Attachment 255771 Details for Bug 283250 – [PATCH] biology/ncbi-blast+: update 2.14.1 → 2.16.0

[patch] [PATCH] biology/ncbi-blast+: update 2.14.1 → 2.16.0

0001-biology-ncbi-blast-update-2.14.1-2.16.0.patch (text/plain), 8.35 KB, created by Älven on 2024-12-11 09:34:54 UTC

(hide)

Description:

Filename:

MIME Type:

Creator: Älven

Created: 2024-12-11 09:34:54 UTC

Size: 8.35 KB

patch

obsolete

>From 9e1958ac05942a7bee84eba1e775b40af4af9498 Mon Sep 17 00:00:00 2001
>From: Ãlven <alster@vinterdalen.se>
>Date: Wed, 11 Dec 2024 13:31:50 +0400
>Subject: [PATCH] biology/ncbi-blast+: update 2.14.1 â 2.16.0
>MIME-Version: 1.0
>Content-Type: text/plain; charset=UTF-8
>Content-Transfer-Encoding: 8bit
>
>* Sort LIB_DEPENDS, USES and SHEBANG_FILES
>---
> biology/ncbi-blast+/Makefile  | 39 +++++++++++++++++------------------
> biology/ncbi-blast+/distinfo  |  6 +++---
> biology/ncbi-blast+/pkg-plist | 14 ++++++++++---
> 3 files changed, 33 insertions(+), 26 deletions(-)
>
>diff --git a/biology/ncbi-blast+/Makefile b/biology/ncbi-blast+/Makefile
>index 8479e38ff8ea..b988ed9a6184 100644
>--- a/biology/ncbi-blast+/Makefile
>+++ b/biology/ncbi-blast+/Makefile
>@@ -1,6 +1,5 @@
> PORTNAME=	ncbi-blast+
>-DISTVERSION=	2.14.1
>-PORTREVISION=	8
>+DISTVERSION=	2.16.0
> 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+/${PORTVERSION}/
>@@ -8,7 +7,7 @@ DISTNAME=	ncbi-blast-${PORTVERSION}+-src
> 
> MAINTAINER=	jwb@FreeBSD.org
> COMMENT=	NCBI implementation of Basic Local Alignment Search Tool
>-WWW=		https://blast.ncbi.nlm.nih.gov
>+WWW=		https://blast.ncbi.nlm.nih.gov/
> 
> LICENSE=	PD
> LICENSE_FILE=	${WRKSRC}/scripts/projects/blast/LICENSE
>@@ -16,35 +15,35 @@ LICENSE_FILE=	${WRKSRC}/scripts/projects/blast/LICENSE
> ONLY_FOR_ARCHS=		aarch64 amd64 powerpc64 powerpc64le riscv64
> ONLY_FOR_ARCHS_REASON=	Requires 64-bit processor
> 
>-LIB_DEPENDS=	libpcre.so:devel/pcre \
>-		liblmdb.so:databases/lmdb \
>-		liblzo2.so:archivers/lzo2 \
>-		libgnutls.so:security/gnutls \
>-		libtspi.so:security/trousers \
>+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 \
>-		libhogweed.so:security/nettle \
>-		libtasn1.so:security/libtasn1 \
>+		libnghttp2.so:www/libnghttp2 \
> 		libp11-kit.so:security/p11-kit \
>-		libgcrypt.so:security/libgcrypt \
>-		libgpg-error.so:security/libgpg-error \
>+		libpcre.so:devel/pcre \
> 		libsqlite3.so:databases/sqlite3 \
>+		libtasn1.so:security/libtasn1 \
>+		libtspi.so:security/trousers \
> 		libuv.so:devel/libuv \
>-		libnghttp2.so:www/libnghttp2 \
>-		libgrpc.so:devel/grpc \
>-		libzstd.so:archivers/zstd \
>-		libdw.so:devel/elfutils
>+		libzstd.so:archivers/zstd
> RUN_DEPENDS=	p5-List-MoreUtils>=0:lang/p5-List-MoreUtils \
> 		p5-JSON>=0:converters/p5-JSON
> 
>-USES=		compiler:c++14-lang gmake localbase:ldflags shebangfix perl5 python
>+USES=		compiler:c++14-lang gmake localbase:ldflags perl5 python shebangfix
> USE_LDCONFIG=	yes
> 
>-SHEBANG_FILES=	src/app/blast/legacy_blast.pl \
>-		src/app/blast/update_blastdb.pl \
>-		src/app/blast/cleanup-blastdb-volumes.py \
>+SHEBANG_FILES=	src/app/blast/cleanup-blastdb-volumes.py \
> 		src/app/blast/get_species_taxids.sh \
>+		src/app/blast/legacy_blast.pl \
>+		src/app/blast/update_blastdb.pl \
> 		src/app/winmasker/windowmasker_2.2.22_adapter.py
> GNU_CONFIGURE=	yes
> 
>diff --git a/biology/ncbi-blast+/distinfo b/biology/ncbi-blast+/distinfo
>index 4af49f2b46ea..fb3f8ad65194 100644
>--- a/biology/ncbi-blast+/distinfo
>+++ b/biology/ncbi-blast+/distinfo
>@@ -1,3 +1,3 @@
>-TIMESTAMP = 1692973880
>-SHA256 (ncbi-blast-2.14.1+-src.tar.gz) = 712c2dbdf0fb13cc1c2d4f4ef5dd1ce4b06c3b57e96dfea8f23e6e99f5b1650e
>-SIZE (ncbi-blast-2.14.1+-src.tar.gz) = 28258487
>+TIMESTAMP = 1733904135
>+SHA256 (ncbi-blast-2.16.0+-src.tar.gz) = 17c93cf009721023e5aecf5753f9c6a255d157561638b91b3ad7276fd6950c2b
>+SIZE (ncbi-blast-2.16.0+-src.tar.gz) = 28307712
>diff --git a/biology/ncbi-blast+/pkg-plist b/biology/ncbi-blast+/pkg-plist
>index a48efb2375e8..88452e690ca1 100644
>--- a/biology/ncbi-blast+/pkg-plist
>+++ b/biology/ncbi-blast+/pkg-plist
>@@ -1,5 +1,4 @@
> bin/blast_formatter
>-bin/blast_report
> bin/blastdb_aliastool
> bin/blastdb_convert
> bin/blastdb_path
>@@ -31,6 +30,7 @@ bin/run_with_lock
> bin/seedtop
> bin/segmasker
> bin/seqdb_demo
>+bin/tax4blast
> bin/tblastn
> bin/tblastx
> bin/update_blastdb.pl
>@@ -255,6 +255,8 @@ 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
>@@ -277,6 +279,7 @@ 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.last
> include/ncbi-tools++/common/ncbi_export.h
>@@ -1162,6 +1165,8 @@ 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
>@@ -3490,11 +3495,13 @@ 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
>@@ -3514,7 +3521,7 @@ 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
>@@ -3588,7 +3595,6 @@ 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
>@@ -4445,6 +4451,7 @@ 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
>@@ -4690,6 +4697,7 @@ 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
>-- 
>2.47.1
>

Flags:

alster: maintainer-approval? (jwb)

Actions: View | Diff

Attachments on bug 283250: 255771