git: bb900f7c9a84 - main - biology/viennarna: Update 2.5.1 → 2.6.2

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From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Sun, 16 Jul 2023 20:50:51 UTC
The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=bb900f7c9a847717df9ed78f5e8ad47261a2921a

commit bb900f7c9a847717df9ed78f5e8ad47261a2921a
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2023-07-16 20:50:40 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2023-07-16 20:50:49 +0000

    biology/viennarna: Update 2.5.1 → 2.6.2
---
 biology/viennarna/Makefile  | 12 +++++++-----
 biology/viennarna/distinfo  |  6 +++---
 biology/viennarna/pkg-plist | 14 ++++++++++++++
 3 files changed, 24 insertions(+), 8 deletions(-)

diff --git a/biology/viennarna/Makefile b/biology/viennarna/Makefile
index b46cd561764d..d24e3125f5f2 100644
--- a/biology/viennarna/Makefile
+++ b/biology/viennarna/Makefile
@@ -1,12 +1,12 @@
 PORTNAME=	viennarna
-DISTVERSION=	2.5.1
+DISTVERSION=	2.6.2
 CATEGORIES=	biology
-MASTER_SITES=	https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_5_x/
+MASTER_SITES=	https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_6_x/
 DISTNAME=	ViennaRNA-${DISTVERSION}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Alignment tools for the structural analysis of RNA
-WWW=		https://github.com/s-will/LocARNA
+WWW=		https://www.tbi.univie.ac.at/RNA/
 
 LICENSE=	ViennaRNALicense
 LICENSE_NAME=	Vienna RNA License
@@ -17,9 +17,11 @@ BUILD_DEPENDS=	bash:shells/bash \
 		libgd>0:graphics/gd # for the static lib
 LIB_DEPENDS=	libgmp.so:math/gmp \
 		libgsl.so:math/gsl \
-		libmpfr.so:math/mpfr
+		liblapack.so:math/lapack \
+		libmpfr.so:math/mpfr \
+		libopenblas.so:math/openblas
 
-USES=		autoreconf compiler:c++11-lang gmake libtool localbase perl5 pkgconfig xorg # w/out autoreconf -lstdc++ is present in configure and Makefiles and this causes link failure
+USES=		autoreconf compiler:c++11-lang fortran gmake libtool localbase perl5 pkgconfig xorg # w/out autoreconf -lstdc++ is present in configure and Makefiles and this causes link failure
 USE_XORG=	x11 xext # only for build
 
 GNU_CONFIGURE=	yes
diff --git a/biology/viennarna/distinfo b/biology/viennarna/distinfo
index 2805208fdbc0..0c7dcfe112a6 100644
--- a/biology/viennarna/distinfo
+++ b/biology/viennarna/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1659253803
-SHA256 (ViennaRNA-2.5.1.tar.gz) = 05400437cf15595e10b1a25df6c9c48856f356130f9d1e380fa8866b6d27f457
-SIZE (ViennaRNA-2.5.1.tar.gz) = 58088049
+TIMESTAMP = 1689538729
+SHA256 (ViennaRNA-2.6.2.tar.gz) = 2ce1f69f4ff87e90f50e8de704e33db7818c7d2f0dfb427a08e0eafc9da9b627
+SIZE (ViennaRNA-2.6.2.tar.gz) = 62105677
diff --git a/biology/viennarna/pkg-plist b/biology/viennarna/pkg-plist
index d05270d41c73..8401e005621b 100644
--- a/biology/viennarna/pkg-plist
+++ b/biology/viennarna/pkg-plist
@@ -28,6 +28,7 @@ bin/RNApvmin
 bin/RNAsnoop
 bin/RNAsubopt
 bin/RNAup
+bin/RNAxplorer
 bin/b2ct
 bin/ct2db
 bin/kinwalker
@@ -58,18 +59,21 @@ include/ViennaRNA/constraints/basic.h
 include/ViennaRNA/constraints/hard.h
 include/ViennaRNA/constraints/ligand.h
 include/ViennaRNA/constraints/soft.h
+include/ViennaRNA/constraints/soft_special.h
 include/ViennaRNA/constraints_SHAPE.h
 include/ViennaRNA/constraints_hard.h
 include/ViennaRNA/constraints_ligand.h
 include/ViennaRNA/constraints_soft.h
 include/ViennaRNA/convert_epars.h
 include/ViennaRNA/data_structures.h
+include/ViennaRNA/datastructures/array.h
 include/ViennaRNA/datastructures/basic.h
 include/ViennaRNA/datastructures/char_stream.h
 include/ViennaRNA/datastructures/hash_tables.h
 include/ViennaRNA/datastructures/heap.h
 include/ViennaRNA/datastructures/lists.h
 include/ViennaRNA/datastructures/stream_output.h
+include/ViennaRNA/datastructures/string.h
 include/ViennaRNA/dist_vars.h
 include/ViennaRNA/dp_matrices.h
 include/ViennaRNA/duplex.h
@@ -107,6 +111,7 @@ include/ViennaRNA/loops/external.h
 include/ViennaRNA/loops/hairpin.h
 include/ViennaRNA/loops/internal.h
 include/ViennaRNA/loops/multibranch.h
+include/ViennaRNA/mconf.h
 include/ViennaRNA/mfe.h
 include/ViennaRNA/mfe_window.h
 include/ViennaRNA/mm.h
@@ -122,6 +127,7 @@ include/ViennaRNA/params/constants.h
 include/ViennaRNA/params/convert.h
 include/ViennaRNA/params/default.h
 include/ViennaRNA/params/io.h
+include/ViennaRNA/params/salt.h
 include/ViennaRNA/part_func.h
 include/ViennaRNA/part_func_co.h
 include/ViennaRNA/part_func_up.h
@@ -212,6 +218,7 @@ man/man1/RNApvmin.1.gz
 man/man1/RNAsnoop.1.gz
 man/man1/RNAsubopt.1.gz
 man/man1/RNAup.1.gz
+man/man1/RNAxplorer.1.gz
 man/man1/ct2db.1.gz
 man/man1/kinwalker.1.gz
 share/ViennaRNA/2Dlandscape.R
@@ -233,6 +240,13 @@ share/ViennaRNA/dna_mathews2004.par
 share/ViennaRNA/rna_andronescu2007.par
 share/ViennaRNA/rna_langdon2018.par
 share/ViennaRNA/rna_misc_special_hairpins.par
+share/ViennaRNA/rna_mod_7DA_parameters.json
+share/ViennaRNA/rna_mod_dihydrouridine_parameters.json
+share/ViennaRNA/rna_mod_inosine_parameters.json
+share/ViennaRNA/rna_mod_m6A_parameters.json
+share/ViennaRNA/rna_mod_pseudouridine_parameters.json
+share/ViennaRNA/rna_mod_purine_parameters.json
+share/ViennaRNA/rna_mod_template_parameters.json
 share/ViennaRNA/rna_turner1999.par
 share/ViennaRNA/rna_turner2004.par
 share/ViennaRNA/viennarna.bib