| Port details on branch 2025Q4 |
- viennarna Alignment tools for the structural analysis of RNA
- 2.7.0_2 biology
 =0      2.7.0_2Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2025-10-18 20:51:07
- Last Update: 2025-10-18 20:48:08
- Commit Hash: 39dc312
- License: ViennaRNALicense
- WWW:
- https://www.tbi.univie.ac.at/RNA/
- https://github.com/ViennaRNA/ViennaRNA
- Description:
- The ViennaRNA Package consists of a C code library and several stand-alone
programs for the prediction and comparison of RNA secondary structures.
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).
  ¦  ¦  ¦  ¦ 
- Manual pages:
-
- pkg-plist: as obtained via:
make generate-plist - USE_RC_SUBR (Service Scripts)
- no SUBR information found for this port
- Dependency lines:
-
- viennarna>0:biology/viennarna
- Conflicts:
- CONFLICTS_INSTALL:
- To install the port:
- cd /usr/ports/biology/viennarna/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/viennarna
- pkg install viennarna
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: viennarna
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1730430067
SHA256 (ViennaRNA-2.7.0.tar.gz) = 9a99fd68ed380894defb4d5e6a8a2871629270028cdf7f16f0a05da6e8c71473
SIZE (ViennaRNA-2.7.0.tar.gz) = 53185587
No package information for this port in our database- Sometimes this happens. Not all ports have packages. Perhaps there is a build error. Check the fallout link:
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- bash : shells/bash
- lapacke>0 : math/lapacke
- libgd>0 : graphics/gd
- swig : devel/swig
- xxd : sysutils/xxd
- bison : devel/bison
- gfortran13 : lang/gcc13
- gmake>=4.4.1 : devel/gmake
- pkgconf>=1.3.0_1 : devel/pkgconf
- as : devel/binutils
- autoconf>=2.72 : devel/autoconf
- automake>=1.17 : devel/automake
- libtoolize : devel/libtool
- perl5>=5.42.r<5.43 : lang/perl5.42
- ice.pc : x11/libICE
- x11.pc : x11/libX11
- xext.pc : x11/libXext
- Runtime dependencies:
-
- gfortran13 : lang/gcc13
- perl5>=5.42.r<5.43 : lang/perl5.42
- ice.pc : x11/libICE
- x11.pc : x11/libX11
- xext.pc : x11/libXext
- indexinfo : print/indexinfo
- Library dependencies:
-
- libdlib.so : science/dlib-cpp
- libgmp.so : math/gmp
- libgsl.so : math/gsl
- liblapack.so : math/lapack
- libmpfr.so : math/mpfr
- There are no ports dependent upon this port
Configuration Options:- ===> The following configuration options are available for viennarna-2.7.0_2:
DOCS=on: Build and/or install documentation
EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
- Options name:
- biology_viennarna
- USES:
- autoreconf bison compiler:c++17-lang fortran gmake libtool localbase perl5 pkgconfig xorg
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Number of commits found: 1
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
2.7.0_2
18 Oct 2025 20:48:08
 |
Yuri Victorovich (yuri) |
biology/viennarna: Unbundle dlib, use port dependency instead
This should fix build.
(cherry picked from commit 042fe38f0395f73b4a9aa2db5c9f4815af33ac6a) |
Number of commits found: 1
|
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