ncbi-blast+: Import patch from FreeBSD build

[Jason W. Bacon (via pkgsrc-wip) <commit-notify%pkgsrc.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Wed Mar 5 18:06:02 2025 -0600
Changeset:	3b0e8ba92948c8d4d0f0400d21ee96197a4fea23

Modified Files:
	ncbi-blast+/distinfo
Added Files:
	ncbi-blast+/patches/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp

Log Message:
ncbi-blast+: Import patch from FreeBSD build

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=3b0e8ba92948c8d4d0f0400d21ee96197a4fea23

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 ncbi-blast+/distinfo                               |  1 +
 ...jtools_blast_seqdb__reader_test_seqdb__perf.cpp | 26 ++++++++++++++++++++++
 2 files changed, 27 insertions(+)

diffs:
diff --git a/ncbi-blast+/distinfo b/ncbi-blast+/distinfo
index 15a954e763..0b92cf047f 100644
--- a/ncbi-blast+/distinfo
+++ b/ncbi-blast+/distinfo
@@ -8,6 +8,7 @@ SHA1 (patch-src_algo_blast_core_blast__kappa.c) = 6fcad996b3a8e5b6c2400608bff9de
 SHA1 (patch-src_build-system_Makefile.in.top) = 71d5246867a8c985c1175c338fb0af664094ca01
 SHA1 (patch-src_build-system_configure) = 95185d53179a69a1b1cfa6870aca36dd962d2c43
 SHA1 (patch-src_build-system_helpers_Makefile.run__with__lock.app) = d69b9e349646c970c3b296707f917defbe39cccd
+SHA1 (patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp) = 7f562585357d70150494bcfcd9f259fc031ca165
 SHA1 (patch-src_util_checksum_cityhash_city.cc) = ff8e84d90a4fc0d9d33e17abd05ed8e9f2de12fc
 SHA1 (patch-src_util_checksum_farmhash_farmhash.cc) = 9b56d69ab7c0da328c35bba4dde04134dd80efc6
 SHA1 (patch-src_util_checksum_farmhash_farmhash.h) = c3ff60de9a9020d3b706c2bff37f6f4cde4e6b6b
diff --git a/ncbi-blast+/patches/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp b/ncbi-blast+/patches/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp
new file mode 100644
index 0000000000..c7fbd64d75
--- /dev/null
+++ b/ncbi-blast+/patches/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp
@@ -0,0 +1,26 @@
+$NetBSD$
+
+# Fix build on FreeBSD
+
+--- src/objtools/blast/seqdb_reader/test/seqdb_perf.cpp.orig	2021-10-14 12:36:57.000000000 +0000
++++ src/objtools/blast/seqdb_reader/test/seqdb_perf.cpp
+@@ -138,7 +138,8 @@ CSeqDBPerfApp::x_ScanDatabase()
+     LOG_POST(Info << "Will go over " << oids2iterate.size() << " sequences");
+ 
+ #if (defined(NCBI_COMPILER_GCC) && (NCBI_COMPILER_VERSION >= 900)) || \
+-    (defined(NCBI_COMPILER_ICC) && (NCBI_COMPILER_VERSION >= 2100))
++    (defined(NCBI_COMPILER_ICC) && (NCBI_COMPILER_VERSION >= 2100)) || \
++    defined(NCBI_COMPILER_LLVM_CLANG)
+     #pragma omp parallel default(none) num_threads(m_DbHandles.size()) \
+                          shared(oids2iterate,kScanUncompressed) if(m_DbHandles.size() > 1)
+ #else
+@@ -210,7 +211,8 @@ CSeqDBPerfApp::x_InitApplicationData()
+ 
+     if (args["multi_threaded_creation"]) {
+ #if (defined(NCBI_COMPILER_GCC) && (NCBI_COMPILER_VERSION >= 900)) || \
+-    (defined(NCBI_COMPILER_ICC) && (NCBI_COMPILER_VERSION >= 2100))
++    (defined(NCBI_COMPILER_ICC) && (NCBI_COMPILER_VERSION >= 2100)) || \
++    defined(NCBI_COMPILER_LLVM_CLANG)
+         #pragma omp parallel default(none) shared(kDbName, kNumThreads, kSeqType) num_threads(kNumThreads)
+ #else
+         #pragma omp parallel default(none) shared(kDbName, kNumThreads) num_threads(kNumThreads)