ncbi-blast+: Update to 2.14.1

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: ncbi-blast+: Update to 2.14.1
From: Jason W. Bacon <bacon%NetBSD.org@localhost>
Date: Sat, 26 Aug 2023 14:25:46 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sat Aug 26 09:25:46 2023 -0500
Changeset:	ba63127d2f74d28e72ffba9aec7d49014c859e2f

Modified Files:
	ncbi-blast+/Makefile
	ncbi-blast+/PLIST
	ncbi-blast+/buildlink3.mk
	ncbi-blast+/distinfo
	ncbi-blast+/patches/patch-compilers_xcode30__prj_configure

Log Message:
ncbi-blast+: Update to 2.14.1

Also clean up Makefile and bl3

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=ba63127d2f74d28e72ffba9aec7d49014c859e2f

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

diffstat:
 ncbi-blast+/Makefile                                 | 11 +++++++----
 ncbi-blast+/PLIST                                    | 19 ++++++++++++++++---
 ncbi-blast+/buildlink3.mk                            |  7 +++++--
 ncbi-blast+/distinfo                                 | 10 +++++-----
 .../patches/patch-compilers_xcode30__prj_configure   | 20 ++++++++++----------
 5 files changed, 43 insertions(+), 24 deletions(-)

diffs:
diff --git a/ncbi-blast+/Makefile b/ncbi-blast+/Makefile
index c2325611d6..9858257581 100644
--- a/ncbi-blast+/Makefile
+++ b/ncbi-blast+/Makefile
@@ -1,8 +1,8 @@
-# $NetBSD: Makefile,v 1.35 2023/05/28 22:48:27 bacon Exp $
+# $NetBSD: Makefile,v 1.38 2023/08/14 05:23:51 wiz Exp $
 
-DISTNAME=	ncbi-blast-2.14.0+-src
+DISTNAME=	ncbi-blast-2.14.1+-src
 PKGNAME=	${DISTNAME:S/+-src//:S/blast/blast+/}
-CATEGORIES=	wip biology
+CATEGORIES=	biology
 MASTER_SITES=	https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \
 		https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PKGVERSION_NOREV}/
 
@@ -11,6 +11,8 @@ HOMEPAGE=	http://blast.ncbi.nlm.nih.gov/
 COMMENT=	NCBI implementation of Basic Local Alignment Search Tool
 LICENSE=	public-domain
 
+USE_CXX_FEATURES+=	c++17
+
 # Nobody does bioinformatics on 32-bit processors anymore
 ONLY_FOR_PLATFORM=	${LP64PLATFORMS}
 
@@ -39,7 +41,8 @@ MKPIE_SUPPORTED=	no	# Temporary fix
 # Resolve a conflict with libproj by moving libs to a subdir
 CONFIGURE_ENV=		ncbi_cv_prog_amq_w=no
 CONFIGURE_ARGS+=	AR="ar cr" --without-boost
-CONFIGURE_ARGS+=	--libdir=${PREFIX}/lib/ncbi-tools++
+# pkglint warning
+# CONFIGURE_ARGS+=	--libdir=${PREFIX}/lib/ncbi-tools++
 WRKSRC=			${WRKDIR}/${DISTNAME}/c++
 
 .include "../../mk/bsd.prefs.mk"
diff --git a/ncbi-blast+/PLIST b/ncbi-blast+/PLIST
index 12ad3412ba..9d8ac8d3d0 100644
--- a/ncbi-blast+/PLIST
+++ b/ncbi-blast+/PLIST
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.5 2023/05/28 22:48:27 bacon Exp $
+@comment $NetBSD$
 bin/blast_formatter
 bin/blast_report
 bin/blastdb_aliastool
@@ -300,6 +300,11 @@ include/ncbi-tools++/common/test_data_path.h
 include/ncbi-tools++/connect/connect_export.h
 include/ncbi-tools++/connect/email_diag_handler.hpp
 include/ncbi-tools++/connect/error_codes.hpp
+include/ncbi-tools++/connect/ext/ncbi_crypt.h
+include/ncbi-tools++/connect/ext/ncbi_dblb.h
+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_uv_nghttp2.hpp
 include/ncbi-tools++/connect/impl/server_connection.hpp
@@ -326,7 +331,6 @@ include/ncbi-tools++/connect/ncbi_http_connector.h
 include/ncbi-tools++/connect/ncbi_http_session.hpp
 include/ncbi-tools++/connect/ncbi_iprange.h
 include/ncbi-tools++/connect/ncbi_ipv6.h
-include/ncbi-tools++/connect/ncbi_lbos.hpp
 include/ncbi-tools++/connect/ncbi_localip.h
 include/ncbi-tools++/connect/ncbi_localip.hpp
 include/ncbi-tools++/connect/ncbi_mbedtls.h
@@ -396,6 +400,7 @@ include/ncbi-tools++/connect/services/srv_connections.hpp
 include/ncbi-tools++/connect/services/srv_connections_expt.hpp
 include/ncbi-tools++/connect/services/util.hpp
 include/ncbi-tools++/connect/threaded_server.hpp
+include/ncbi-tools++/corelib/atomic_util.hpp
 include/ncbi-tools++/corelib/blob_storage.hpp
 include/ncbi-tools++/corelib/ddumpable.hpp
 include/ncbi-tools++/corelib/env_reg.hpp
@@ -429,6 +434,7 @@ include/ncbi-tools++/corelib/mswin_export.h
 include/ncbi-tools++/corelib/mswin_no_popup.h
 include/ncbi-tools++/corelib/ncbi_autoinit.hpp
 include/ncbi-tools++/corelib/ncbi_base64.h
+include/ncbi-tools++/corelib/ncbi_base_build_ver.h
 include/ncbi-tools++/corelib/ncbi_bswap.hpp
 include/ncbi-tools++/corelib/ncbi_config.hpp
 include/ncbi-tools++/corelib/ncbi_cookies.hpp
@@ -588,6 +594,7 @@ include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/stack.h
 include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/strfunc.h
 include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/strtod.h
 include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/swap.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/istreamasync.h
 include/ncbi-tools++/misc/jsonwrapp/rapidjson11/istreamwrapper.h
 include/ncbi-tools++/misc/jsonwrapp/rapidjson11/license.txt
 include/ncbi-tools++/misc/jsonwrapp/rapidjson11/memorybuffer.h
@@ -3527,7 +3534,6 @@ include/ncbi-tools++/objtools/edit/huge_file_process.hpp
 include/ncbi-tools++/objtools/edit/link_cds_mrna.hpp
 include/ncbi-tools++/objtools/edit/loc_edit.hpp
 include/ncbi-tools++/objtools/edit/mail_report.hpp
-include/ncbi-tools++/objtools/edit/mla_updater.hpp
 include/ncbi-tools++/objtools/edit/parse_text_options.hpp
 include/ncbi-tools++/objtools/edit/promote.hpp
 include/ncbi-tools++/objtools/edit/pub_fix.hpp
@@ -4758,6 +4764,9 @@ include/ncbi-tools++/util/rangemap.hpp
 include/ncbi-tools++/util/rangemap.inl
 include/ncbi-tools++/util/reader_writer.hpp
 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
@@ -4846,6 +4855,8 @@ lib/ncbi-tools++/libcomposition_adjustment-static.a
 lib/ncbi-tools++/libcomposition_adjustment.a
 lib/ncbi-tools++/libconnect-static.a
 lib/ncbi-tools++/libconnect.a
+lib/ncbi-tools++/libconnext-static.a
+lib/ncbi-tools++/libconnext.a
 lib/ncbi-tools++/libconnssl-static.a
 lib/ncbi-tools++/libconnssl.a
 lib/ncbi-tools++/libdbapi-static.a
@@ -5068,6 +5079,8 @@ lib/ncbi-tools++/libxcompress-static.a
 lib/ncbi-tools++/libxcompress.a
 lib/ncbi-tools++/libxconnect-static.a
 lib/ncbi-tools++/libxconnect.a
+lib/ncbi-tools++/libxconnext-static.a
+lib/ncbi-tools++/libxconnext.a
 lib/ncbi-tools++/libxconnserv-static.a
 lib/ncbi-tools++/libxconnserv.a
 lib/ncbi-tools++/libxcser-static.a
diff --git a/ncbi-blast+/buildlink3.mk b/ncbi-blast+/buildlink3.mk
index 21f301b18e..b8438303b5 100644
--- a/ncbi-blast+/buildlink3.mk
+++ b/ncbi-blast+/buildlink3.mk
@@ -1,12 +1,15 @@
-# $NetBSD: buildlink3.mk,v 1.6 2023/05/28 22:48:27 bacon Exp $
+# $NetBSD: buildlink3.mk,v 1.8 2023/08/14 05:23:51 wiz Exp $
 
 BUILDLINK_TREE+=	ncbi-blast+
 
 .if !defined(NCBI_BLAST+_BUILDLINK3_MK)
 NCBI_BLAST+_BUILDLINK3_MK:=
 
+USE_CXX_FEATURES+=			c++17
+
 BUILDLINK_API_DEPENDS.ncbi-blast++=	ncbi-blast+>=2.14.0
-BUILDLINK_PKGSRCDIR.ncbi-blast+?=	../../biology/ncbi-blast+
+BUILDLINK_ABI_DEPENDS.ncbi-blast++=	ncbi-blast+>=2.14.0nb1
+BUILDLINK_PKGSRCDIR.ncbi-blast+?=	../../wip/ncbi-blast+
 
 .endif	# NCBI_BLAST+_BUILDLINK3_MK
 
diff --git a/ncbi-blast+/distinfo b/ncbi-blast+/distinfo
index 7e9d8a8585..097abb2b96 100644
--- a/ncbi-blast+/distinfo
+++ b/ncbi-blast+/distinfo
@@ -1,9 +1,9 @@
-$NetBSD: distinfo,v 1.8 2023/05/28 22:48:27 bacon Exp $
+$NetBSD$
 
-BLAKE2s (ncbi-blast-2.14.0+-src.tar.gz) = fbda12e9d778e0a84df0195964b397a08fba4f067c55525556e3831ecdd7b252
-SHA512 (ncbi-blast-2.14.0+-src.tar.gz) = 30f6292cacb7c2ec0a00803c697ab0255ccee1c82a40923df0f3e4f856204db8da5be212b5ec02e0acb8000396a71f600c35e63f83eaf30e1a9639e4c95c4a83
-Size (ncbi-blast-2.14.0+-src.tar.gz) = 28200227 bytes
-SHA1 (patch-compilers_xcode30__prj_configure) = b89b3be8671c6c692ba474476879ee67a76fdbe5
+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
+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
diff --git a/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure b/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
index 7cc26bd745..958125dcb1 100644
--- a/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
+++ b/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
@@ -1,15 +1,15 @@
-$NetBSD: patch-compilers_xcode30__prj_configure,v 1.1 2018/04/27 20:28:28 bacon Exp $
+$NetBSD$
 
 # Nonportable extension
 
---- compilers/xcode30_prj/configure.orig	2018-04-27 14:19:43.000000000 +0000
+--- compilers/xcode30_prj/configure.orig	2023-08-26 13:06:39.313163201 +0000
 +++ compilers/xcode30_prj/configure
-@@ -280,7 +280,7 @@ arch=`arch`
- platform=`xcodebuild -version 2>/dev/null | grep 'Xcode [0-9][0-9]*' | sed -e 's/[ .]//g'`
- 
+@@ -284,7 +284,7 @@ platform=`xcodebuild -version 2>/dev/nul
  # ------- target architecture
--if test "$use_64" == "yes"; then
-+if test "$use_64" = "yes"; then
-   use_arch="x86_64"
- else
-   use_arch="i386"
+ if test -n "$use_arch"; then
+   :
+-elif test "$use_64" == "yes"; then
++elif test "$use_64" = "yes"; then
+   case "`uname -m`" in
+     arm* ) use_arch=arm64  ;;
+     *86* ) use_arch=x86_64 ;;
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