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Port details
crux Software toolkit for phylogenetic inference
1.2.0_7 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

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 08 Jun 2009 23:51:06
Also Listed In: python
License: BSD2CLAUSE BSD3CLAUSE
Crux is a software toolkit for molecular phylogenetic inference. It is
structured as a set of Python modules, which makes it possible to quickly
develop Python scripts that perform unique, non-canned analyses. Features
include:
* Tree log-likelihoods can be computed under a variety of models,
  including all specializations of GTR+I+G and mixture models. Tree
  likelihoods can be computed in parallel via pthreads.
* Bayesian Markov chain Monte Carlo (MCMC) methods (with Metropolis
  coupling) can sample among non-nested models using reversible model
  jumps.
* Crux is capable of simulating character data under any model its
  likelihood engine is capable of.
* The neighbor joining (NJ) and relaxed neighbor joining (RNJ)
  implementations are among the fastest in existence.
* Pairwise distances between sequences can be computed based on percent
  identity, or using methods that correct for multiple hits
  (Jukes-Cantor, Kimura, and logDet).

WWW: http://www.canonware.com/Crux/
SVNWeb : Homepage : PortsMon

To install the port: cd /usr/ports/biology/crux/ && make install clean
To add the package: pkg install crux

PKGNAME: crux

distinfo:

SHA256 (crux-1.2.0.tar.bz2) = 11f677e8bf62db69e75271670ea50fb5a23c8a2c526fa9d16ccf2e736e5212c5
SIZE (crux-1.2.0.tar.bz2) = 1187274


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. gfortran5 : lang/gcc5
  2. gmake : devel/gmake
  3. python2.7 : lang/python27
  4. as : devel/binutils
Runtime dependencies:
  1. gfortran5 : lang/gcc5
  2. python2.7 : lang/python27
There are no ports dependent upon this port

Configuration Options
===> The following configuration options are available for crux-1.2.0_7:
     SYS_LINALG=off: Enable system ATLAS/LAPACK
===> Use 'make config' to modify these settings

USES:
fortran gmake python tar:bzip2

Master Sites:
  1. http://www.canonware.com/download/Crux/

Number of commits found: 30

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
26 May 2017 20:02:44
Original commit files touched by this commit  1.2.0_7
Revision:441814
linimon search for other commits by this committer
Mark some ports failing on armv6, for errors classified as "???".

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)
01 May 2017 19:24:01
Original commit files touched by this commit  1.2.0_7
Revision:439905
linimon search for other commits by this committer
Provide error messages for some ports failing on aarch64, and, in a
few cases, other tier-2 archs.

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)
01 Apr 2017 15:23:32
Original commit files touched by this commit  1.2.0_7
Revision:437439
gerald search for other commits by this committer
Bump PORTREVISIONs for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.9.4 to GCC 5.4 (at least under some
circumstances such as versions of FreeBSD or platforms).

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using using Mk/bsd.octave.mk which in turn has USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++14-lang,
   c++11-lang, c++0x, c11, or gcc-c++11-lib.

PR:		216707
07 Dec 2016 13:24:57
Original commit files touched by this commit  1.2.0_6
Revision:428057
gerald search for other commits by this committer
Bump PORTREVISIONS for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.8.5 to GCC 4.9.4 (at least under some
circumstances such as versions of FreeBSD or platforms), part II.

The first part covered  ports with USE_GCC=yes, USE_GCC=any, or one of
gcc-c++11-lib, openmp, nestedfct, c++11-lib as well as c++14-lang,
c++11-lang, c++0x, c11 requested via USES=compiler.

This adds ports with USES=fortran and ports using Mk/bsd.octave.mk
which in turn has USES=fortran.

PR:		214965
Reported by:	thierry
01 Apr 2016 13:29:17
Original commit files touched by this commit  1.2.0_5
Revision:412344
mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
30 Dec 2015 19:49:17
Original commit files touched by this commit  1.2.0_5
Revision:404876
marino search for other commits by this committer
biology/crux is not jobs safe

This cython-based port has failed on me a couple of times in a bulk build.
I'm not sure what the actual problem is but the issue is itermittent.
02 Sep 2015 09:23:06
Original commit files touched by this commit  1.2.0_5
Revision:395826
danfe search for other commits by this committer
Unbreak the build on PowerPC, it had nothing to do with "error in pthreads":
configure script was passing `-faltivec' to the compiler, while this flag is
non-standard and only supported on Mac OS X/Darwin systems.

Also replace Apple-specific Altivec detection with querying the "hw.altivec"
sysctl instead.
02 Sep 2015 03:04:10
Original commit files touched by this commit  1.2.0_5
Revision:395817
amdmi3 search for other commits by this committer
- Switch to options helpers
20 Oct 2014 07:10:48
Original commit files touched by this commit  1.2.0_5
Revision:371237
bapt search for other commits by this committer
Cleanup plist
10 Sep 2014 20:50:37
Original commit files touched by this commit  1.2.0_5
Revision:367888
gerald search for other commits by this committer
Update the default version of GCC in the Ports Collection from GCC 4.7.4
to GCC 4.8.3.

Part II, Bump PORTREVISIONs.

PR:		192025
Tested by:	antoine (-exp runs)
Approved by:	portmgr (implicit)
26 Aug 2014 20:39:05
Original commit files touched by this commit  1.2.0_4
Revision:366266
rene search for other commits by this committer
biology/crux: stage, modernize, add license (BSD[23]CLAUSE), cleanups

PR:		193026
Submitted by:	Ports Fury
29 Jul 2014 18:41:17
Original commit files touched by this commit  1.2.0_3
Revision:363371  Sanity Test Failure
adamw search for other commits by this committer
Convert a bunch of USE_BZIP2 to USES=tar:bzip2

Approved by:	portmgr (not really, but touches unstaged ports)
23 Jul 2014 16:44:28
Original commit files touched by this commit  1.2.0_3
Revision:362705
bapt search for other commits by this committer
Reset maintainership for ports not staged with no pending PR

With hat:	portmgr
10 Mar 2014 20:55:22
Original commit files touched by this commit  1.2.0_3
Revision:347809
gerald search for other commits by this committer
Update the default version of GCC used in the Ports Collection from
GCC 4.6.4 to GCC 4.7.3.  This entails updating the lang/gcc port as
well as changing the default in Mk/bsd.default-versions.mk.

Part II, Bump PORTREVISIONs.

PR:		182136
Supported by:	Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports)
Tested by:	bdrewery (two -exp runs)
16 Feb 2014 17:15:32
Original commit files touched by this commit  1.2.0_2
Revision:344614
tijl search for other commits by this committer
Convert all USE_FORTRAN=yes to "USES=fortran, USE_GCC=yes".  In most cases
USE_GCC=yes has been omitted though.

Remove USE_FORTRAN handling from bsd.port.mk and bsd.gcc.mk.

Minor cleanups in some ports like USE_GMAKE, NOPORTDOCS,...

Exp-run:	bdrewery
Approved by:	portmgr (bdrewery)
21 Jan 2014 23:18:05
Original commit files touched by this commit  1.2.0_2
Revision:340671
bapt search for other commits by this committer
Fix properties on pkg-plist
13 Jan 2014 21:00:04
Original commit files touched by this commit  1.2.0_2
Revision:339634
rene search for other commits by this committer
Python cleanup:
- USE_PYTHON* = 2.X -> USE_PYTHON* = 2
- USE_PYTHON* = 2.X+ -> USE_PYTHON* = yes
Reviewed by:	python (mva, rm)
Approved by:	portmgr-lurkers (mat)
11 Dec 2013 14:43:51
Original commit files touched by this commit  1.2.0_2
Revision:336171
bapt search for other commits by this committer
In preparation for making libtool generate libraries with a sane name, fix all
LIB_DEPENDS in biology
26 Oct 2013 00:52:36
Original commit files touched by this commit  1.2.0_2
Revision:331644
gerald search for other commits by this committer
Update to libmpc version 1.0.1 which brings the following fixes:

 - Switched to automake 1.11.6, see CVE-2012-3386.
 - #14669: Fixed extraction of CC from gmp.h.
 - Fixed case of intermediate zero real or imaginary part in mpc_fma,
   found by hydra with GMP_CHECK_RANDOMIZE=1346362345.

This is on top of the following changes from version 1.0

 - Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no
   invariant sections) for the documentation.
 - 100% of all lines are covered by tests
 - Renamed functions
   . mpc_mul_2exp to mpc_mul_2ui
   . mpc_div_2exp to mpc_div_2ui
(Only the first 15 lines of the commit message are shown above View all of this commit message)
20 Sep 2013 15:55:44
Original commit files touched by this commit  1.2.0_1
Revision:327709
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
18 Mar 2013 06:48:55
Original commit files touched by this commit  1.2.0_1
Revision:314529
jgh search for other commits by this committer
- adoption of optionsNG
- trim historical header
- use tabs in favor of spaces

Approved by:	portmgr (miwi)
10 Nov 2011 14:30:51
Original commit files touched by this commit  1.2.0_1
linimon search for other commits by this committer
Does not build on powerpc-9: error in pthreads.

Hat:            portmgr
Feature safe:   yes
23 Sep 2011 22:26:39
Original commit files touched by this commit  1.2.0_1
amdmi3 search for other commits by this committer
- Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS)
- Fix all ports that add {CPP,LD}FLAGS to *_ENV to modify flags instead

PR:             157936
Submitted by:   myself
Exp-runs by:    pav
Approved by:    pav
19 Mar 2011 12:38:54
Original commit files touched by this commit  1.2.0_1
miwi search for other commits by this committer
- Get Rid MD5 support
19 Sep 2009 17:58:14
Original commit files touched by this commit  1.2.0_1
jasone search for other commits by this committer
Update to Crux 1.2.0.

Feature safe:   yes
13 Sep 2009 00:08:01
Original commit files touched by this commit  1.1.0_1
gerald search for other commits by this committer
Bump PORTREVISION for everything that sets USE_FORTRAN=yes which now
implies lang/gcc44 up from lang/gcc43.

Approved by:    portmgr
08 Aug 2009 13:26:13
Original commit files touched by this commit  1.1.0
erwin search for other commits by this committer
Fix PKGORIGIN

Submitted by:   pointyhat
21 Jun 2009 06:18:51
Original commit files touched by this commit  1.1.0
jasone search for other commits by this committer
Update to Crux 1.1.0.

Fix the ATLAS/LAPACK build option.
10 Jun 2009 01:25:02
Original commit files touched by this commit  1.0.1
jasone search for other commits by this committer
Change CONFIGURE_ENV --> USE_CSTD. [1]

Add missing pkg-plist entry for Parsing.so. [2]

Change RUN_DEPENDS --> LIB_DEPENDS for optional math/atlas dependency.

Submitted by:   [1] erwin
Reported by:    [2] QAT
08 Jun 2009 23:49:59
Original commit files touched by this commit  1.0.1
jasone search for other commits by this committer
Add the biology/crux port.

Number of commits found: 30

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