| Port details |
- viennarna Alignment tools for the structural analysis of RNA
- 2.7.0_1 biology
 =2      2.7.0Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2019-06-24 09:29:23
- Last Update: 2025-01-24 12:18:28
- Commit Hash: 6cce1f5
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- 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:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - 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
Packages (timestamps in pop-ups are UTC):
- 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>=5.36<5.37 : lang/perl5.36
- ice.pc : x11/libICE
- x11.pc : x11/libX11
- xext.pc : x11/libXext
- Runtime dependencies:
-
- gfortran13 : lang/gcc13
- perl5>=5.36<5.37 : lang/perl5.36
- ice.pc : x11/libICE
- x11.pc : x11/libX11
- xext.pc : x11/libXext
- indexinfo : print/indexinfo
- Library dependencies:
-
- libgmp.so : math/gmp
- libgsl.so : math/gsl
- liblapack.so : math/lapack
- libmpfr.so : math/mpfr
- This port is required by:
- for Build
-
- biology/locarna
Configuration Options:- ===> The following configuration options are available for viennarna-2.7.0_1:
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:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
2.7.0_1
24 Jan 2025 12:18:28
 |
Thierry Thomas (thierry) |
*/*: bump PORTREVISION to chase blas/lapack, Suitesparse and BLIS |
2.7.0
02 Nov 2024 08:51:51
|
Yuri Victorovich (yuri) |
biology/viennarna: Broken on 15
Reported by: fallout |
2.7.0
01 Nov 2024 04:12:15
|
Yuri Victorovich (yuri) |
biology/viennarna: update 2.6.4 → 2.7.0 |
2.6.4_2
02 Mar 2024 20:35:56
|
Nuno Teixeira (eduardo) |
biology/viennarna: Move man pages to share/man
Approved by: portmgr (blanket) |
2.6.4_1
01 Jan 2024 11:49:51
|
Thierry Thomas (thierry) |
*/*: chase the upgrade of BLAS / LAPACK to 3.12.0
PR: 275860 |
2.6.4
03 Nov 2023 22:02:11
|
Yuri Victorovich (yuri) |
biology/viennarna: update 2.6.3 → 2.6.4 |
2.6.3
18 Aug 2023 06:57:13
|
Muhammad Moinur Rahman (bofh) |
biology/viennarna: Mark BROKEN on 14
Fails to compile with:
error: no member named 'bind2nd' in namespace 'std'
Approved by: portmgr (blanket)
Sponsored by: The FreeBSD Foundation |
2.6.3
22 Jul 2023 08:55:02
|
Yuri Victorovich (yuri) |
biology/viennarna: Update 2.6.2 → 2.6.3 |
2.6.2_1
16 Jul 2023 21:38:39
|
Yuri Victorovich (yuri) |
biology/viennarna: Remove unnecessary library from .pc file; Correct pkg-descr |
2.6.2
16 Jul 2023 20:50:49
|
Yuri Victorovich (yuri) |
biology/viennarna: Update 2.5.1 → 2.6.2 |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner) |
2.5.1
07 Sep 2022 21:10:59
|
Stefan Eßer (se) |
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above  ) |
2.5.1
31 Jul 2022 08:12:49
|
Yuri Victorovich (yuri) |
biology/viennarna: Update 2.5.0 -> 2.5.1
Also add test target. |
2.5.0
06 Feb 2022 18:36:07
|
Stefan Eßer (se) |
Update CONFLICTS definitions in categories a* to c*
Update the CONFLICTS definitions of ports in the following categories:
- accessibility
- archivers
- audio
- benchmarks
- biology
- cad
- chinese
- comms
- converters
An attempt has been made to use generic conflicts patterns that do not
have to be updated whenever a new version of a conflicting port is
added to the ports system.
There is a misunderstanding that the port being built/installed has to
be omitted from the conflicts pattern. This is not true - the port
being built is implicitly non-conflicting due to logic in bsd.port.mk.
Approved by: portmgr (implicit) |
2.5.0
25 Jan 2022 05:44:21
|
Yuri Victorovich (yuri) |
biology/viennarna: Update 2.4.18 -> 2.5.0 |
2.4.18_2
12 Jan 2022 19:41:22
|
Tobias C. Berner (tcberner) |
math/gsl: bump portrevision of consumers after update to 2.7.1
PR: 260201 |
2.4.18_1
16 Jun 2021 19:31:27
|
Tobias C. Berner (tcberner) |
math/gsl: update to 2.7
From [1]
* What is new in gsl-2.7:
* fixed doc bug for gsl_histogram_min_bin (lhcsky at 163.com)
* fixed bug #60335 (spmatrix test failure, J. Lamb)
* fixed bug #36577
* clarified documentation on interpolation accelerators (V. Krishnan)
* fixed bug #45521 (erroneous GSL_ERROR_NULL in ode-initval2, thanks to M.
Sitte)
* fixed doc bug #59758
* fixed bug #58202 (rstat median for n=5)
* added support for native C complex number types in gsl_complex
when using a C11 compiler
* upgraded to autoconf 2.71, automake 1.16.3, libtool 2.4.6 (Only the first 15 lines of the commit message are shown above ) |
2.4.18
24 Apr 2021 01:57:38
|
Yuri Victorovich (yuri) |
biology/viennarna: Update 2.4.17 -> 2.4.18 |
2.4.17
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
2.4.17
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
2.4.17
06 Dec 2020 20:14:53
 |
yuri |
biology/viennarna: Update 2.4.16 -> 2.4.17 |
2.4.16
11 Nov 2020 23:27:39
|
yuri |
biology/viennarna: Update 2.4.15 -> 2.4.16 |
2.4.15
07 Sep 2020 21:49:08
|
yuri |
biology/viennarna: Update 2.4.14 -> 2.4.15 |
2.4.14_1
04 May 2020 21:31:39
|
dinoex |
- update libgd to 2.3.0
- new option RAQM
- resurrect deprecated gdlib-config
- bump dependend ports |
2.4.14
06 Jan 2020 04:17:49
|
yuri |
biology/viennarna: Update 2.4.13 -> 2.4.14
Reported by: repology |
2.4.13_2
04 Nov 2019 21:08:20
|
zeising |
Add USES=xorg USES=gl, ports categories b
Add USES=xorg, USES=gl and in a few cases USES=gnome to ports in categories
starting with 'b'. |
2.4.13_2
25 Oct 2019 23:41:34
|
tcberner |
math/gsl: update to 2.6
- math/p5-Math-GSL does not seem to have any upstream activity to make it work
with this version -> mark it broken
- this also breaks the two consumers of this port
- biology/gemma: has a conflict with cblas, and is makred broken.
PR: 241363
Exp-run by: antoine |
2.4.13_1
26 Jul 2019 20:46:57
|
gerald |
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.
This includes ports
- with USE_GCC=yes or USE_GCC=any,
- with USES=fortran,
- using Mk/bsd.octave.mk which in turn features USES=fortran, and
- with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.
PR: 238330 |
2.4.13
24 Jun 2019 19:30:15
|
yuri |
biology/viennarna: Make it less/not prone to failures due to hardcoded C++
library name
configure and Makefile.in provided in tarballs have -lstdc++ hard-coded in them.
The previous version of the port patches these to be -lc++, which still might
fail on gcc systems, depending on which C++ library is used.
This change adds USES=autoreconf which makes it to regenerate configure and
Makefile.in and hopefully have the proper C++ library in these files.
GNU libtool links with the C compiler, not with the C++ compiler, in this
project. This is what I think triggers link failures due to a wrong C++
library getting into the link lines. GNU libtool likely chooses C compiler
because this project has its 'main' functions in .c files,
but also includes C++ object modules. This likely causes GNU tools confusion and
it uses the C compiler to link and fails due to wrong C++ libraries added there. |
2.4.13
24 Jun 2019 09:29:05
|
yuri |
New port: biology/viennarna: Alignment tools for the structural analysis of RNA |
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