svn commit: r524533 - in head/biology/hmmer: . files

[Fernando Apesteguía]

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 at 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 at niid.go.jp
+MAINTAINER=	mzaki at 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