git: 3e4f91e805a3 - main - biology/viennarna: Remove unnecessary library from .pc file; Correct pkg-descr

The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=3e4f91e805a3663672f9efdae1d4bb5b44d0c81a

commit 3e4f91e805a3663672f9efdae1d4bb5b44d0c81a
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2023-07-16 21:38:39 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2023-07-16 21:38:39 +0000

    biology/viennarna: Remove unnecessary library from .pc file; Correct pkg-descr
---
 biology/viennarna/Makefile                         |  4 ++++
 .../viennarna/files/patch-RNA-Tutorial_Makefile.am |  4 ++--
 biology/viennarna/pkg-descr                        | 25 +++++++++++-----------
 3 files changed, 19 insertions(+), 14 deletions(-)

diff --git a/biology/viennarna/Makefile b/biology/viennarna/Makefile
index d24e3125f5f2..fbf0bae747ed 100644
--- a/biology/viennarna/Makefile
+++ b/biology/viennarna/Makefile
@@ -1,5 +1,6 @@
 PORTNAME=	viennarna
 DISTVERSION=	2.6.2
+PORTREVISION=	1
 CATEGORIES=	biology
 MASTER_SITES=	https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_6_x/
 DISTNAME=	ViennaRNA-${DISTVERSION}
@@ -43,4 +44,7 @@ OPTIONS_DEFINE=	DOCS EXAMPLES
 PORTDOCS=	*
 PORTEXAMPLES=	*
 
+post-configure: # remove -lstdc++ from .pc file
+	@${REINPLACE_CMD} -e 's| -lstdc++||' ${WRKSRC}/RNAlib2.pc
+
 .include <bsd.port.mk>
diff --git a/biology/viennarna/files/patch-RNA-Tutorial_Makefile.am b/biology/viennarna/files/patch-RNA-Tutorial_Makefile.am
index 170cccfc6eb7..8857bf17c682 100644
--- a/biology/viennarna/files/patch-RNA-Tutorial_Makefile.am
+++ b/biology/viennarna/files/patch-RNA-Tutorial_Makefile.am
@@ -1,6 +1,6 @@
---- RNA-Tutorial/Makefile.am.orig	2019-06-24 18:48:09 UTC
+--- RNA-Tutorial/Makefile.am.orig	2020-11-23 22:41:05 UTC
 +++ RNA-Tutorial/Makefile.am
-@@ -95,7 +95,7 @@ vrna_htmltutorial_uninst:
+@@ -90,7 +90,7 @@ vrna_htmltutorial_uninst:
  
  if WITH_TUTORIAL_PDF
  
diff --git a/biology/viennarna/pkg-descr b/biology/viennarna/pkg-descr
index dd5376f2a390..acceb30f5685 100644
--- a/biology/viennarna/pkg-descr
+++ b/biology/viennarna/pkg-descr
@@ -1,13 +1,14 @@
-LocARNA is a collection of alignment tools for the structural analysis of RNA.
-Given a set of RNA sequences, LocARNA simultaneously aligns and predicts common
-structures for your RNAs. In this way, LocARNA performs Sankoff-like alignment
-and is in particular suited for analyzing sets of related RNAs without known
-common structure.
+The ViennaRNA Package consists of a C code library and several stand-alone
+programs for the prediction and comparison of RNA secondary structures.
 
-LocARNA distinguishes itself from many other Sankoff-style multiple alignment
-programs by its performance and low memory complexity, high accuracy, and
-richness of features. As unique features, it offers structure-local alignment,
-flexible structure and anchor constraints, and provides efficient computation of
-reliabilities in sequence-structure alignment. The package offers a robust core
-of features and is used as experimental platform for the incorporation of new
-features in RNA sequence-structure alignment.
+RNA secondary structure prediction through energy minimization is the most used
+function in the package. We provide three kinds of dynamic programming
+algorithms for structure prediction: the minimum free energy algorithm of
+(Zuker & Stiegler 1981) which yields a single optimal structure, the partition
+function algorithm of (McCaskill 1990) which calculates base pair probabilities
+in the thermodynamic ensemble, and the suboptimal folding algorithm of (Wuchty
+et.al 1999) which generates all suboptimal structures within a given energy
+range of the optimal energy. For secondary structure comparison, the package
+contains several measures of distance (dissimilarities) using either string
+alignment or tree-editing (Shapiro & Zhang 1990). Finally, we provide an
+algorithm to design sequences with a predefined structure (inverse folding).