From nobody Tue Jan 14 17:47:33 2025 X-Original-To: dev-commits-ports-all@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4YXc5x6M0qz5kCwH; Tue, 14 Jan 2025 17:47:33 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R11" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4YXc5x5bbPz43qt; Tue, 14 Jan 2025 17:47:33 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1736876853; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=9lNQB8mZPyLfU+1LqrKAguHHVqRVmYeC68jocdg1plI=; b=I3FPtDpbaoJ4qb9Varljucgfrwbc+dy54dvku6V5qhEZA0MmWfqPuqrKW9EyAjpg3fscDE PjfbzWtAnEuH1ElO+ucTJda0OUzG226DuKNsQ8KkUCpXj3hx28JGlI6jaUWJmTQvehodBN iS9iWJxDj75li8aKg2R7Obifx8dRlZtGXxSqXnzhuXz1lkmTXdwQmx+w85YnecGxRExybn s1LKGDASRKMi2lho4oFFkO3j7w4KgMnwPbuNnVa7c7vrAkOjXSd8w7v7/MuDk2DDWkHSXV ufaJfmejRZ8X9pizMMlSJX0ZH2nuX6yc12bZ9/lpNW+rWpRxZQjSYnwO+lh+4Q== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1736876853; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=9lNQB8mZPyLfU+1LqrKAguHHVqRVmYeC68jocdg1plI=; b=FjXKaRIfI/h9KFo7C9gbJQxW7fQ+W/dIL1x6U1vCE8Xgd3E3bvLrq2FZ1ljqIuyJRlzKyS cpoAJt95/eFmYu0Qpbg3Awl8+RcBqbBEpTZ8pE+KVCN8v6F4YeMQOJC5NQFUAyANdF+3uy DACB9Zt4uM3HBHGiDMOJC34X4hjUlsKaQ/+ZeRJnBvfJfr1M/bL2p5a8iDJdYVX2VfoypN pfoXIFhyCZ/jnpRO4RCGGLqXBC1lMAupIsP27xGeXkXMXZqWy0z2lN/1Dl4fg26q4pH8uW TpyJ9GkJAuE8c/IooziRxiqIrhibMZAWqX0sTFg58VdwJ+QDSA5paqxRZAGjGg== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1736876853; a=rsa-sha256; cv=none; b=QLw0Vp3seLbYfaRCxBi6it1mN/FmZaa4qU+8kkq3fnPRXYm7IOQy9QE54HfAumW1CfZoRB /Tbj20UTMNHOU7oNXuehZ3DTZ/kTcOTNVLKaXv3YioZlpAz3PZfJuYqlRrrsFExJ9mMOGs VqGEDv4jCnuG5AXcvPz3pJHIQ5W2y4kBtDFzN35XaD4XOKHzxcoSzloE2Ow/EkDFOKl+oT bQhVX6obsDnGctxXI7EHzWY7gvBKQiytfxScs12WRxJIQDzJwiMTpPdtpJ3j8wSuhnK6Ek HNOpPmm5led6HMiOJxaCylpzQRy6qGz0SYLdcti/+vSFZnZM/GxW9kf4+CmMeQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4YXc5x5BGlz1Q29; Tue, 14 Jan 2025 17:47:33 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.18.1/8.18.1) with ESMTP id 50EHlXaH054136; Tue, 14 Jan 2025 17:47:33 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 50EHlXi0054133; Tue, 14 Jan 2025 17:47:33 GMT (envelope-from git) Date: Tue, 14 Jan 2025 17:47:33 GMT Message-Id: <202501141747.50EHlXi0054133@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: b324d354c77d - main - biology/ncbi-blast+: Update to 2.16.0 List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-all@freebsd.org Sender: owner-dev-commits-ports-all@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: b324d354c77d38829dfde770cdd9799e69462442 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=b324d354c77d38829dfde770cdd9799e69462442 commit b324d354c77d38829dfde770cdd9799e69462442 Author: Jason W. Bacon AuthorDate: 2025-01-14 17:43:59 +0000 Commit: Jason W. Bacon CommitDate: 2025-01-14 17:43:59 +0000 biology/ncbi-blast+: Update to 2.16.0 Several minor improvements and bug fixes Changes: https://www.ncbi.nlm.nih.gov/books/NBK131777/ Minor clean up in port Makefile PR: 283250 Reported by: alster@vinterdalen.se --- biology/ncbi-blast+/Makefile | 41 ++++++++++++++++++++--------------------- biology/ncbi-blast+/distinfo | 6 +++--- biology/ncbi-blast+/pkg-plist | 14 +++++++++++--- 3 files changed, 34 insertions(+), 27 deletions(-) diff --git a/biology/ncbi-blast+/Makefile b/biology/ncbi-blast+/Makefile index 8479e38ff8ea..e6ef9db191cc 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 -USE_LDCONFIG= yes +USES= compiler:c++14-lang gmake localbase:ldflags perl5 python shebangfix +USE_LDCONFIG= ${PREFIX}/lib/ncbi-tools++ -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