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-rw-r--r--biology/ncbi-blast+/Makefile17
-rw-r--r--biology/ncbi-blast+/distinfo6
-rw-r--r--biology/ncbi-blast+/files/patch-grpc26
-rw-r--r--biology/ncbi-blast+/files/patch-src_serial_grpc__integration_grpc__integration.cpp32
-rw-r--r--biology/ncbi-blast+/pkg-plist61
5 files changed, 64 insertions, 78 deletions
diff --git a/biology/ncbi-blast+/Makefile b/biology/ncbi-blast+/Makefile
index b87a9c2d6b60..1627922c6d5e 100644
--- a/biology/ncbi-blast+/Makefile
+++ b/biology/ncbi-blast+/Makefile
@@ -1,6 +1,5 @@
PORTNAME= ncbi-blast+
-DISTVERSION= 2.16.0
-PORTREVISION= 3
+DISTVERSION= 2.17.0
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}/
@@ -16,23 +15,13 @@ LICENSE_FILE= ${WRKSRC}/scripts/projects/blast/LICENSE
ONLY_FOR_ARCHS= aarch64 amd64 powerpc64 powerpc64le riscv64
ONLY_FOR_ARCHS_REASON= Requires 64-bit processor
+BUILD_DEPENDS= grpc>0:devel/grpc
LIB_DEPENDS= libdw.so:devel/elfutils \
- libgcrypt.so:security/libgcrypt \
- libgmp.so:math/gmp \
- libgnutls.so:security/gnutls \
- libgpg-error.so:security/libgpg-error \
- libgrpc.so:devel/grpc \
- libhogweed.so:security/nettle \
- libidn2.so:dns/libidn2 \
liblmdb.so:databases/lmdb \
liblzo2.so:archivers/lzo2 \
- libnettle.so:security/nettle \
libnghttp2.so:www/libnghttp2 \
- libp11-kit.so:security/p11-kit \
- libpcre.so:devel/pcre \
+ libpcre2-8.so:devel/pcre2 \
libsqlite3.so:databases/sqlite3 \
- libtasn1.so:security/libtasn1 \
- libtspi.so:security/trousers \
libuv.so:devel/libuv \
libzstd.so:archivers/zstd
RUN_DEPENDS= p5-List-MoreUtils>=0:lang/p5-List-MoreUtils \
diff --git a/biology/ncbi-blast+/distinfo b/biology/ncbi-blast+/distinfo
index fb3f8ad65194..bd9b8a595168 100644
--- a/biology/ncbi-blast+/distinfo
+++ b/biology/ncbi-blast+/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1733904135
-SHA256 (ncbi-blast-2.16.0+-src.tar.gz) = 17c93cf009721023e5aecf5753f9c6a255d157561638b91b3ad7276fd6950c2b
-SIZE (ncbi-blast-2.16.0+-src.tar.gz) = 28307712
+TIMESTAMP = 1753183842
+SHA256 (ncbi-blast-2.17.0+-src.tar.gz) = 502057a88e9990e34e62758be21ea474cc0ad68d6a63a2e37b2372af1e5ea147
+SIZE (ncbi-blast-2.17.0+-src.tar.gz) = 29571791
diff --git a/biology/ncbi-blast+/files/patch-grpc b/biology/ncbi-blast+/files/patch-grpc
deleted file mode 100644
index 22e9dc6aee66..000000000000
--- a/biology/ncbi-blast+/files/patch-grpc
+++ /dev/null
@@ -1,26 +0,0 @@
---- src/serial/grpc_integration/grpc_integration.cpp.orig 2023-05-18 18:14:23 UTC
-+++ src/serial/grpc_integration/grpc_integration.cpp
-@@ -113,23 +113,8 @@ static CGRPCInitializer s_GRPCInitializer;
- grpc::Server::GlobalCallbacks* volatile CGRPCInitializer::sm_ServerCallbacks;
- static CGRPCInitializer s_GRPCInitializer;
-
--extern "C" {
-- static void s_NCBI_GPR_Log_Function(gpr_log_func_args *args) {
-- static const char* unk_func = g_DiagUnknownFunction();
-- CDiagCompileInfo diag_info(args->file, args->line, unk_func, "GRPC");
-- EDiagSev sev = eDiag_Error;
-- switch (args->severity) {
-- case GPR_LOG_SEVERITY_DEBUG: sev = eDiag_Trace; break;
-- case GPR_LOG_SEVERITY_INFO: sev = eDiag_Info; break;
-- case GPR_LOG_SEVERITY_ERROR: sev = eDiag_Error; break;
-- }
-- CNcbiDiag(diag_info) << Severity(sev) << args->message << Endm;
-- }
--}
--
- CGRPCInitializer::CGRPCInitializer(void)
- {
-- gpr_set_log_function(s_NCBI_GPR_Log_Function);
- sm_ServerCallbacks = new CGRPCServerCallbacks;
- grpc::Server::SetGlobalCallbacks(sm_ServerCallbacks);
- // NB: on the client side, we encourage the use of
diff --git a/biology/ncbi-blast+/files/patch-src_serial_grpc__integration_grpc__integration.cpp b/biology/ncbi-blast+/files/patch-src_serial_grpc__integration_grpc__integration.cpp
new file mode 100644
index 000000000000..18f4558d0310
--- /dev/null
+++ b/biology/ncbi-blast+/files/patch-src_serial_grpc__integration_grpc__integration.cpp
@@ -0,0 +1,32 @@
+--- src/serial/grpc_integration/grpc_integration.cpp.orig 2025-07-22 11:26:40 UTC
++++ src/serial/grpc_integration/grpc_integration.cpp
+@@ -87,21 +87,6 @@ static CNCBILogSink s_NCBILogSink;
+
+ #else //ABSEIL_LOG
+
+-extern "C" {
+- static void s_NCBI_GPR_Log_Function(gpr_log_func_args *args) {
+- static const char* unk_func = ncbi::g_DiagUnknownFunction();
+- ncbi::CDiagCompileInfo diag_info(args->file, args->line, unk_func, "GRPC");
+- ncbi::EDiagSev sev = ncbi::eDiag_Error;
+- switch (args->severity) {
+- case GPR_LOG_SEVERITY_DEBUG: sev = ncbi::eDiag_Trace; break;
+- case GPR_LOG_SEVERITY_INFO: sev = ncbi::eDiag_Info; break;
+- case GPR_LOG_SEVERITY_ERROR: sev = ncbi::eDiag_Error; break;
+- }
+- ncbi::CNcbiDiag(diag_info) << ncbi::Severity(sev) << args->message << ncbi::Endm;
+- }
+-}
+-#define GPR_SET_LOG_FUNCION gpr_set_log_function(s_NCBI_GPR_Log_Function)
+-
+ #endif //ABSEIL_LOG
+ #endif //HAVE_LIBGRPC
+
+@@ -172,7 +157,6 @@ CGRPCInitializer::CGRPCInitializer(void)
+
+ CGRPCInitializer::CGRPCInitializer(void)
+ {
+- GPR_SET_LOG_FUNCION;
+ sm_ServerCallbacks = new CGRPCServerCallbacks;
+ grpc::Server::SetGlobalCallbacks(sm_ServerCallbacks);
+ // NB: on the client side, we encourage the use of
diff --git a/biology/ncbi-blast+/pkg-plist b/biology/ncbi-blast+/pkg-plist
index a44c7748df28..64e087878999 100644
--- a/biology/ncbi-blast+/pkg-plist
+++ b/biology/ncbi-blast+/pkg-plist
@@ -14,7 +14,6 @@ bin/datatool
bin/deltablast
bin/dustmasker
bin/gc_cli
-bin/gene_info_reader
bin/get_species_taxids.sh
bin/legacy_blast.pl
bin/lmdbxx_sample
@@ -267,6 +266,7 @@ include/ncbi-tools++/cgi/cgiapp_cached.hpp
include/ncbi-tools++/cgi/cgictx.hpp
include/ncbi-tools++/cgi/error_codes.hpp
include/ncbi-tools++/cgi/fcgiapp_mt.hpp
+include/ncbi-tools++/cgi/fcgiapp_st.hpp
include/ncbi-tools++/cgi/impl/cgi_entry_reader.hpp
include/ncbi-tools++/cgi/ncbicgi.hpp
include/ncbi-tools++/cgi/ncbicgir.hpp
@@ -287,6 +287,7 @@ include/ncbi-tools++/common/ncbi_export.h
include/ncbi-tools++/common/ncbi_package_ver.h
include/ncbi-tools++/common/ncbi_pch_impl.hpp
include/ncbi-tools++/common/ncbi_revision.h
+include/ncbi-tools++/common/ncbi_sample_api.hpp
include/ncbi-tools++/common/ncbi_sanitizers.h
include/ncbi-tools++/common/ncbi_sc_version.h
include/ncbi-tools++/common/ncbi_skew_guard.h
@@ -305,6 +306,7 @@ include/ncbi-tools++/connect/ext/ncbi_dblb_svcmapper.hpp
include/ncbi-tools++/connect/ext/ncbi_ifconf.h
include/ncbi-tools++/connect/ext/ncbi_localnet.h
include/ncbi-tools++/connect/impl/connect_misc.hpp
+include/ncbi-tools++/connect/impl/ncbi_servicep.h
include/ncbi-tools++/connect/impl/ncbi_uv_nghttp2.hpp
include/ncbi-tools++/connect/impl/server_connection.hpp
include/ncbi-tools++/connect/impl/thread_pool_for_server.hpp
@@ -346,6 +348,7 @@ include/ncbi-tools++/connect/ncbi_service.h
include/ncbi-tools++/connect/ncbi_service.hpp
include/ncbi-tools++/connect/ncbi_service_connector.h
include/ncbi-tools++/connect/ncbi_service_cxx.hpp
+include/ncbi-tools++/connect/ncbi_sftp.hpp
include/ncbi-tools++/connect/ncbi_socket.h
include/ncbi-tools++/connect/ncbi_socket.hpp
include/ncbi-tools++/connect/ncbi_socket_connector.h
@@ -425,6 +428,7 @@ include/ncbi-tools++/corelib/impl/ncbi_param_impl.hpp
include/ncbi-tools++/corelib/impl/ncbi_toolkit_impl.hpp
include/ncbi-tools++/corelib/impl/ncbierror_impl.hpp
include/ncbi-tools++/corelib/impl/rwstreambuf.hpp
+include/ncbi-tools++/corelib/impl/std_backport.hpp
include/ncbi-tools++/corelib/impl/stringutf8_deprecated.hpp
include/ncbi-tools++/corelib/impl/stringutf8_deprecated.inl
include/ncbi-tools++/corelib/interprocess_lock.hpp
@@ -452,6 +456,7 @@ include/ncbi-tools++/corelib/ncbi_signal.hpp
include/ncbi-tools++/corelib/ncbi_stack.hpp
include/ncbi-tools++/corelib/ncbi_strings.h
include/ncbi-tools++/corelib/ncbi_system.hpp
+include/ncbi-tools++/corelib/ncbi_test.hpp
include/ncbi-tools++/corelib/ncbi_toolkit.hpp
include/ncbi-tools++/corelib/ncbi_tree.hpp
include/ncbi-tools++/corelib/ncbi_url.hpp
@@ -494,6 +499,7 @@ include/ncbi-tools++/corelib/ncbiutil.hpp
include/ncbi-tools++/corelib/obj_pool.hpp
include/ncbi-tools++/corelib/obj_store.hpp
include/ncbi-tools++/corelib/perf_log.hpp
+include/ncbi-tools++/corelib/phone_home_policy.hpp
include/ncbi-tools++/corelib/plugin_manager.hpp
include/ncbi-tools++/corelib/plugin_manager_impl.hpp
include/ncbi-tools++/corelib/plugin_manager_store.hpp
@@ -1901,23 +1907,6 @@ include/ncbi-tools++/objects/mim/mim__.hpp
include/ncbi-tools++/objects/misc/error_codes.hpp
include/ncbi-tools++/objects/misc/sequence_macros.hpp
include/ncbi-tools++/objects/misc/sequence_util_macros.hpp
-include/ncbi-tools++/objects/mla/.gitignore
-include/ncbi-tools++/objects/mla/Error_val.hpp
-include/ncbi-tools++/objects/mla/Error_val_.hpp
-include/ncbi-tools++/objects/mla/Mla_back.hpp
-include/ncbi-tools++/objects/mla/Mla_back_.hpp
-include/ncbi-tools++/objects/mla/Mla_request.hpp
-include/ncbi-tools++/objects/mla/Mla_request_.hpp
-include/ncbi-tools++/objects/mla/NCBI_MedArchive_module.hpp
-include/ncbi-tools++/objects/mla/Title_msg.hpp
-include/ncbi-tools++/objects/mla/Title_msg_.hpp
-include/ncbi-tools++/objects/mla/Title_msg_list.hpp
-include/ncbi-tools++/objects/mla/Title_msg_list_.hpp
-include/ncbi-tools++/objects/mla/Title_type.hpp
-include/ncbi-tools++/objects/mla/Title_type_.hpp
-include/ncbi-tools++/objects/mla/mla__.hpp
-include/ncbi-tools++/objects/mla/mla_client.hpp
-include/ncbi-tools++/objects/mla/mla_client_.hpp
include/ncbi-tools++/objects/mmdb1/.gitignore
include/ncbi-tools++/objects/mmdb1/Atom.hpp
include/ncbi-tools++/objects/mmdb1/Atom_.hpp
@@ -3339,6 +3328,7 @@ include/ncbi-tools++/objmgr/impl/bioseq_edit_commands.hpp
include/ncbi-tools++/objmgr/impl/bioseq_info.hpp
include/ncbi-tools++/objmgr/impl/bioseq_set_edit_commands.hpp
include/ncbi-tools++/objmgr/impl/bioseq_set_info.hpp
+include/ncbi-tools++/objmgr/impl/bioseq_sort.hpp
include/ncbi-tools++/objmgr/impl/data_source.hpp
include/ncbi-tools++/objmgr/impl/edit_commands_impl.hpp
include/ncbi-tools++/objmgr/impl/handle_range.hpp
@@ -3483,11 +3473,7 @@ include/ncbi-tools++/objtools/blast/blastdb_format/blastdb_seqid.hpp
include/ncbi-tools++/objtools/blast/blastdb_format/invalid_data_exception.hpp
include/ncbi-tools++/objtools/blast/blastdb_format/seq_formatter.hpp
include/ncbi-tools++/objtools/blast/blastdb_format/seq_writer.hpp
-include/ncbi-tools++/objtools/blast/gene_info_reader/file_utils.hpp
-include/ncbi-tools++/objtools/blast/gene_info_reader/gene_info.hpp
-include/ncbi-tools++/objtools/blast/gene_info_reader/gene_info_reader.hpp
include/ncbi-tools++/objtools/blast/seqdb_reader/column_reader.hpp
-include/ncbi-tools++/objtools/blast/seqdb_reader/impl/lmdb++.h
include/ncbi-tools++/objtools/blast/seqdb_reader/impl/seqdb_lmdb.hpp
include/ncbi-tools++/objtools/blast/seqdb_reader/impl/seqdbatlas.hpp
include/ncbi-tools++/objtools/blast/seqdb_reader/impl/seqdbcol.hpp
@@ -3551,7 +3537,13 @@ include/ncbi-tools++/objtools/data_loaders/genbank/impl/incr_time.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/info_cache.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/processor.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/processors.hpp
+include/ncbi-tools++/objtools/data_loaders/genbank/impl/psg_blob_processor.hpp
+include/ncbi-tools++/objtools/data_loaders/genbank/impl/psg_cache.hpp
+include/ncbi-tools++/objtools/data_loaders/genbank/impl/psg_cdd.hpp
+include/ncbi-tools++/objtools/data_loaders/genbank/impl/psg_evloop.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/psg_loader_impl.hpp
+include/ncbi-tools++/objtools/data_loaders/genbank/impl/psg_processor.hpp
+include/ncbi-tools++/objtools/data_loaders/genbank/impl/psg_processors.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/reader_id1_base.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/reader_id2_base.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/reader_service.hpp
@@ -4513,6 +4505,7 @@ include/ncbi-tools++/objtools/readers/aln_reader.hpp
include/ncbi-tools++/objtools/readers/alnread.hpp
include/ncbi-tools++/objtools/readers/bed_reader.hpp
include/ncbi-tools++/objtools/readers/cigar.hpp
+include/ncbi-tools++/objtools/readers/co_generator.hpp
include/ncbi-tools++/objtools/readers/error_container.hpp
include/ncbi-tools++/objtools/readers/fasta.hpp
include/ncbi-tools++/objtools/readers/fasta_exception.hpp
@@ -4687,6 +4680,7 @@ include/ncbi-tools++/sra/readers/bam/bgzf.hpp
include/ncbi-tools++/sra/readers/bam/cache_with_lock.hpp
include/ncbi-tools++/sra/readers/bam/vdbfile.hpp
include/ncbi-tools++/sra/readers/ncbi_traces_path.hpp
+include/ncbi-tools++/sra/readers/ncbi_traces_path.hpp.bak
include/ncbi-tools++/sra/readers/sra/csraread.hpp
include/ncbi-tools++/sra/readers/sra/exception.hpp
include/ncbi-tools++/sra/readers/sra/graphread.hpp
@@ -4784,6 +4778,10 @@ include/ncbi-tools++/util/compress/zlib.hpp
include/ncbi-tools++/util/compress/zlib/zconf.h
include/ncbi-tools++/util/compress/zlib/zlib.h
include/ncbi-tools++/util/compress/zlib/zutil.h
+include/ncbi-tools++/util/compress/zlib_cloudflare.hpp
+include/ncbi-tools++/util/compress/zlib_cloudflare/zconf_cf.h
+include/ncbi-tools++/util/compress/zlib_cloudflare/zlib_cf.h
+include/ncbi-tools++/util/compress/zlib_cloudflare/zutil_cf.h
include/ncbi-tools++/util/compress/zstd.hpp
include/ncbi-tools++/util/creaders/alnread.h
include/ncbi-tools++/util/creaders/creaders_export.h
@@ -4801,15 +4799,13 @@ include/ncbi-tools++/util/histogram_binning.hpp
include/ncbi-tools++/util/icanceled.hpp
include/ncbi-tools++/util/id_mux.hpp
include/ncbi-tools++/util/impl/compile_time_bits.hpp
-include/ncbi-tools++/util/impl/const_tuple.hpp
-include/ncbi-tools++/util/impl/ct_bitset_cxx14.hpp
include/ncbi-tools++/util/impl/ct_bitset_cxx17.hpp
include/ncbi-tools++/util/impl/ct_crc32.hpp
-include/ncbi-tools++/util/impl/ct_string_cxx14.hpp
include/ncbi-tools++/util/impl/ct_string_cxx17.hpp
include/ncbi-tools++/util/impl/ctsort_cxx14.hpp
include/ncbi-tools++/util/impl/floating_point_comparison.hpp
include/ncbi-tools++/util/impl/generated_fsm.hpp
+include/ncbi-tools++/util/incr_time.hpp
include/ncbi-tools++/util/itransaction.hpp
include/ncbi-tools++/util/itree.hpp
include/ncbi-tools++/util/itree.inl
@@ -4826,6 +4822,7 @@ include/ncbi-tools++/util/math/matrix.hpp
include/ncbi-tools++/util/math/miscmath.h
include/ncbi-tools++/util/math/promote.hpp
include/ncbi-tools++/util/md5.hpp
+include/ncbi-tools++/util/memory_streambuf.hpp
include/ncbi-tools++/util/message_queue.hpp
include/ncbi-tools++/util/miscmath.h
include/ncbi-tools++/util/multi_writer.hpp
@@ -4847,10 +4844,8 @@ include/ncbi-tools++/util/regexp.hpp
include/ncbi-tools++/util/regexp/ctre/LICENSE
include/ncbi-tools++/util/regexp/ctre/ctre-unicode.hpp
include/ncbi-tools++/util/regexp/ctre/ctre.hpp
-include/ncbi-tools++/util/regexp/pcre.h
-include/ncbi-tools++/util/regexp/pcrecpp.h
-include/ncbi-tools++/util/regexp/pcrecpparg.h
-include/ncbi-tools++/util/regexp/pcreposix.h
+include/ncbi-tools++/util/regexp/pcre2.h
+include/ncbi-tools++/util/regexp/pcre2posix.h
include/ncbi-tools++/util/request_control.hpp
include/ncbi-tools++/util/resize_iter.hpp
include/ncbi-tools++/util/resource_pool.hpp
@@ -4984,8 +4979,6 @@ lib/ncbi-tools++/libgbseq-static.a
lib/ncbi-tools++/libgbseq.a
lib/ncbi-tools++/libgencoll_client-static.a
lib/ncbi-tools++/libgencoll_client.a
-lib/ncbi-tools++/libgene_info-static.a
-lib/ncbi-tools++/libgene_info.a
lib/ncbi-tools++/libgeneral-static.a
lib/ncbi-tools++/libgeneral.a
lib/ncbi-tools++/libgenesbyloc-static.a
@@ -5020,10 +5013,6 @@ lib/ncbi-tools++/libmedline-static.a
lib/ncbi-tools++/libmedline.a
lib/ncbi-tools++/libmim-static.a
lib/ncbi-tools++/libmim.a
-lib/ncbi-tools++/libmla-static.a
-lib/ncbi-tools++/libmla.a
-lib/ncbi-tools++/libmlacli-static.a
-lib/ncbi-tools++/libmlacli.a
lib/ncbi-tools++/libmmdb-static.a
lib/ncbi-tools++/libmmdb.a
lib/ncbi-tools++/libncbi_xblobstorage_netcache-static.a
@@ -5206,3 +5195,5 @@ lib/ncbi-tools++/libxxconnect.a
lib/ncbi-tools++/libxxconnect2-dll.so
lib/ncbi-tools++/libxxconnect2-static.a
lib/ncbi-tools++/libxxconnect2.a
+lib/ncbi-tools++/libzcf-static.a
+lib/ncbi-tools++/libzcf.a
generated by cgit v1.2.3 (git 2.25.1) at 2025-08-30 02:06:42 +0000