git: 95b2e3a08855 - main - biology/infernal: Update to 1.1.4

The branch main has been updated by eduardo:

URL: https://cgit.FreeBSD.org/ports/commit/?id=95b2e3a08855793600b2587fc598eb23ef83f388

commit 95b2e3a08855793600b2587fc598eb23ef83f388
Author:     Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
AuthorDate: 2022-10-12 10:06:23 +0000
Commit:     Nuno Teixeira <eduardo@FreeBSD.org>
CommitDate: 2022-10-12 10:15:54 +0000

    biology/infernal: Update to 1.1.4
    
    ChangeLog:      http://eddylab.org/infernal/RELEASE-1.1.4.md
    PR:             266967
---
 biology/infernal/Makefile                      | 16 ++++++++--------
 biology/infernal/distinfo                      |  6 +++---
 biology/infernal/files/patch-hmmer_src_hmmc2.c | 11 -----------
 biology/infernal/files/patch-src_Makefile.in   | 19 -------------------
 4 files changed, 11 insertions(+), 41 deletions(-)

diff --git a/biology/infernal/Makefile b/biology/infernal/Makefile
index 528494dbb63a..af7f5630d313 100644
--- a/biology/infernal/Makefile
+++ b/biology/infernal/Makefile
@@ -1,5 +1,5 @@
 PORTNAME=	infernal
-PORTVERSION=	1.1.3
+PORTVERSION=	1.1.4
 CATEGORIES=	biology
 MASTER_SITES=	http://eddylab.org/infernal/
 
@@ -14,14 +14,14 @@ ONLY_FOR_ARCHS=	amd64 i386 powerpc powerpc64 powerpc64le powerpcspe
 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
 
@@ -34,14 +34,11 @@ 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
 
-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/*
 
@@ -53,4 +50,7 @@ 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/infernal/distinfo b/biology/infernal/distinfo
index 9f362448abc8..80865c942e66 100644
--- a/biology/infernal/distinfo
+++ b/biology/infernal/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1578660730
-SHA256 (infernal-1.1.3.tar.gz) = 3b98a6a3a0e7b01aa077a0caf1e958223c4d8f80a69a4eb602ca59a3475da85e
-SIZE (infernal-1.1.3.tar.gz) = 29910035
+TIMESTAMP = 1665487539
+SHA256 (infernal-1.1.4.tar.gz) = f9493c7dee9fbf25f6405706818883d24b9f5e455121a0662c96c8f0307f95fc
+SIZE (infernal-1.1.4.tar.gz) = 29499238
diff --git a/biology/infernal/files/patch-hmmer_src_hmmc2.c b/biology/infernal/files/patch-hmmer_src_hmmc2.c
deleted file mode 100644
index 5bd86cf55247..000000000000
--- a/biology/infernal/files/patch-hmmer_src_hmmc2.c
+++ /dev/null
@@ -1,11 +0,0 @@
---- 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
deleted file mode 100644
index 7afaa0ab41ea..000000000000
--- a/biology/infernal/files/patch-src_Makefile.in
+++ /dev/null
@@ -1,19 +0,0 @@
---- 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}