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 <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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