diff options
Diffstat (limited to 'biology/ncbi-blast+/patches')
3 files changed, 56 insertions, 11 deletions
diff --git a/biology/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c b/biology/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c index 328c1f2a826..b5ee840aba4 100644 --- a/biology/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c +++ b/biology/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c @@ -1,8 +1,8 @@ -$NetBSD: patch-src_algo_blast_core_blast__kappa.c,v 1.1 2018/04/27 20:28:28 bacon Exp $ +$NetBSD: patch-src_algo_blast_core_blast__kappa.c,v 1.2 2019/01/07 15:00:10 bacon Exp $ # Work around NetBSD stderr def choking macro ---- src/algo/blast/core/blast_kappa.c.orig 2018-03-26 21:55:44.000000000 +0000 +--- src/algo/blast/core/blast_kappa.c.orig 2019-01-02 04:00:17.000000000 +0000 +++ src/algo/blast/core/blast_kappa.c @@ -32,6 +32,7 @@ * system for each match in blastpgp @@ -12,7 +12,16 @@ $NetBSD: patch-src_algo_blast_core_blast__kappa.c,v 1.1 2018/04/27 20:28:28 baco #include <float.h> #include <algo/blast/core/ncbi_math.h> #include <algo/blast/core/blast_hits.h> -@@ -3404,13 +3405,15 @@ Blast_RedoAlignmentCore_MT(EBlastProgram +@@ -57,7 +58,7 @@ + * shared(...) list. */ + # define STDERR_COMMA + # else +-# define STDERR_COMMA stderr, ++# define STDERR_COMMA my_stderr, + # endif + #endif + +@@ -3412,6 +3413,8 @@ Blast_RedoAlignmentCore_MT(EBlastProgram } Boolean interrupt = FALSE; @@ -21,11 +30,3 @@ $NetBSD: patch-src_algo_blast_core_blast__kappa.c,v 1.1 2018/04/27 20:28:28 baco #pragma omp parallel \ default(none) num_threads(actual_num_threads) \ if(actual_num_threads>1) \ - shared(interrupt, seqsrc_tld, score_params_tld, hit_params_tld, \ - gap_align_tld, results_tld, \ - redoneMatches_tld, \ -- stderr, \ -+ my_stderr, \ - numQueries, numMatches, theseMatches, \ - numFrames, program_number, subjectBlk_tld, positionBased, \ - default_db_genetic_code, localScalingFactor, queryInfo, \ diff --git a/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-unix.sh b/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-unix.sh new file mode 100644 index 00000000000..0e184ea4aff --- /dev/null +++ b/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-unix.sh @@ -0,0 +1,15 @@ +$NetBSD: patch-src_build-system_cmake_cmake-cfg-unix.sh,v 1.1 2019/01/07 15:00:10 bacon Exp $ + +# Portability + +--- src/build-system/cmake/cmake-cfg-unix.sh.orig 2019-01-02 01:22:44.549100012 +0000 ++++ src/build-system/cmake/cmake-cfg-unix.sh +@@ -166,7 +166,7 @@ CMAKE_ARGS="$CMAKE_ARGS -DBUILD_SHARED_L + CMAKE_ARGS="$CMAKE_ARGS -DCMAKE_USE_CCACHE=$USE_CCACHE" + CMAKE_ARGS="$CMAKE_ARGS -DCMAKE_USE_DISTCC=$USE_DISTCC" + build_root=CMake-${CC_NAME}${CC_VERSION}-${BUILD_TYPE} +-if [ "$BUILD_SHARED_LIBS" == "ON" ]; then ++if [ "$BUILD_SHARED_LIBS" = "ON" ]; then + build_root="$build_root"DLL + fi + #build_root="$build_root"64 diff --git a/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.h b/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.h new file mode 100644 index 00000000000..dcd0a43378f --- /dev/null +++ b/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.h @@ -0,0 +1,29 @@ +$NetBSD: patch-src_util_checksum_farmhash_farmhash.h,v 1.1 2019/01/07 15:00:11 bacon Exp $ + +# __GNUC__ does not imply location of endian.h. Check for BSD first. + +--- src/util/checksum/farmhash/farmhash.h.orig 2018-09-26 12:38:06.000000000 +0000 ++++ src/util/checksum/farmhash/farmhash.h +@@ -305,15 +305,18 @@ inline uint128_t Fingerprint128(const St + #if !defined(FARMHASH_BIG_ENDIAN) + #define FARMHASH_BIG_ENDIAN + #endif +-#elif defined(__linux__) || defined(__CYGWIN__) || defined( __GNUC__ ) || defined( __GNU_LIBRARY__ ) +- #include <endian.h> // libc6-dev, GLIBC ++#elif defined(__OpenBSD__) || defined(__NetBSD__) || defined(__FreeBSD__) || defined(__DragonFly__) || defined(__s390x__) ++ #include <sys/endian.h> + #if BYTE_ORDER == BIG_ENDIAN + #if !defined(FARMHASH_BIG_ENDIAN) + #define FARMHASH_BIG_ENDIAN + #endif + #endif +-#elif defined(__OpenBSD__) || defined(__NetBSD__) || defined(__FreeBSD__) || defined(__DragonFly__) || defined(__s390x__) +- #include <sys/endian.h> ++// __GNUC__ actually does not imply the location of endian.h. It could ++// be set on any system running GCC. I'm wondering why this was added ++// Working around breakage for BSD systems by checking for BSD first. ++#elif defined(__linux__) || defined(__CYGWIN__) || defined( __GNUC__ ) || defined( __GNU_LIBRARY__ ) ++ #include <endian.h> // libc6-dev, GLIBC + #if BYTE_ORDER == BIG_ENDIAN + #if !defined(FARMHASH_BIG_ENDIAN) + #define FARMHASH_BIG_ENDIAN |