| Port details |
- hyphy Hypothesis testing using Phylogenies
- 2.3.14.16_2 biology
 =0    2.3.14.16Version of this port present on the latest quarterly branch.- Maintainer: jrm@FreeBSD.org
- Port Added: 2018-05-11 00:05:33
- Last Update: 2019-07-26 21:46:57
- SVN Revision: 507372
- License: MIT
- Description:
- HyPhy is an open-source software package for the analysis of genetic sequences
using techniques in phylogenetics, molecular evolution, and machine learning. It
features a rich scripting language for limitless customization of
analyses. Additionally, HyPhy features support for parallel computing
environments via message passing interface, MPI and it can be compiled as a
shared library and called from other programming environments such as Python and
R.
WWW: http://www.hyphy.org/
- SVNWeb : Homepage
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- To install the port:
cd /usr/ports/biology/hyphy/ && make install clean - To add the package:
pkg install hyphy - PKGNAME: hyphy
- Flavors: there is no flavor information for this port.
- ONLY_FOR_ARCHS: amd64 i386
- distinfo:
- TIMESTAMP = 1540036335
SHA256 (veg-hyphy-2.3.14-16-g3d88d3e6_GH0.tar.gz) = 459cd0a261ae5f31dc230847acbd294a4dc1e17fa69ef0c3db173c2b8808c826
SIZE (veg-hyphy-2.3.14-16-g3d88d3e6_GH0.tar.gz) = 8041349
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- cmake : devel/cmake
- ninja : devel/ninja
- Library dependencies:
-
- libcurl.so : ftp/curl
- There are no ports dependent upon this port
- Configuration Options
- No options to configure
- USES:
- compiler:c++14-lang cmake localbase:ldflags ssl
- Master Sites:
- https://codeload.github.com/veg/hyphy/tar.gz/2.3.14-16-g3d88d3e6?dummy=/
|
Number of commits found: 7
| Commit History - (may be incomplete: see SVNWeb link above for full details) |
| Date | By | Description |
26 Jul 2019 20:46:57
  2.3.14.16_2
|
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 |
25 Dec 2018 20:25:40
2.3.14.16_1
|
tcberner |
Change cmake default behaviour to outsource.
Ports that build out of source now simply can use "USES=cmake"
instead of "USES=cmake:outsource". Ports that fail to build
out of source now need to specify "USES=cmake:insource".
I tried to only set insource where explictely needed.
PR: 232038
Exp-run by: antoine |
12 Dec 2018 01:35:36
2.3.14.16_1
|
gerald |
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.
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, as a double check, everything INDEX-11 showed depending on lang/gcc7.
PR: 231590 |
20 Oct 2018 12:21:15
2.3.14.16
|
jrm |
biology/hyphy: Update to version 2.3.14.16
This pulls in fixes after the 2.3.14 release.
Upstream changes for version 2.3.14:
https://github.com/veg/hyphy/releases/tag/2.3.14
Subsequent fixes:
https://github.com/veg/hyphy/commit/1ecac31
https://github.com/veg/hyphy/commit/bec6833
https://github.com/veg/hyphy/commit/9847438
https://github.com/veg/hyphy/commit/02dcedd
https://github.com/veg/hyphy/commit/8f44d3c
https://github.com/veg/hyphy/commit/5297c30
https://github.com/veg/hyphy/commit/3d88d3e |
22 May 2018 22:55:18
2.3.13
|
jrm |
biology/hyphy: Update to version 2.3.13 |
14 May 2018 16:52:40
2.3.12_1
|
jrm |
biology/hyphy: Bump PORTREVISION after upstream rerolled release
Also, remove patch that upstream incorporated in new tarball.
Upstream issue: https://github.com/veg/hyphy/issues/796 |
11 May 2018 00:05:16
2.3.12
|
jrm |
New port, biology/hyphy: Hypothesis testing using Phylogenies
WWW: http://www.hyphy.org/ |
Number of commits found: 7
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| Latest Vulnerabilities |
|
8 vulnerabilities affecting 24 ports have been reported in the past 14 days
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* - modified, not new All vulnerabilities
Last updated:
2019-10-15 15:43:31
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