CVS commit: pkgsrc/biology/ncbi-blast+

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Thu Jan 16 01:06:31 UTC 2025

Modified Files:
        pkgsrc/biology/ncbi-blast+: Makefile PLIST buildlink3.mk distinfo
        pkgsrc/biology/ncbi-blast+/patches:
            patch-compilers_xcode30__prj_configure
Removed Files:
        pkgsrc/biology/ncbi-blast+/patches:
            patch-src_build-system_cmake_cmake-cfg-xcode.sh

Log Message:
biology/ncbi-blast+: Update to 2.16.0

Several minor improvements and bug fixes
Changes: https://www.ncbi.nlm.nih.gov/books/NBK131777/


To generate a diff of this commit:
cvs rdiff -u -r1.46 -r1.47 pkgsrc/biology/ncbi-blast+/Makefile
cvs rdiff -u -r1.6 -r1.7 pkgsrc/biology/ncbi-blast+/PLIST
cvs rdiff -u -r1.9 -r1.10 pkgsrc/biology/ncbi-blast+/buildlink3.mk \
    pkgsrc/biology/ncbi-blast+/distinfo
cvs rdiff -u -r1.2 -r1.3 \
    pkgsrc/biology/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
cvs rdiff -u -r1.3 -r0 \
    pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh

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

Modified files:

Index: pkgsrc/biology/ncbi-blast+/Makefile
diff -u pkgsrc/biology/ncbi-blast+/Makefile:1.46 pkgsrc/biology/ncbi-blast+/Makefile:1.47
--- pkgsrc/biology/ncbi-blast+/Makefile:1.46    Thu Nov 14 22:18:47 2024
+++ pkgsrc/biology/ncbi-blast+/Makefile Thu Jan 16 01:06:31 2025
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.46 2024/11/14 22:18:47 wiz Exp $
+# $NetBSD: Makefile,v 1.47 2025/01/16 01:06:31 bacon Exp $
 
-DISTNAME=      ncbi-blast-2.14.1+-src
+DISTNAME=      ncbi-blast-2.16.0+-src
 PKGNAME=       ${DISTNAME:S/+-src//:S/blast/blast+/}
-PKGREVISION=   7
 CATEGORIES=    biology
 MASTER_SITES=  https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \
                https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PKGVERSION_NOREV}/

Index: pkgsrc/biology/ncbi-blast+/PLIST
diff -u pkgsrc/biology/ncbi-blast+/PLIST:1.6 pkgsrc/biology/ncbi-blast+/PLIST:1.7
--- pkgsrc/biology/ncbi-blast+/PLIST:1.6        Thu Sep 14 00:39:17 2023
+++ pkgsrc/biology/ncbi-blast+/PLIST    Thu Jan 16 01:06:31 2025
@@ -1,6 +1,5 @@
-@comment $NetBSD: PLIST,v 1.6 2023/09/14 00:39:17 bacon Exp $
+@comment $NetBSD: PLIST,v 1.7 2025/01/16 01:06:31 bacon Exp $
 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_ma
 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/ncbic
 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/Fold
 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/seqd
 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/cl
 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_
 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/fea
 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/lim
 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

Index: pkgsrc/biology/ncbi-blast+/buildlink3.mk
diff -u pkgsrc/biology/ncbi-blast+/buildlink3.mk:1.9 pkgsrc/biology/ncbi-blast+/buildlink3.mk:1.10
--- pkgsrc/biology/ncbi-blast+/buildlink3.mk:1.9        Thu Sep 14 00:39:17 2023
+++ pkgsrc/biology/ncbi-blast+/buildlink3.mk    Thu Jan 16 01:06:31 2025
@@ -1,4 +1,4 @@
-# $NetBSD: buildlink3.mk,v 1.9 2023/09/14 00:39:17 bacon Exp $
+# $NetBSD: buildlink3.mk,v 1.10 2025/01/16 01:06:31 bacon Exp $
 
 BUILDLINK_TREE+=       ncbi-blast+
 
@@ -7,8 +7,8 @@ NCBI_BLAST+_BUILDLINK3_MK:=
 
 USE_CXX_FEATURES=                      c++17
 
-BUILDLINK_API_DEPENDS.ncbi-blast++=    ncbi-blast+>=2.14.1
-BUILDLINK_ABI_DEPENDS.ncbi-blast++=    ncbi-blast+>=2.14.1
+BUILDLINK_API_DEPENDS.ncbi-blast++=    ncbi-blast+>=2.16.0
+BUILDLINK_ABI_DEPENDS.ncbi-blast++=    ncbi-blast+>=2.16.0
 BUILDLINK_PKGSRCDIR.ncbi-blast+?=      ../../biology/ncbi-blast+
 
 .endif # NCBI_BLAST+_BUILDLINK3_MK
Index: pkgsrc/biology/ncbi-blast+/distinfo
diff -u pkgsrc/biology/ncbi-blast+/distinfo:1.9 pkgsrc/biology/ncbi-blast+/distinfo:1.10
--- pkgsrc/biology/ncbi-blast+/distinfo:1.9     Thu Sep 14 00:39:17 2023
+++ pkgsrc/biology/ncbi-blast+/distinfo Thu Jan 16 01:06:31 2025
@@ -1,12 +1,11 @@
-$NetBSD: distinfo,v 1.9 2023/09/14 00:39:17 bacon Exp $
+$NetBSD: distinfo,v 1.10 2025/01/16 01:06:31 bacon Exp $
 
-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

Index: pkgsrc/biology/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
diff -u pkgsrc/biology/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure:1.2 pkgsrc/biology/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure:1.3
--- pkgsrc/biology/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure:1.2       Thu Sep 14 00:39:17 2023
+++ pkgsrc/biology/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure   Thu Jan 16 01:06:31 2025
@@ -1,4 +1,4 @@
-$NetBSD: patch-compilers_xcode30__prj_configure,v 1.2 2023/09/14 00:39:17 bacon Exp $
+$NetBSD: patch-compilers_xcode30__prj_configure,v 1.3 2025/01/16 01:06:31 bacon Exp $
 
 # Nonportable extension