2
+     ${PROJECT_NAME}_sse4.1
+     ${PROJECT_NAME}_sse2)
++  add_dependencies(${PROJECT_NAME}_static
++    ${PROJECT_NAME}_avx2
++    ${PROJECT_NAME}_sse4.1
++    ${PROJECT_NAME}_sse2)
+ 
+   target_link_libraries(${PROJECT_NAME}
+     cpu_features)
++  target_link_libraries(${PROJECT_NAME}_static
++    cpu_features)
+ endif ()
+ 
  include(GNUInstallDirs)
  install(TARGETS ${PROJECT_NAME}
    DESTINATION ${CMAKE_INSTALL_LIBDIR})


=====================================
debian/rules
=====================================
@@ -10,8 +10,7 @@ DEB_CMAKE_EXTRA_FLAGS = -DCMAKE_BUILD_TYPE=Release \
                         -Dspoa_build_tests=ON \
 			-Dspoa_use_simde_nonvec=ON \
 			-Dspoa_use_simde_openmp=ON \
-			-Dspoa_optimize_for_native=OFF \
-			-DBUILD_SHARED_LIBS=ON
+			-Dspoa_optimize_for_native=OFF
 
 ifneq (,$(filter $(DEB_HOST_ARCH),i386 amd64))
 	DEB_CMAKE_EXTRA_FLAGS += -Dspoa_generate_dispatch=ON



View it on GitLab: https://salsa.debian.org/med-team/spoa/-/compare/375af60330d4d21574acb7d31af52a721bd3dea7...bed75419522098b096e91b684bb090fa59c44af4

-- 
View it on GitLab: https://salsa.debian.org/med-team/spoa/-/compare/375af60330d4d21574acb7d31af52a721bd3dea7...bed75419522098b096e91b684bb090fa59c44af4
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