git: b532c5dd966e - main - biology/hmmer: Update to 3.3.2

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=b532c5dd966eb638a5616fc7819657f007c08848

commit b532c5dd966eb638a5616fc7819657f007c08848
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2022-10-11 18:58:39 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2022-10-11 20:13:01 +0000

    biology/hmmer: Update to 3.3.2
    
    No release notes.  See commits for changes:
    https://github.com/EddyRivasLab/hmmer
    
    PR:             266968
    Reported by:    mzaki@e-mail.ne.jp
---
 biology/hmmer/Makefile                | 16 ++++++++--------
 biology/hmmer/distinfo                |  6 +++---
 biology/hmmer/files/patch-src_hmmc2.c | 11 -----------
 3 files changed, 11 insertions(+), 22 deletions(-)

diff --git a/biology/hmmer/Makefile b/biology/hmmer/Makefile
index 3773440431c7..21a16114e1d5 100644
--- a/biology/hmmer/Makefile
+++ b/biology/hmmer/Makefile
@@ -1,5 +1,5 @@
 PORTNAME=	hmmer
-PORTVERSION=	3.3
+PORTVERSION=	3.3.2
 CATEGORIES=	biology
 MASTER_SITES=	http://eddylab.org/software/hmmer/
 
@@ -14,14 +14,14 @@ ONLY_FOR_ARCHS=	amd64 i386 powerpc powerpc64
 ONLY_FOR_ARCHS_REASON=	requires SSE2 or AltiVec instructions
 
 USES=		compiler:c11 gmake perl5 python:3.5+,test shebangfix
+USE_PERL5=	test
+SHEBANG_FILES=	easel/devkit/*
+SHEBANG_GLOB=	*.pl *.py
 
 GNU_CONFIGURE=	yes
 MAKE_ARGS=	V=1
 
 TEST_TARGET=	check
-USE_PERL5=	test
-SHEBANG_GLOB=	*.pl *.py
-SHEBANG_FILES=	easel/devkit/*
 
 OPTIONS_DEFINE=	DOCS EXAMPLES TEST
 
@@ -30,14 +30,11 @@ 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}
+TEST_VARS=	use_perl5=build
 
 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/*
 
@@ -49,4 +46,7 @@ post-install-EXAMPLES-on:
 	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
 	${INSTALL_DATA} ${EXAMPLES:S,^,${WRKSRC}/tutorial/,} ${STAGEDIR}${EXAMPLESDIR}
 
+pre-test:
+	${FIND} ${WRKSRC} -type f \( -name Makefile -or -name sqc \) -exec ${GREP} -q 'python3 ' {} \; -print | ${XARGS} ${SED} -i.bak 's/python3 /${PYTHON_VERSION} /'
+
 .include <bsd.port.mk>
diff --git a/biology/hmmer/distinfo b/biology/hmmer/distinfo
index 4af97cebbada..edb75ddf6465 100644
--- a/biology/hmmer/distinfo
+++ b/biology/hmmer/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1578579116
-SHA256 (hmmer-3.3.tar.gz) = 0186bf40af67032666014971ed8ddc3cf2834bebc2be5b3bc0304a93e763736c
-SIZE (hmmer-3.3.tar.gz) = 18614771
+TIMESTAMP = 1665491511
+SHA256 (hmmer-3.3.2.tar.gz) = 92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69
+SIZE (hmmer-3.3.2.tar.gz) = 18213049
diff --git a/biology/hmmer/files/patch-src_hmmc2.c b/biology/hmmer/files/patch-src_hmmc2.c
deleted file mode 100644
index 8d16156a130c..000000000000
--- a/biology/hmmer/files/patch-src_hmmc2.c
+++ /dev/null
@@ -1,11 +0,0 @@
---- 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);