ncbi-blast+: Update to 2.16.0

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: ncbi-blast+: Update to 2.16.0
From: Jason W. Bacon (via pkgsrc-wip) <commit-notify%pkgsrc.org@localhost>
Date: Wed, 15 Jan 2025 12:10:50 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <jtocino%gmx.com@localhost>
Pushed By:	outpaddling
Date:		Wed Jan 15 06:10:25 2025 -0600
Changeset:	9678f0919663fd6e6175198ef9e9282d12af03d6

Modified Files:
	ncbi-blast+/Makefile
	ncbi-blast+/PLIST
	ncbi-blast+/distinfo
Removed Files:
	ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh

Log Message:
ncbi-blast+: Update to 2.16.0

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=9678f0919663fd6e6175198ef9e9282d12af03d6

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

diffstat:
 ncbi-blast+/Makefile                                |  2 +-
 ncbi-blast+/PLIST                                   | 14 +++++++++++---
 ncbi-blast+/distinfo                                |  7 +++----
 .../patch-src_build-system_cmake_cmake-cfg-xcode.sh | 21 ---------------------
 4 files changed, 15 insertions(+), 29 deletions(-)

diffs:
diff --git a/ncbi-blast+/Makefile b/ncbi-blast+/Makefile
index 6f6eeb28cd..e31914274a 100644
--- a/ncbi-blast+/Makefile
+++ b/ncbi-blast+/Makefile
@@ -1,6 +1,6 @@
 # $NetBSD: Makefile,v 1.38 2023/08/14 05:23:51 wiz Exp $
 
-DISTNAME=	ncbi-blast-2.14.1+-src
+DISTNAME=	ncbi-blast-2.16.0+-src
 PKGNAME=	${DISTNAME:S/+-src//:S/blast/blast+/}
 CATEGORIES=	biology
 MASTER_SITES=	https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \
diff --git a/ncbi-blast+/PLIST b/ncbi-blast+/PLIST
index 9d8ac8d3d0..18b2ae009f 100644
--- a/ncbi-blast+/PLIST
+++ b/ncbi-blast+/PLIST
@@ -1,6 +1,5 @@
 @comment $NetBSD$
 bin/blast_formatter
-bin/blast_report
 bin/blastdb_aliastool
 bin/blastdb_convert
 bin/blastdb_path
@@ -33,6 +32,7 @@ bin/seedtop
 bin/segmasker
 bin/seqdb_demo
 bin/seqdb_perf
+bin/tax4blast
 bin/tblastn
 bin/tblastx
 bin/update_blastdb.pl
@@ -257,6 +257,8 @@ include/ncbi-tools++/algo/winmask/win_mask_dup_table.hpp
 include/ncbi-tools++/algo/winmask/win_mask_gen_counts.hpp
 include/ncbi-tools++/algo/winmask/win_mask_util.hpp
 include/ncbi-tools++/cgi/caf.hpp
+include/ncbi-tools++/cgi/caf_encoded.hpp
+include/ncbi-tools++/cgi/caf_plain.hpp
 include/ncbi-tools++/cgi/cgi_exception.hpp
 include/ncbi-tools++/cgi/cgi_serial.hpp
 include/ncbi-tools++/cgi/cgi_session.hpp
@@ -280,6 +282,7 @@ include/ncbi-tools++/common/config/ncbiconf_xcode.h
 include/ncbi-tools++/common/header_template.hpp
 include/ncbi-tools++/common/metamodules_doxygen.h
 include/ncbi-tools++/common/ncbi_build_info.h
+include/ncbi-tools++/common/ncbi_build_ver.cmake_nodep
 include/ncbi-tools++/common/ncbi_build_ver.h
 include/ncbi-tools++/common/ncbi_build_ver.h.in
 include/ncbi-tools++/common/ncbi_build_ver.h.last
@@ -1151,6 +1154,8 @@ include/ncbi-tools++/objects/gbproj/FolderInfo.hpp
 include/ncbi-tools++/objects/gbproj/FolderInfo_.hpp
 include/ncbi-tools++/objects/gbproj/GBProject_ver2.hpp
 include/ncbi-tools++/objects/gbproj/GBProject_ver2_.hpp
+include/ncbi-tools++/objects/gbproj/HugeFileProjectItem.hpp
+include/ncbi-tools++/objects/gbproj/HugeFileProjectItem_.hpp
 include/ncbi-tools++/objects/gbproj/LoaderDescriptor.hpp
 include/ncbi-tools++/objects/gbproj/LoaderDescriptor_.hpp
 include/ncbi-tools++/objects/gbproj/NCBI_GBProject_module.hpp
@@ -3429,11 +3434,13 @@ include/ncbi-tools++/objtools/blast/seqdb_reader/impl/seqdbgeneral.hpp
 include/ncbi-tools++/objtools/blast/seqdb_reader/impl/seqdbisam.hpp
 include/ncbi-tools++/objtools/blast/seqdb_reader/impl/seqdbtax.hpp
 include/ncbi-tools++/objtools/blast/seqdb_reader/impl/seqdbvol.hpp
+include/ncbi-tools++/objtools/blast/seqdb_reader/itax4blast.hpp
 include/ncbi-tools++/objtools/blast/seqdb_reader/seqdb.hpp
 include/ncbi-tools++/objtools/blast/seqdb_reader/seqdbblob.hpp
 include/ncbi-tools++/objtools/blast/seqdb_reader/seqdbcommon.hpp
 include/ncbi-tools++/objtools/blast/seqdb_reader/seqdbexpert.hpp
 include/ncbi-tools++/objtools/blast/seqdb_reader/seqidlist_reader.hpp
+include/ncbi-tools++/objtools/blast/seqdb_reader/tax4blastsqlite.hpp
 include/ncbi-tools++/objtools/blast/seqdb_writer/build_db.hpp
 include/ncbi-tools++/objtools/blast/seqdb_writer/impl/criteria.hpp
 include/ncbi-tools++/objtools/blast/seqdb_writer/multisource_util.hpp
@@ -3453,7 +3460,7 @@ include/ncbi-tools++/objtools/cleanup/cleanup_change.hpp
 include/ncbi-tools++/objtools/cleanup/cleanup_message.hpp
 include/ncbi-tools++/objtools/cleanup/cleanup_pub.hpp
 include/ncbi-tools++/objtools/cleanup/fix_feature_id.hpp
-include/ncbi-tools++/objtools/cleanup/huge_file_cleanup.hpp
+include/ncbi-tools++/objtools/cleanup/influenza_set.hpp
 include/ncbi-tools++/objtools/data_loaders/blastdb/bdbloader.hpp
 include/ncbi-tools++/objtools/data_loaders/blastdb/bdbloader_rmt.hpp
 include/ncbi-tools++/objtools/data_loaders/blastdb/blastdb_adapter.hpp
@@ -3527,7 +3534,6 @@ include/ncbi-tools++/objtools/edit/gaps_edit.hpp
 include/ncbi-tools++/objtools/edit/gb_block_field.hpp
 include/ncbi-tools++/objtools/edit/gene_utils.hpp
 include/ncbi-tools++/objtools/edit/huge_asn_loader.hpp
-include/ncbi-tools++/objtools/edit/huge_asn_macro_reader.hpp
 include/ncbi-tools++/objtools/edit/huge_asn_reader.hpp
 include/ncbi-tools++/objtools/edit/huge_file.hpp
 include/ncbi-tools++/objtools/edit/huge_file_process.hpp
@@ -4374,6 +4380,7 @@ include/ncbi-tools++/objtools/format/feature_gather.hpp
 include/ncbi-tools++/objtools/format/flat_expt.hpp
 include/ncbi-tools++/objtools/format/flat_file_config.hpp
 include/ncbi-tools++/objtools/format/flat_file_generator.hpp
+include/ncbi-tools++/objtools/format/flat_file_html.hpp
 include/ncbi-tools++/objtools/format/format_item_ostream.hpp
 include/ncbi-tools++/objtools/format/formatter.hpp
 include/ncbi-tools++/objtools/format/ftable_formatter.hpp
@@ -4619,6 +4626,7 @@ include/ncbi-tools++/sra/readers/sra/limited_resource_map.hpp
 include/ncbi-tools++/sra/readers/sra/sdk.hpp
 include/ncbi-tools++/sra/readers/sra/snpread.hpp
 include/ncbi-tools++/sra/readers/sra/sraread.hpp
+include/ncbi-tools++/sra/readers/sra/vdbcache.hpp
 include/ncbi-tools++/sra/readers/sra/vdbread.hpp
 include/ncbi-tools++/sra/readers/sra/wgsread.hpp
 include/ncbi-tools++/sra/readers/sra/wgsresolver.hpp
diff --git a/ncbi-blast+/distinfo b/ncbi-blast+/distinfo
index 097abb2b96..15a954e763 100644
--- a/ncbi-blast+/distinfo
+++ b/ncbi-blast+/distinfo
@@ -1,12 +1,11 @@
 $NetBSD$
 
-BLAKE2s (ncbi-blast-2.14.1+-src.tar.gz) = 56f2cde7da4eb06f3ba14f89b64c29f8093938f8ff0188e64fe380fe9b100c29
-SHA512 (ncbi-blast-2.14.1+-src.tar.gz) = e0d7371da98fc80ce0e1fc600347d84836e38f162f023edb2dc9b2863af6146499c975f2d3f067283770d7452a677f746bb09b50d5935b21fd113c2ad5a9aca4
-Size (ncbi-blast-2.14.1+-src.tar.gz) = 28258487 bytes
+BLAKE2s (ncbi-blast-2.16.0+-src.tar.gz) = d58d567e760bcdc020ee1bf1a6cf7a0da5d7c7d21a60aeac797d8c53fc82f5a9
+SHA512 (ncbi-blast-2.16.0+-src.tar.gz) = 1e632f24efded51a20e51840477b07f63b56ae794e6a182ec47d663fca8adb9dd266d984fdb42b274f8b8013eddb54ba022721f263a521d3331f505b880261de
+Size (ncbi-blast-2.16.0+-src.tar.gz) = 28307712 bytes
 SHA1 (patch-compilers_xcode30__prj_configure) = a689f10f48930148fd7f61b82eb20e1d3ac208cf
 SHA1 (patch-src_algo_blast_core_blast__kappa.c) = 6fcad996b3a8e5b6c2400608bff9de62ebf6927f
 SHA1 (patch-src_build-system_Makefile.in.top) = 71d5246867a8c985c1175c338fb0af664094ca01
-SHA1 (patch-src_build-system_cmake_cmake-cfg-xcode.sh) = b50a53ac7f2bd191d0d85cf490ac891f2cf20bfa
 SHA1 (patch-src_build-system_configure) = 95185d53179a69a1b1cfa6870aca36dd962d2c43
 SHA1 (patch-src_build-system_helpers_Makefile.run__with__lock.app) = d69b9e349646c970c3b296707f917defbe39cccd
 SHA1 (patch-src_util_checksum_cityhash_city.cc) = ff8e84d90a4fc0d9d33e17abd05ed8e9f2de12fc
diff --git a/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh b/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh
deleted file mode 100644
index cdea4f8853..0000000000
--- a/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh
+++ /dev/null
@@ -1,21 +0,0 @@
-$NetBSD: patch-src_build-system_cmake_cmake-cfg-xcode.sh,v 1.3 2023/05/28 22:48:27 bacon Exp $
-
-# sh portability
-
---- src/build-system/cmake/cmake-cfg-xcode.sh.orig	2023-05-26 12:05:14.109542442 +0000
-+++ src/build-system/cmake/cmake-cfg-xcode.sh
-@@ -249,12 +249,12 @@ CMAKE_ARGS="$CMAKE_ARGS -DBUILD_SHARED_L
- if [ -z "$BUILD_ROOT" ]; then
-   if [ -z "$BUILD_TYPE" ]; then
-     BUILD_ROOT=CMake-${CC_NAME}${CC_VERSION}
--    if [ "$BUILD_SHARED_LIBS" == "ON" ]; then
-+    if [ "$BUILD_SHARED_LIBS" = "ON" ]; then
-       BUILD_ROOT="$BUILD_ROOT"-DLL
-     fi
-   else
-     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
-   fi
Prev by Date: rust183: remove superfluous patch-config.example.toml
Next by Date: auto-admin: Update to 0.8.0.86
Previous by Thread: rust183: remove superfluous patch-config.example.toml
Next by Thread: auto-admin: Update to 0.8.0.86
Indexes:
Home | Main Index | Thread Index | Old Index