[med-svn] [Git][med-team/sra-sdk][master] 5 commits: Start work on sra-sdk 3.0.3+dfsg-3.
Aaron M. Ucko (@ucko)
gitlab at salsa.debian.org
Sun Jan 22 18:30:48 GMT 2023
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk
Commits:
9f5e1645 by Aaron M. Ucko at 2023-01-22T13:13:19-05:00
Start work on sra-sdk 3.0.3+dfsg-3.
- - - - -
84d6d236 by Aaron M. Ucko at 2023-01-22T13:15:28-05:00
d/patches/use_c_locale_for_comma (new): Stick with the C locale.
en_US.UTF-8 isn't necessarily available, particularly on the buildds,
and C is perfectly sufficient to ensure recognition of comma as a
thousands separator. (Recent versions of glibc supply a middle-ground
C.utf8, but even that looks like overkill at the moment.)
- - - - -
dcb99276 by Aaron M. Ucko at 2023-01-22T13:16:48-05:00
debian/patches/no_sse4.2.patch (new): Don't use SSE 4.2.
It's a baseline violation on x86, and entirely unavailable elsewhere.
- - - - -
8da20705 by Aaron M. Ucko at 2023-01-22T13:22:02-05:00
debian/copyright: Account for bam-loader's BitMagic from 2022.
Account for a second(!) version of BitMagic under
tools/loaders/bam-loader, with copyright running through 2022.
- - - - -
4148a38e by Aaron M. Ucko at 2023-01-22T13:26:17-05:00
Finalize sra-sdk 3.0.3+dfsg-3 for unstable.
- - - - -
5 changed files:
- debian/changelog
- debian/copyright
- + debian/patches/no_sse4.2.patch
- debian/patches/series
- + debian/patches/use_c_locale_for_comma.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+sra-sdk (3.0.3+dfsg-3) unstable; urgency=medium
+
+ * debian/copyright: Account for a second(!) version of BitMagic under
+ tools/loaders/bam-loader, with copyright running through 2022.
+ * debian/patches/no_sse4.2.patch (new): Don't use SSE 4.2. It's a
+ baseline violation on x86, and entirely unavailable elsewhere.
+ * debian/patches/use_c_locale_for_comma (new): Stick with the C locale.
+ en_US.UTF-8 isn't necessarily available, particularly on the buildds,
+ and C is perfectly sufficient to ensure recognition of comma as a
+ thousands separator. (Recent versions of glibc supply a middle-ground
+ C.utf8, but even that looks like overkill at the moment.)
+
+ -- Aaron M. Ucko <ucko at debian.org> Sun, 22 Jan 2023 13:26:16 -0500
+
sra-sdk (3.0.3+dfsg-2) unstable; urgency=medium
* Upload to unstable.
=====================================
debian/copyright
=====================================
@@ -103,8 +103,8 @@ License: BSD-3-clause-CLI11
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-Files: tools/loaders/sharq/bm/*
-Copyright: 2002-2021 Anatoliy Kuznetsov (anatoliy_kuznetsov at yahoo.com)
+Files: tools/loaders/*/bm/*
+Copyright: 2002-2022 Anatoliy Kuznetsov (anatoliy_kuznetsov at yahoo.com)
License: Apache-2
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
=====================================
debian/patches/no_sse4.2.patch
=====================================
@@ -0,0 +1,49 @@
+Index: b/test/loaders/sharq/CMakeLists.txt
+===================================================================
+--- a/test/loaders/sharq/CMakeLists.txt
++++ b/test/loaders/sharq/CMakeLists.txt
+@@ -31,7 +31,7 @@ if( SINGLE_CONFIG )
+ if ( ZLIB_FOUND AND BZip2_FOUND AND Threads_FOUND )
+
+ set(CMAKE_CXX_STANDARD 17)
+- add_definitions(-msse4.2 -DBMSSE42OPT)
++ # add_definitions(-msse4.2 -DBMSSE42OPT)
+
+ # assume tools/sharq built libre2
+ set(LOCAL_BUILD_DIR ${CMAKE_ARCHIVE_OUTPUT_DIRECTORY})
+Index: b/tools/loaders/bam-loader/CMakeLists.txt
+===================================================================
+--- a/tools/loaders/bam-loader/CMakeLists.txt
++++ b/tools/loaders/bam-loader/CMakeLists.txt
+@@ -58,9 +58,9 @@ if( NOT WIN32)
+
+ GenerateExecutableWithDefs( bam-load "${SRC}" "" "${CMAKE_SOURCE_DIR}/libs/inc" "loader;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_WRITE}" )
+ target_compile_features(bam-load PUBLIC cxx_std_17)
+- if (COMPILER_OPTION_SSE42_SUPPORTED)
+- target_compile_options( bam-load PUBLIC -msse4.2 -DBMSSE42OPT)
+- endif()
++ #if (COMPILER_OPTION_SSE42_SUPPORTED)
++ # target_compile_options( bam-load PUBLIC -msse4.2 -DBMSSE42OPT)
++ #endif()
+ target_include_directories( bam-load PRIVATE ${CMAKE_SOURCE_DIR}/libs/inc)
+ target_link_libraries( bam-load loader OpenSSL::SSL ${COMMON_LINK_LIBRARIES} ${COMMON_LIBS_WRITE} -lz )
+
+Index: b/tools/loaders/sharq/CMakeLists.txt
+===================================================================
+--- a/tools/loaders/sharq/CMakeLists.txt
++++ b/tools/loaders/sharq/CMakeLists.txt
+@@ -52,10 +52,10 @@ if ( ZLIB_FOUND AND BZip2_FOUND AND Thre
+ #set(CMAKE_VERBOSE_MAKEFILE ON)
+ set(CMAKE_CXX_STANDARD 17)
+
+-#specific to BitMagic
+-if (COMPILER_OPTION_SSE42_SUPPORTED)
+- add_definitions(-msse4.2 -DBMSSE42OPT)
+-endif()
++##specific to BitMagic
++#if (COMPILER_OPTION_SSE42_SUPPORTED)
++# add_definitions(-msse4.2 -DBMSSE42OPT)
++#endif()
+
+ set(LOCAL_BUILD_DIR ${CMAKE_ARCHIVE_OUTPUT_DIRECTORY})
+ set(LOCAL_INCDIR ${LOCAL_BUILD_DIR}/include)
=====================================
debian/patches/series
=====================================
@@ -36,3 +36,5 @@ label_online_tests.patch
# reflect_code_donations.patch
prefer_dynamic_libraries.patch
fix_ngs-c++-underlinkage.patch
+use_c_locale_for_comma.patch
+no_sse4.2.patch
=====================================
debian/patches/use_c_locale_for_comma.patch
=====================================
@@ -0,0 +1,26 @@
+Index: b/tools/loaders/bam-loader/loader-imp.c
+===================================================================
+--- a/tools/loaders/bam-loader/loader-imp.c
++++ b/tools/loaders/bam-loader/loader-imp.c
+@@ -4014,7 +4014,7 @@ static rc_t ArchiveBAM(VDBManager *mgr,
+ bool *has_alignments,
+ bool continuing)
+ {
+- std::locale::global(std::locale("en_US.UTF-8")); // enable comma as thousand separator
++ std::locale::global(std::locale("C")); // enable comma as thousand separator
+ if (G.hasExtraLogging) {
+ auto logger = spdlog::stderr_logger_mt("stderr"); // send log to stderr
+ spdlog::set_default_logger(logger);
+Index: b/tools/loaders/sharq/fastq_parse.cpp
+===================================================================
+--- a/tools/loaders/sharq/fastq_parse.cpp
++++ b/tools/loaders/sharq/fastq_parse.cpp
+@@ -567,7 +567,7 @@ void CFastqParseApp::xCheckErrorLimits(f
+ int main(int argc, const char* argv[])
+ {
+ ios_base::sync_with_stdio(false); // turn off synchronization with standard C streams
+- std::locale::global(std::locale("en_US.UTF-8")); // enable comma as thousand separator
++ std::locale::global(std::locale("C")); // enable comma as thousand separator
+ auto stderr_logger = spdlog::stderr_logger_mt("stderr"); // send log to stderr
+ spdlog::set_default_logger(stderr_logger);
+
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/e256ccbec8ae099d418b11286348faee40007be7...4148a38e72cf924b794e802299aed16186d8d567
--
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/e256ccbec8ae099d418b11286348faee40007be7...4148a38e72cf924b794e802299aed16186d8d567
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