From owner-svn-ports-all@freebsd.org Wed Jan 29 05:55:13 2020 Return-Path: Delivered-To: svn-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 6E0F41C20B8; Wed, 29 Jan 2020 05:55:13 +0000 (UTC) (envelope-from fernape@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) server-signature RSA-PSS (4096 bits) client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 486t4K2K2cz4B2m; Wed, 29 Jan 2020 05:55:13 +0000 (UTC) (envelope-from fernape@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 464147799; Wed, 29 Jan 2020 05:55:13 +0000 (UTC) (envelope-from fernape@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id 00T5tD5L035070; Wed, 29 Jan 2020 05:55:13 GMT (envelope-from fernape@FreeBSD.org) Received: (from fernape@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id 00T5tCxE035064; Wed, 29 Jan 2020 05:55:12 GMT (envelope-from fernape@FreeBSD.org) Message-Id: <202001290555.00T5tCxE035064@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: fernape set sender to fernape@FreeBSD.org using -f From: =?UTF-8?Q?Fernando_Apestegu=c3=ada?= Date: Wed, 29 Jan 2020 05:55:12 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r524533 - in head/biology/hmmer: . files X-SVN-Group: ports-head X-SVN-Commit-Author: fernape X-SVN-Commit-Paths: in head/biology/hmmer: . files X-SVN-Commit-Revision: 524533 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 29 Jan 2020 05:55:13 -0000 Author: fernape Date: Wed Jan 29 05:55:12 2020 New Revision: 524533 URL: https://svnweb.freebsd.org/changeset/ports/524533 Log: biology/hmmer: update to 3.3 PR: 243244 Submitted by: mzaki@e-mail.ne.jp (maintainer) Added: head/biology/hmmer/files/ head/biology/hmmer/files/patch-src_hmmc2.c (contents, props changed) Modified: head/biology/hmmer/Makefile head/biology/hmmer/distinfo head/biology/hmmer/pkg-plist Modified: head/biology/hmmer/Makefile ============================================================================== --- head/biology/hmmer/Makefile Wed Jan 29 03:38:41 2020 (r524532) +++ head/biology/hmmer/Makefile Wed Jan 29 05:55:12 2020 (r524533) @@ -2,12 +2,11 @@ # $FreeBSD$ PORTNAME= hmmer -PORTVERSION= 3.2.1 -PORTREVISION= 1 +PORTVERSION= 3.3 CATEGORIES= biology MASTER_SITES= http://eddylab.org/software/hmmer/ -MAINTAINER= mzaki@niid.go.jp +MAINTAINER= mzaki@e-mail.ne.jp COMMENT= Profile hidden Markov models for biological sequence analysis LICENSE= BSD3CLAUSE @@ -16,14 +15,14 @@ LICENSE_FILE= ${WRKSRC}/LICENSE ONLY_FOR_ARCHS= amd64 i386 powerpc powerpc64 powerpcspe ONLY_FOR_ARCHS_REASON= requires SSE2 or AltiVec instructions -USES= compiler:c11 gmake perl5 shebangfix +USES= compiler:c11 gmake perl5 python:3.5+,test shebangfix GNU_CONFIGURE= yes MAKE_ARGS= V=1 TEST_TARGET= check USE_PERL5= test -SHEBANG_GLOB= *.pl +SHEBANG_GLOB= *.pl *.py SHEBANG_FILES= easel/devkit/* OPTIONS_DEFINE= DOCS EXAMPLES TEST @@ -34,8 +33,12 @@ EXAMPLES= 7LESS_DROME HBB_HUMAN MADE1.hmm MADE1.sto \ globins4.hmm globins4.sto globins45.fa TEST_VARS= use_perl5=build +TEST_BUILD_DEPENDS= ${PYTHON_VERSION}:lang/python${PYTHON_SUFFIX} -post-build-TEST-on: do-test +post-build-TEST-on: pre-test do-test + +pre-test: + ${FIND} ${WRKSRC} -type f \( -name Makefile -or -name sqc \) -exec ${GREP} -q 'python3 ' {} \; -print | ${XARGS} ${SED} -i.bak 's/python3 /${PYTHON_VERSION} /' post-install: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/* Modified: head/biology/hmmer/distinfo ============================================================================== --- head/biology/hmmer/distinfo Wed Jan 29 03:38:41 2020 (r524532) +++ head/biology/hmmer/distinfo Wed Jan 29 05:55:12 2020 (r524533) @@ -1,3 +1,3 @@ -TIMESTAMP = 1531293655 -SHA256 (hmmer-3.2.1.tar.gz) = a56129f9d786ec25265774519fc4e736bbc16e4076946dcbd7f2c16efc8e2b9c -SIZE (hmmer-3.2.1.tar.gz) = 7670274 +TIMESTAMP = 1578579116 +SHA256 (hmmer-3.3.tar.gz) = 0186bf40af67032666014971ed8ddc3cf2834bebc2be5b3bc0304a93e763736c +SIZE (hmmer-3.3.tar.gz) = 18614771 Added: head/biology/hmmer/files/patch-src_hmmc2.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/hmmer/files/patch-src_hmmc2.c Wed Jan 29 05:55:12 2020 (r524533) @@ -0,0 +1,11 @@ +--- src/hmmc2.c.orig 2019-11-18 13:23:12 UTC ++++ src/hmmc2.c +@@ -334,7 +334,7 @@ int main(int argc, char *argv[]) + n = sizeof(sstatus); + total += n; + if ((size = readn(sock, &sstatus, n)) == -1) { +- if(errno == 104 || errno == 0){ ++ if(errno == ECONNRESET || errno == 0){ + // connection was reset, usually because server exited + fprintf(stderr, "Daemon exited, shutting down\n"); + exit(0); Modified: head/biology/hmmer/pkg-plist ============================================================================== --- head/biology/hmmer/pkg-plist Wed Jan 29 03:38:41 2020 (r524532) +++ head/biology/hmmer/pkg-plist Wed Jan 29 05:55:12 2020 (r524533) @@ -6,6 +6,7 @@ bin/hmmemit bin/hmmfetch bin/hmmlogo bin/hmmpgmd +bin/hmmpgmd_shard bin/hmmpress bin/hmmscan bin/hmmsearch @@ -19,12 +20,14 @@ bin/phmmer man/man1/alimask.1.gz man/man1/hmmalign.1.gz man/man1/hmmbuild.1.gz +man/man1/hmmc2.1.gz man/man1/hmmconvert.1.gz man/man1/hmmemit.1.gz man/man1/hmmer.1.gz man/man1/hmmfetch.1.gz man/man1/hmmlogo.1.gz man/man1/hmmpgmd.1.gz +man/man1/hmmpgmd_shard.1.gz man/man1/hmmpress.1.gz man/man1/hmmscan.1.gz man/man1/hmmsearch.1.gz