Date: Sun, 16 Jul 2023 20:50:51 GMT From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: bb900f7c9a84 - main - =?utf-8?Q?biology/viennarna:=20Update=202.5.1=20=E2=86=92=202.6.2?= Message-ID: <202307162050.36GKoppi005925@gitrepo.freebsd.org>
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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
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