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Port details
crux Software toolkit for phylogenetic inference
1.2.0_9 biology Deleted 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 1.2.0Version of this port present on the latest quarterly branch.
Broken BROKEN: No public distfiles
Deprecated DEPRECATED: Broken for more than 6 months
Expired This port expired on: 2018-06-06
Ignore 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
search for ports maintained by this maintainer
Port Added: 2009-06-08 23:51:06
Last Update: 2018-06-07 01:34:18
SVN Revision: 471892
Also Listed In: python
License: BSD2CLAUSE BSD3CLAUSE
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (60 items)
  1. /usr/local/share/licenses/crux-1.2.0_9/catalog.mk
  2. /usr/local/share/licenses/crux-1.2.0_9/LICENSE
  3. /usr/local/share/licenses/crux-1.2.0_9/BSD2CLAUSE
  4. /usr/local/share/licenses/crux-1.2.0_9/BSD3CLAUSE
  5. bin/crux
  6. bin/redpoint
  7. bin/MrRogers
  8. lib/Crux/lib/libCx.so
  9. lib/Crux/parsers/Fasta.log
  10. lib/Crux/parsers/Fasta.pickle
  11. lib/python2.7/site-packages/Crux/CTMatrix.so
  12. lib/python2.7/site-packages/Crux/Character.so
  13. lib/python2.7/site-packages/Crux/Config.py
  14. @rmtry lib/python2.7/site-packages/Crux/Config.pyo
  15. lib/python2.7/site-packages/Crux/Copying.py
  16. @rmtry lib/python2.7/site-packages/Crux/Copying.pyo
  17. lib/python2.7/site-packages/Crux/DistMatrix/Nj.so
  18. lib/python2.7/site-packages/Crux/DistMatrix/__init__.py
  19. lib/python2.7/site-packages/Crux/DistMatrix/__init__.so
  20. lib/python2.7/site-packages/Crux/Fasta.so
  21. lib/python2.7/site-packages/Crux/Mc3/Chain.so
  22. lib/python2.7/site-packages/Crux/Mc3/Post.so
  23. lib/python2.7/site-packages/Crux/Mc3/__init__.py
  24. lib/python2.7/site-packages/Crux/Mc3/__init__.so
  25. lib/python2.7/site-packages/Crux/Newick.so
  26. lib/python2.7/site-packages/Crux/Taxa.so
  27. lib/python2.7/site-packages/Crux/Tree/Bipart.so
  28. lib/python2.7/site-packages/Crux/Tree/Lik.so
  29. lib/python2.7/site-packages/Crux/Tree/Sumt.so
  30. lib/python2.7/site-packages/Crux/Tree/__init__.py
  31. lib/python2.7/site-packages/Crux/Tree/__init__.so
  32. lib/python2.7/site-packages/Crux/include/Crux/CTMatrix.pxd
  33. lib/python2.7/site-packages/Crux/include/Crux/Character.pxd
  34. lib/python2.7/site-packages/Crux/include/Crux/Crux/CxMath.pxd
  35. lib/python2.7/site-packages/Crux/include/Crux/Crux/CxMat.pxd
  36. lib/python2.7/site-packages/Crux/include/Crux/Crux/CxNewickLexer.pxd
  37. lib/python2.7/site-packages/Crux/include/Crux/Crux/CxRi.pxd
  38. lib/python2.7/site-packages/Crux/include/Crux/Crux/Cx.pxd
  39. lib/python2.7/site-packages/Crux/include/Crux/Crux/DistMatrix/CxDistMatrixLexer.pxd
  40. lib/python2.7/site-packages/Crux/include/Crux/Crux/Tree/CxLik.pxd
  41. lib/python2.7/site-packages/Crux/include/Crux/DistMatrix/Nj.pxd
  42. lib/python2.7/site-packages/Crux/include/Crux/DistMatrix/__init__.pxd
  43. lib/python2.7/site-packages/Crux/include/Crux/Fasta.pxd
  44. lib/python2.7/site-packages/Crux/include/Crux/Mc3/Chain.pxd
  45. lib/python2.7/site-packages/Crux/include/Crux/Mc3/Post.pxd
  46. lib/python2.7/site-packages/Crux/include/Crux/Mc3/__init__.pxd
  47. lib/python2.7/site-packages/Crux/include/Crux/Newick.pxd
  48. lib/python2.7/site-packages/Crux/include/Crux/SFMT/SFMT.pxd
  49. lib/python2.7/site-packages/Crux/include/Crux/Taxa.pxd
  50. lib/python2.7/site-packages/Crux/include/Crux/Tree/Bipart.pxd
  51. lib/python2.7/site-packages/Crux/include/Crux/Tree/Lik.pxd
  52. lib/python2.7/site-packages/Crux/include/Crux/Tree/Sumt.pxd
  53. lib/python2.7/site-packages/Crux/include/Crux/Tree/__init__.pxd
  54. lib/python2.7/site-packages/Crux/include/Crux/__init__.pxd
  55. lib/python2.7/site-packages/Crux/include/Crux/libc.pxd
  56. lib/python2.7/site-packages/Crux/include/Crux/libm.pxd
  57. lib/python2.7/site-packages/Crux/include/Parsing.pxd
  58. lib/python2.7/site-packages/Crux/__init__.py
  59. lib/python2.7/site-packages/Crux/__init__.so
  60. lib/python2.7/site-packages/Parsing.so
Collapse this list.
Dependency lines:
  • crux>0:biology/crux
  • libCx.so:biology/crux
No installation instructions: this port has been deleted.
The package name of this deleted port was:
PKGNAME: crux
Flavors: there is no flavor information for this port.
distinfo:

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gfortran6 : lang/gcc6
  2. gmake : devel/gmake
  3. python2.7 : lang/python27
  4. as : devel/binutils
Runtime dependencies:
  1. gfortran6 : lang/gcc6
  2. python2.7 : lang/python27
There are no ports dependent upon this port

Configuration Options

USES:

Master Sites:
  1. http://www.canonware.com/download/Crux/
Port Moves
  • port deleted on 2018-06-07
    REASON: Has expired: Broken for more than 6 months

Number of commits found: 36

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
07 Jun 2018 00:34:18
Original commit files touched by this commit  1.2.0_9
Revision:471892
rene search for other commits by this committer
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 View all of this commit message)
05 May 2018 10:49:36
Original commit files touched by this commit  1.2.0_9
Revision:469100
antoine search for other commits by this committer
Deprecate ports broken for more than 6 months
10 Mar 2018 17:46:06
Original commit files touched by this commit  1.2.0_9
Revision:464084
gerald search for other commits by this committer
Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079).
30 Nov 2017 06:13:35
Original commit files touched by this commit  1.2.0_8
Revision:455167  Sanity Test Failure
linimon search for other commits by this committer
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
13 Oct 2017 11:14:53
Original commit files touched by this commit  1.2.0_8
Revision:451982  Sanity Test Failure
bapt search for other commits by this committer
Mark as broken ports with no public distfiles
10 Sep 2017 20:55:39
Original commit files touched by this commit  1.2.0_8
Revision:449591
gerald search for other commits by this committer
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
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: 36

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