Index: head/biology/hmmer/Makefile
===================================================================
--- head/biology/hmmer/Makefile	(revision 524532)
+++ head/biology/hmmer/Makefile	(revision 524533)
@@ -1,51 +1,54 @@
 # Created by: barnhart@genetics.wustl.edu
 # $FreeBSD$
 
 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
 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
 
 DOCFILES=	Userguide.pdf
 EXAMPLES=	7LESS_DROME HBB_HUMAN MADE1.hmm MADE1.sto \
 		Pkinase.hmm Pkinase.sto dna_target.fa fn3.hmm fn3.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/*
 
 post-install-DOCS-on:
 	@${MKDIR} ${STAGEDIR}${DOCSDIR}
 	${INSTALL_DATA} ${DOCFILES:S,^,${WRKSRC}/,} ${STAGEDIR}${DOCSDIR}
 
 post-install-EXAMPLES-on:
 	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
 	${INSTALL_DATA} ${EXAMPLES:S,^,${WRKSRC}/tutorial/,} ${STAGEDIR}${EXAMPLESDIR}
 
 .include <bsd.port.mk>
Index: head/biology/hmmer/distinfo
===================================================================
--- head/biology/hmmer/distinfo	(revision 524532)
+++ head/biology/hmmer/distinfo	(revision 524533)
@@ -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
Index: head/biology/hmmer/files/patch-src_hmmc2.c
===================================================================
--- head/biology/hmmer/files/patch-src_hmmc2.c	(nonexistent)
+++ head/biology/hmmer/files/patch-src_hmmc2.c	(revision 524533)
@@ -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);

Property changes on: head/biology/hmmer/files/patch-src_hmmc2.c
___________________________________________________________________
Added: fbsd:nokeywords
## -0,0 +1 ##
+yes
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Index: head/biology/hmmer/pkg-plist
===================================================================
--- head/biology/hmmer/pkg-plist	(revision 524532)
+++ head/biology/hmmer/pkg-plist	(revision 524533)
@@ -1,50 +1,53 @@
 bin/alimask
 bin/hmmalign
 bin/hmmbuild
 bin/hmmconvert
 bin/hmmemit
 bin/hmmfetch
 bin/hmmlogo
 bin/hmmpgmd
+bin/hmmpgmd_shard
 bin/hmmpress
 bin/hmmscan
 bin/hmmsearch
 bin/hmmsim
 bin/hmmstat
 bin/jackhmmer
 bin/makehmmerdb
 bin/nhmmer
 bin/nhmmscan
 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
 man/man1/hmmsim.1.gz
 man/man1/hmmstat.1.gz
 man/man1/jackhmmer.1.gz
 man/man1/makehmmerdb.1.gz
 man/man1/nhmmer.1.gz
 man/man1/nhmmscan.1.gz
 man/man1/phmmer.1.gz
 %%PORTDOCS%%%%DOCSDIR%%/Userguide.pdf
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/7LESS_DROME
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/HBB_HUMAN
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MADE1.hmm
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MADE1.sto
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/Pkinase.hmm
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/Pkinase.sto
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dna_target.fa
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.hmm
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.sto
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.hmm
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.sto
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins45.fa