git: 8de761e7d400 - main - biology/ncbi-blast+: Update to 2.16.0_3

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=8de761e7d400ab1896932ea94995aeeb3d5a01d6

commit 8de761e7d400ab1896932ea94995aeeb3d5a01d6
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2025-03-06 12:42:48 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2025-03-06 12:42:48 +0000

    biology/ncbi-blast+: Update to 2.16.0_3
    
    Fix build of seqdb_perf
    Disable build system attempts to access NCBI file servers,
    causing NFS timeouts where autofs is enabled
---
 biology/ncbi-blast+/Makefile                       | 30 +++++++++++++++++-----
 ...jtools_blast_seqdb__reader_test_seqdb__perf.cpp |  2 +-
 biology/ncbi-blast+/pkg-plist                      |  1 +
 3 files changed, 25 insertions(+), 8 deletions(-)

diff --git a/biology/ncbi-blast+/Makefile b/biology/ncbi-blast+/Makefile
index a3ff911a4960..b87a9c2d6b60 100644
--- a/biology/ncbi-blast+/Makefile
+++ b/biology/ncbi-blast+/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=	ncbi-blast+
 DISTVERSION=	2.16.0
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	biology perl5 python
 MASTER_SITES=	https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \
 		https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/
@@ -69,13 +69,29 @@ CONFIGURE_ARGS+=	--without-openmp
 LDFLAGS+=	-latomic # Only exists in gcc libs
 .endif
 
+# Build system attempts to access NCBI file server paths such as
+# /net/snowman in many places.  :-/
+# This causes NFS timeouts if autofs is enabled.
+pre-configure:
+	${REINPLACE_CMD} -e 's|/net/|/nonexistent/net/|g' \
+	      ${WRKSRC}/include/sra/readers/ncbi_traces_path.hpp \
+	      ${WRKSRC}/scripts/common/impl/create_flat_makefile.sh \
+	      ${WRKSRC}/src/objects/genomecoll/gc_cli/Makefile.in \
+	      ${WRKSRC}/src/objtools/blast/seqdb_reader/configuration.txt \
+	      ${WRKSRC}/src/objtools/align_format/unit_test/data/large_gi.asn \
+	      ${WRKSRC}/src/build-system/project_tree_builder.ini \
+	      ${WRKSRC}/src/build-system/cmake/CMake.NCBIptb.datatool.cmake \
+	      ${WRKSRC}/src/build-system/new_module.sh.in \
+	      ${WRKSRC}/src/build-system/Makefile.meta_l \
+	      ${WRKSRC}/src/build-system/config.site.ncbi
+
 post-install:
-	@${RM} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/*/*/.cvsignore.extra
-	@${RM} -rf ${STAGEDIR}${PREFIX}/lib/X11
-	@${RM} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/common/config/ncbiconf_msvc_site.h.in
-	@${RM} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/common/ncbi_build_ver.h.in
-	@${RM} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/common/ncbi_revision.h.in
-	@${RMDIR} ${STAGEDIR}${PREFIX}/lib/debug
+	${RM} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/*/*/.cvsignore.extra
+	${RM} -rf ${STAGEDIR}${PREFIX}/lib/X11
+	${RM} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/common/config/ncbiconf_msvc_site.h.in
+	${RM} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/common/ncbi_build_ver.h.in
+	${RM} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/common/ncbi_revision.h.in
+	${RMDIR} ${STAGEDIR}${PREFIX}/lib/debug
 	${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/ncbi-tools++/*.so
 
 .include <bsd.port.post.mk>
diff --git a/biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp b/biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp
index 3ea6f61a5619..956fa6004e1a 100644
--- a/biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp
+++ b/biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp
@@ -15,7 +15,7 @@
      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_ICC) && (NCBI_COMPILER_VERSION >= 2100)) || \
 +    defined(NCBI_COMPILER_LLVM_CLANG)
          #pragma omp parallel default(none) shared(kDbName, kNumThreads, kSeqType) num_threads(kNumThreads)
  #else
diff --git a/biology/ncbi-blast+/pkg-plist b/biology/ncbi-blast+/pkg-plist
index 88452e690ca1..a44c7748df28 100644
--- a/biology/ncbi-blast+/pkg-plist
+++ b/biology/ncbi-blast+/pkg-plist
@@ -30,6 +30,7 @@ bin/run_with_lock
 bin/seedtop
 bin/segmasker
 bin/seqdb_demo
+bin/seqdb_perf
 bin/tax4blast
 bin/tblastn
 bin/tblastx