5 files changed, 53 insertions, 22 deletions

diff --git a/biology/infernal/Makefile b/biology/infernal/Makefile
index 9e65537af33d..8ecde37b71ac 100644
--- a/biology/infernal/Makefile
+++ b/biology/infernal/Makefile
@@ -1,23 +1,31 @@
 # $FreeBSD$
 
 PORTNAME=	infernal
-PORTVERSION=	1.1.2
+PORTVERSION=	1.1.3
 CATEGORIES=	biology
 MASTER_SITES=	http://eddylab.org/infernal/
 
-MAINTAINER=	mzaki@niid.go.jp
+MAINTAINER=	mzaki@e-mail.ne.jp
 COMMENT=	Search sequence databases for structural RNA homologs
 
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
-ONLY_FOR_ARCHS=	amd64 i386 powerpc64
+ONLY_FOR_ARCHS=	amd64 i386 powerpc powerpc64 powerpcspe
 ONLY_FOR_ARCHS_REASON=	requires SSE2 or AltiVec instructions
 
-USES=		gmake
+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 *.py
+SHEBANG_FILES=	easel/devkit/*
+
+OPTIONS_DEFINE=	DOCS EXAMPLES TEST
+
 DOCFILES=	Userguide.pdf
 EXAMPLES=	5S_rRNA.c.cm 5S_rRNA.sto \
 		Cobalamin.c.cm Cobalamin.fa Cobalamin.sto \
@@ -27,13 +35,16 @@ EXAMPLES=	5S_rRNA.c.cm 5S_rRNA.sto \
 		tRNA5-hand.c.cm tRNA5-hand.sto tRNA5-mrum.out \
 		tRNA5-noss.sto tRNA5.c.cm tRNA5.sto
 
-OPTIONS_DEFINE=	DOCS EXAMPLES TEST
+TEST_VARS=	use_perl5=build
+TEST_BUILD_DEPENDS=	${PYTHON_VERSION}:lang/python${PYTHON_SUFFIX}
+
+post-build-TEST-on:	pre-test do-test
 
-TEST_TEST_TARGET=	check
-TEST_USES=	shebangfix perl5
-TEST_VARS=	shebang_glob=*.pl shebang_files=easel/devkit/* use_perl5=build
+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-build-TEST-on:	do-test
+post-install:
+	@${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*
 
 post-install-DOCS-on:
 	@${MKDIR} ${STAGEDIR}${DOCSDIR}
diff --git a/biology/infernal/distinfo b/biology/infernal/distinfo
index a99bece6070f..9f362448abc8 100644
--- a/biology/infernal/distinfo
+++ b/biology/infernal/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1528251928
-SHA256 (infernal-1.1.2.tar.gz) = ac8c24f484205cfb7124c38d6dc638a28f2b9035b9433efec5dc753c7e84226b
-SIZE (infernal-1.1.2.tar.gz) = 19364073
+TIMESTAMP = 1578660730
+SHA256 (infernal-1.1.3.tar.gz) = 3b98a6a3a0e7b01aa077a0caf1e958223c4d8f80a69a4eb602ca59a3475da85e
+SIZE (infernal-1.1.3.tar.gz) = 29910035
diff --git a/biology/infernal/files/patch-configure b/biology/infernal/files/patch-configure
deleted file mode 100644
index f9fdfd5f3f0d..000000000000
--- a/biology/infernal/files/patch-configure
+++ /dev/null
@@ -1,10 +0,0 @@
---- configure.orig	2016-07-01 20:26:34 UTC
-+++ configure
-@@ -3855,6 +3855,7 @@ fi
- if test "$impl_choice" = "none"; then
-   case $host in
-     ia64-*-*)      impl_choice=sse;;
-+    amd64-*-*)     impl_choice=sse;;
-     i?86-*-*)      impl_choice=sse;;
-     x86*-*-*)      impl_choice=sse;;
-     powerpc*-*-*)  impl_choice=vmx;;
diff --git a/biology/infernal/files/patch-hmmer_src_hmmc2.c b/biology/infernal/files/patch-hmmer_src_hmmc2.c
new file mode 100644
index 000000000000..5bd86cf55247
--- /dev/null
+++ b/biology/infernal/files/patch-hmmer_src_hmmc2.c
@@ -0,0 +1,11 @@
+--- hmmer/src/hmmc2.c.orig	2019-11-19 19:30:04 UTC
++++ hmmer/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);
diff --git a/biology/infernal/files/patch-src_Makefile.in b/biology/infernal/files/patch-src_Makefile.in
new file mode 100644
index 000000000000..7afaa0ab41ea
--- /dev/null
+++ b/biology/infernal/files/patch-src_Makefile.in
@@ -0,0 +1,19 @@
+--- src/Makefile.in.orig	2019-11-19 19:28:55 UTC
++++ src/Makefile.in
+@@ -27,6 +27,7 @@ CC             = @CC@
+ CFLAGS         = @CFLAGS@
+ PTHREAD_CFLAGS = @PTHREAD_CFLAGS@ 
+ PIC_CFLAGS     = @PIC_CFLAGS@
++SIMD_CFLAGS    = @SSE_CFLAGS@ @VMX_CFLAGS@
+ CPPFLAGS       = @CPPFLAGS@
+ LDFLAGS        = @LDFLAGS@
+ DEFS           = @DEFS@
+@@ -200,7 +201,7 @@ ${PROGS}: % : %.o libinfernal.a ../${HMM
+ 	${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${DEFS} ${LDFLAGS} ${MYLIBDIRS} -o $@ $@.o ${MPILIBS} ${LIBS}
+ 
+ .c.o:
+-	${QUIET_CC}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${DEFS} ${CPPFLAGS} ${MYINCDIRS} -o $@ -c $<
++	${QUIET_CC}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${MYINCDIRS} -o $@ -c $<
+ 
+ ${ITESTS}: % : %.o libinfernal.a ../${HMMERDIR}/src/libhmmer.a ../${ESLDIR}/libeasel.a ${HDRS} config.h
+ 	${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${DEFS} ${LDFLAGS} ${MYLIBDIRS} -o $@ $@.o ${MPILIBS} ${LIBS}