| Port details |
- treekin Efficient computation of RNA folding dynamics
- 0.5.1_7 biology
 =2      0.5.1_6Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2019-06-15 20:37:22
- 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: LatticeLib
- WWW:
- https://www.tbi.univie.ac.at/RNA/Treekin/
- Description:
- treekin computes folding dynamics on coarse grained version of an energy
landscape, where all conformations belonging to the same local minimum have
been contracted into a single macro-state.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- treekin>0:biology/treekin
- To install the port:
- cd /usr/ports/biology/treekin/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/treekin
- pkg install treekin
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: treekin
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1560629735
SHA256 (Treekin-0.5.1.tar.gz) = aae56c1a746829b02a9b97c6a54d1d58348718d4ca585ef41a5dbdd41d5c9f06
SIZE (Treekin-0.5.1.tar.gz) = 222232
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:
-
- lapacke>0 : math/lapacke
- gfortran13 : lang/gcc13
- gmake>=4.4.1 : devel/gmake
- as : devel/binutils
- Runtime dependencies:
-
- gfortran13 : lang/gcc13
- Library dependencies:
-
- libblas.so : math/blas
- liblapack.so : math/lapack
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_treekin
- USES:
- blaslapack:netlib compiler:c++11-lang fortran gmake localbase:ldflags
- 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 |
|---|
0.5.1_7
24 Jan 2025 12:18:28
 |
Thierry Thomas (thierry) |
*/*: bump PORTREVISION to chase blas/lapack, Suitesparse and BLIS |
0.5.1_6
02 Mar 2024 20:02:27
|
Nuno Teixeira (eduardo) |
biology/treekin: Move man pages to share/man
Approved by: portmgr (blanket) |
0.5.1_5
01 Jan 2024 11:49:51
|
Thierry Thomas (thierry) |
*/*: chase the upgrade of BLAS / LAPACK to 3.12.0
PR: 275860 |
0.5.1_4
23 Apr 2023 09:09:58
|
Gerald Pfeifer (gerald) |
*: Bump PORTREVISIONs for math/mpc update to 1.3.1 |
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) |
0.5.1_3
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  ) |
0.5.1_3
15 Oct 2021 15:50:24
|
Yuri Victorovich (yuri) |
biology/treekin: Unbreak
Recent Lapack API changes broke it.
PR: 259179 |
0.5.1_3
13 Jun 2021 17:48:12
|
Thierry Thomas (thierry) |
math/lapack: +math/blas et al., upgrade to 3.9.1
- Upgrade math/blas, math/cblas, math/lapack, math/lapacke and math/xlapack
to 3.9.1;
Latest release notes at <http://www.netlib.org/lapack/lapack-3.9.1.html>
- Chase this upgrade in biology/treekin;
- Add a test target;
- Remove a conflict with math/openblas (PR 244296);
- Fix the build with Gcc10 (PR 247485).
PR: 247542
Approved by: expr-run by antoine@ |
0.5.1_2
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
0.5.1_2
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
0.5.1_2
30 Jan 2020 14:17:44
 |
swills |
Fix math/openblas and bump dependent ports
* Fix build on i386 [1]
* Fix science/code_saturne build with new openblas [2]
* Avoid installing private headers [3]
* Prevent build from optimizing for host by correcting build confg [4]
* Bump portrevision of dependent ports [5]
This is correcting issues from r523749 [1][2][4] and r515970 [3]
PR: 231371
Reported by: build cluster [1]
Reported by: Dima Pasechnik <dimpase+freebsd@gmail.com> [2]
Reported by: many [5]
Reviewed by: mat, bapt
Approved by: implicit, since this is a build fix |
0.5.1_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 |
0.5.1
19 Jul 2019 08:49:33
|
pkubaj |
biology/treekin: fix build on GCC architectures
Needs C++11 compiler:
configure: error: *** A compiler with support for C++11 language features is
required.
Approved by: mentors (implicit approval) |
0.5.1
15 Jun 2019 20:37:06
|
yuri |
New port: biology/treekin: Efficient computation of RNA folding dynamics |
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