Date: Wed, 29 Jan 2020 05:55:12 +0000 (UTC) From: =?UTF-8?Q?Fernando_Apestegu=c3=ada?= <fernape@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r524533 - in head/biology/hmmer: . files Message-ID: <202001290555.00T5tCxE035064@repo.freebsd.org>
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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
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