git: 8e8bb4267860 - main - biology/infernal: update 1.1.4 → 1.1.5

The branch main has been updated by fernape:

URL: https://cgit.FreeBSD.org/ports/commit/?id=8e8bb42678606d55936e7602672c7a5a1deb1498

commit 8e8bb42678606d55936e7602672c7a5a1deb1498
Author:     Älven <alster@vinterdalen.se>
AuthorDate: 2025-01-29 10:56:37 +0000
Commit:     Fernando Apesteguía <fernape@FreeBSD.org>
CommitDate: 2025-01-30 07:35:31 +0000

    biology/infernal: update 1.1.4 → 1.1.5
    
    ChangeLog:
    https://github.com/EddyRivasLab/infernal/blob/master/release-notes/RELEASE-1.1.5.md
    
    PR:             283483
    Reported by:    alster@vinterdalen.se
    Approved by:    mzaki@e-mail.ne.jp (maintainer, timeout > 2 weeks)
---
 biology/infernal/Makefile  | 22 +++++++++++-----------
 biology/infernal/distinfo  |  6 +++---
 biology/infernal/pkg-plist |  3 +++
 3 files changed, 17 insertions(+), 14 deletions(-)

diff --git a/biology/infernal/Makefile b/biology/infernal/Makefile
index 74ed79a152b0..4e3e096bf7f6 100644
--- a/biology/infernal/Makefile
+++ b/biology/infernal/Makefile
@@ -1,12 +1,12 @@
 PORTNAME=	infernal
-PORTVERSION=	1.1.4
-PORTREVISION=	1
+DISTVERSION=	1.1.5
 CATEGORIES=	biology
 MASTER_SITES=	http://eddylab.org/infernal/
 
 MAINTAINER=	mzaki@e-mail.ne.jp
 COMMENT=	Search sequence databases for structural RNA homologs
-WWW=		http://eddylab.org/infernal/
+WWW=		http://eddylab.org/infernal/ \
+		https://github.com/EddyRivasLab/infernal/
 
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENSE
@@ -16,28 +16,28 @@ ONLY_FOR_ARCHS_REASON=	requires SSE2 or AltiVec instructions
 
 USES=		compiler:c11 gmake perl5 python:test shebangfix
 USE_PERL5=	test
+
 SHEBANG_FILES=	easel/devkit/*
 SHEBANG_GLOB=	*.pl *.py
 
 GNU_CONFIGURE=	yes
-GNU_CONFIGURE_MANPREFIX=${PREFIX}/share
-MAKE_ARGS=	V=1
 
+MAKE_ARGS=	V=1
 TEST_TARGET=	check
 
 OPTIONS_DEFINE=	DOCS EXAMPLES TEST
 
+TEST_BUILD_DEPENDS=	${PYTHON_VERSION}:lang/python${PYTHON_SUFFIX}
+TEST_VARS=	use_perl5=build
+
 DOCFILES=	Userguide.pdf
 EXAMPLES=	5S_rRNA.c.cm 5S_rRNA.sto \
-		Cobalamin.c.cm Cobalamin.fa Cobalamin.sto \
+		Cobalamin.c.cm Cobalamin.fa Cobalamin.sto Rfam.14.9.clanin \
 		metag-example.fa minifam-metag.out minifam.cm \
 		minifam.cm.i1f minifam.cm.i1i minifam.cm.i1m minifam.cm.i1p \
 		mrum-genome.fa mrum-tRNAs10.fa mrum-tRNAs10.out \
-		tRNA5-hand.c.cm tRNA5-hand.sto tRNA5-mrum.out \
-		tRNA5-noss.sto tRNA5.c.cm tRNA5.sto
-
-TEST_BUILD_DEPENDS=	${PYTHON_VERSION}:lang/python${PYTHON_SUFFIX}
-TEST_VARS=	use_perl5=build
+		tRNA5-hand.c.cm tRNA5-hand.frag.sto tRNA5-hand.fraggiven.sto \
+		tRNA5-hand.sto tRNA5-mrum.out tRNA5-noss.sto tRNA5.c.cm tRNA5.sto
 
 post-build-TEST-on:	pre-test do-test
 
diff --git a/biology/infernal/distinfo b/biology/infernal/distinfo
index 80865c942e66..71b26908f86e 100644
--- a/biology/infernal/distinfo
+++ b/biology/infernal/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1665487539
-SHA256 (infernal-1.1.4.tar.gz) = f9493c7dee9fbf25f6405706818883d24b9f5e455121a0662c96c8f0307f95fc
-SIZE (infernal-1.1.4.tar.gz) = 29499238
+TIMESTAMP = 1734834453
+SHA256 (infernal-1.1.5.tar.gz) = ad4ddae02f924ca7c85bc8c4a79c9f875af8df96aeb726702fa985cbe752497f
+SIZE (infernal-1.1.5.tar.gz) = 31300142
diff --git a/biology/infernal/pkg-plist b/biology/infernal/pkg-plist
index 9282b4f46c55..9df5582a1c80 100644
--- a/biology/infernal/pkg-plist
+++ b/biology/infernal/pkg-plist
@@ -25,6 +25,7 @@ share/man/man1/infernal.1.gz
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/Cobalamin.c.cm
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/Cobalamin.fa
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/Cobalamin.sto
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Rfam.14.9.clanin
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/metag-example.fa
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam-metag.out
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.cm
@@ -36,6 +37,8 @@ share/man/man1/infernal.1.gz
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mrum-tRNAs10.fa
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mrum-tRNAs10.out
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/tRNA5-hand.c.cm
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tRNA5-hand.frag.sto
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tRNA5-hand.fraggiven.sto
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/tRNA5-hand.sto
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/tRNA5-mrum.out
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/tRNA5-noss.sto