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Port details
cruxSoftware toolkit for phylogenetic inference
1.2.0_9biologyΣ=0 1.2.0_9Version of this port present on the latest quarterly branch.
BROKEN: No public distfiles DEPRECATED: Broken for more than 6 months This port expired on: 2018-06-06 IGNORE: is marked as broken: No public distfiles
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
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/
===> The following configuration options are available for crux-1.2.0_9:
SYS_LINALG=off: Enable system ATLAS/LAPACK
===> Use 'make config' to modify these settings
Remove expired ports:
2018-06-06 biology/ssaha: Broken for more than 6 months
2018-06-06 biology/crux: Broken for more than 6 months
2018-06-06 biology/ariadne: Broken for more than 6 months
2018-06-06 cad/sceptre: Broken for more than 6 months
2018-06-06 cad/cider: Broken for more than 6 months
2018-06-06 chinese/scim-array: Broken for more than 6 months
2018-06-06 chinese/xpdf: Broken for more than 6 months
2018-06-06 chinese/telnet: Broken for more than 6 months
2018-06-06 comms/java-commapi-freebsd: Depends on BROKEN and expiring
comms/java-commapi
2018-06-06 comms/soundmodem: Broken for more than 6 months
2018-06-06 comms/jsdr: Broken for more than 6 months
2018-06-06 comms/java-commapi: Broken for more than 6 months
2018-06-06 converters/pdf2djvu: Broken for more than 6 months
2018-06-06 databases/rdb: Broken for more than 6 months
(Only the first 15 lines of the commit message are shown above )
For ports that are marked BROKEN on armv6, and also fail to build on
armv7, mark them so.
This is part two of a multipart commit to bring armv7 ports to parity
with armv6.
Approved by: portmgr (tier-2 blanket)
Obtained from: lonesome.com -exp run
Bump PORTREVISION for ports depending on the canonical version of GCC
(via Mk/bsd.default-versions.mk and lang/gcc) which has moved from
GCC 5.4 to GCC 6.4 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, c++11-lib, c++11-lang,
c++14-lang, c++0x, c11, or gcc-c++11-lib.
PR: 219275
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)
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
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
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.
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.
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)
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)
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)
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 )
- 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
