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Port details
treekin Efficient computation of RNA folding dynamics
0.5.1_6 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.5.1_4Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-06-15 20:37:22
Last Update: 2024-03-02 20:02:27
Commit Hash: 5c2b06d
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (5 items)
Collapse this list.
  1. bin/treekin
  2. share/man/man1/treekin.1.gz
  3. /usr/local/share/licenses/treekin-0.5.1_6/catalog.mk
  4. /usr/local/share/licenses/treekin-0.5.1_6/LICENSE
  5. /usr/local/share/licenses/treekin-0.5.1_6/LatticeLib
Collapse this list.
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):
treekin
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest0.5.1_60.5.1_60.5.1_20.5.1_60.5.1_6-0.5.1_2-
FreeBSD:13:quarterly0.5.1_50.5.1_5-0.5.1_50.5.1_5-0.5.1_50.5.1_5
FreeBSD:14:latest0.5.1_60.5.1_6-0.5.1_60.5.1_6---
FreeBSD:14:quarterly0.5.1_50.5.1_5-0.5.1_50.5.1_5-0.5.1_50.5.1_5
FreeBSD:15:latest0.5.1_60.5.1_6n/a0.5.1_5n/a-0.5.1_50.5.1_5
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. lapacke>0 : math/lapacke
  2. gfortran13 : lang/gcc13
  3. gmake>=4.3 : devel/gmake
  4. as : devel/binutils
Runtime dependencies:
  1. gfortran13 : lang/gcc13
Library dependencies:
  1. libblas.so : math/blas
  2. 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:
Expand this list (1 items)
Collapse this list.
  1. https://www.tbi.univie.ac.at/RNA/packages/source/
Collapse this list.

Number of commits found: 13

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
0.5.1_6
02 Mar 2024 20:02:27
commit hash: 5c2b06d5382d9bce11d5c7c4fce440823029e086commit hash: 5c2b06d5382d9bce11d5c7c4fce440823029e086commit hash: 5c2b06d5382d9bce11d5c7c4fce440823029e086commit hash: 5c2b06d5382d9bce11d5c7c4fce440823029e086 files touched by this commit
Nuno Teixeira (eduardo) search for other commits by this committer
biology/treekin: Move man pages to share/man

Approved by:	portmgr (blanket)
0.5.1_5
01 Jan 2024 11:49:51
commit hash: f2489ab0c721f5ec60a9f8074e904cfbe5d21dfdcommit hash: f2489ab0c721f5ec60a9f8074e904cfbe5d21dfdcommit hash: f2489ab0c721f5ec60a9f8074e904cfbe5d21dfdcommit hash: f2489ab0c721f5ec60a9f8074e904cfbe5d21dfd files touched by this commit
Thierry Thomas (thierry) search for other commits by this committer
*/*: chase the upgrade of BLAS / LAPACK to 3.12.0

PR:		275860
0.5.1_4
23 Apr 2023 09:09:58
commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b files touched by this commit
Gerald Pfeifer (gerald) search for other commits by this committer
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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 View all of this commit message)
0.5.1_3
15 Oct 2021 15:50:24
commit hash: c16b145a0f292e0aaf321c7b48681ccd63f7280bcommit hash: c16b145a0f292e0aaf321c7b48681ccd63f7280bcommit hash: c16b145a0f292e0aaf321c7b48681ccd63f7280bcommit hash: c16b145a0f292e0aaf321c7b48681ccd63f7280b files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/treekin: Unbreak

Recent Lapack API changes broke it.

PR:		259179
0.5.1_3
13 Jun 2021 17:48:12
commit hash: c2488a6020830af2cf09699b887adec7af806bf3commit hash: c2488a6020830af2cf09699b887adec7af806bf3commit hash: c2488a6020830af2cf09699b887adec7af806bf3commit hash: c2488a6020830af2cf09699b887adec7af806bf3 files touched by this commit
Thierry Thomas (thierry) search for other commits by this committer
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
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
0.5.1_2
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
0.5.1_2
30 Jan 2020 14:17:44
Revision:524642Original commit files touched by this commit
swills search for other commits by this committer
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
Revision:507372Original commit files touched by this commit
gerald search for other commits by this committer
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
Revision:506914Original commit files touched by this commit
pkubaj search for other commits by this committer
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
Revision:504268Original commit files touched by this commit
yuri search for other commits by this committer
New port: biology/treekin: Efficient computation of RNA folding dynamics

Number of commits found: 13