From owner-dev-commits-ports-all@freebsd.org Wed Aug 25 20:28:37 2021 Return-Path: Delivered-To: dev-commits-ports-all@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 7B78365AACF; Wed, 25 Aug 2021 20:28:37 +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 "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4GvyH914Rsz3vB8; Wed, 25 Aug 2021 20:28:37 +0000 (UTC) (envelope-from git@FreeBSD.org) 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 0C32722D5C; Wed, 25 Aug 2021 20:28:37 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 17PKSa8h010857; Wed, 25 Aug 2021 20:28:36 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 17PKSau0010856; Wed, 25 Aug 2021 20:28:36 GMT (envelope-from git) Date: Wed, 25 Aug 2021 20:28:36 GMT Message-Id: <202108252028.17PKSau0010856@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: cc5fdc14d943 - main - biology/ncbi-cxx-toolkit: Update 22.0.0 -> 25.0.0 MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: cc5fdc14d94309a7dbae28f96689202781c1e299 Auto-Submitted: auto-generated X-BeenThere: dev-commits-ports-all@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Commit messages for all branches of the ports repository List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 25 Aug 2021 20:28:37 -0000 The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=cc5fdc14d94309a7dbae28f96689202781c1e299 commit cc5fdc14d94309a7dbae28f96689202781c1e299 Author: Yuri Victorovich AuthorDate: 2021-08-25 19:54:09 +0000 Commit: Yuri Victorovich CommitDate: 2021-08-25 20:28:23 +0000 biology/ncbi-cxx-toolkit: Update 22.0.0 -> 25.0.0 --- biology/ncbi-cxx-toolkit/Makefile | 25 ++++++++++++++++++------- biology/ncbi-cxx-toolkit/distinfo | 6 +++--- 2 files changed, 21 insertions(+), 10 deletions(-) diff --git a/biology/ncbi-cxx-toolkit/Makefile b/biology/ncbi-cxx-toolkit/Makefile index d8ab6730f753..4148f33e2d63 100644 --- a/biology/ncbi-cxx-toolkit/Makefile +++ b/biology/ncbi-cxx-toolkit/Makefile @@ -1,7 +1,7 @@ PORTNAME= ncbi-cxx-toolkit -DISTVERSION= 22_0_0 +DISTVERSION= 25_0_0 CATEGORIES= biology science devel -MASTER_SITES= ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/2019/Mar_28_2019/ +MASTER_SITES= ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/2021/Aug_18_2021/ DISTNAME= ncbi_cxx--${DISTVERSION} MAINTAINER= yuri@FreeBSD.org @@ -10,25 +10,36 @@ COMMENT= NCBI C++ Toolkit LICENSE= PD LICENSE_FILE= ${WRKSRC}/doc/public/LICENSE -LIB_DEPENDS= liblmdb.so:databases/lmdb \ +LIB_DEPENDS= libcdd.so:math/cddlib \ + liblmdb.so:databases/lmdb \ libpcre.so:devel/pcre RUN_DEPENDS= bash:shells/bash USES= compiler:c++11-lang gmake mysql perl5 python shebangfix ssl xorg -SHEBANG_FILES= 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 USE_XORG= x11 xpm +SHEBANG_FILES= src/app/blast/get_species_taxids.sh +SHEBANG_GLOB= *.pl *.py + GNU_CONFIGURE= yes -CONFIGURE_ARGS= --without-debug --with-dll --without-static +CONFIGURE_ARGS= --without-debug --with-dll --without-static \ + --without-vdb + +WRKSRC= ${WRKDIR}/public-${DISTVERSION:S/_/./g}-2021-08-18-11-21-29 post-install: # strip @${FIND} ${STAGEDIR}${PREFIX}/bin -type f | ${GREP} -v -E '\.(sh|py|pl)$$' | ${XARGS} ${STRIP_CMD} @${FIND} ${STAGEDIR}${PREFIX}/lib -name "*.so" | ${XARGS} ${STRIP_CMD} # remove an empty directory - @${RMDIR} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/objtools/data_loaders/genbank/psg + #@${RMDIR} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/objtools/data_loaders/genbank/psg + @${RMDIR} \ + ${STAGEDIR}${PREFIX}/include/ncbi-tools++/algo/ms/formats \ + ${STAGEDIR}${PREFIX}/include/ncbi-tools++/algo/ms # remove the conflicting file - @${RM} ${STAGEDIR}${PREFIX}/lib/liblmdb.so + @${RM} \ + ${STAGEDIR}${PREFIX}/lib/libcdd.so \ + ${STAGEDIR}${PREFIX}/lib/liblmdb.so # autoplist: thousands of files @cd ${STAGEDIR}${PREFIX} && \ ${RMDIR} include/ncbi-tools++/algo/blast/bl2api include/ncbi-tools++/objtools/test && \ diff --git a/biology/ncbi-cxx-toolkit/distinfo b/biology/ncbi-cxx-toolkit/distinfo index 5ded16bce9b4..d85ae212645c 100644 --- a/biology/ncbi-cxx-toolkit/distinfo +++ b/biology/ncbi-cxx-toolkit/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1600993142 -SHA256 (ncbi_cxx--22_0_0.tar.gz) = ef39429bbc7f13c44c0d327432d9cfb430f9f20d10d825e6b2c4ddd7ccce457f -SIZE (ncbi_cxx--22_0_0.tar.gz) = 56042079 +TIMESTAMP = 1629878632 +SHA256 (ncbi_cxx--25_0_0.tar.gz) = 0158971349839b69ea96b3b88db774ac1692befd9910c040a00186e841ef5ed5 +SIZE (ncbi_cxx--25_0_0.tar.gz) = 95801019