Update R-genetics to 1.3.4

genetics 1.3.4 - 2008-08-20
---------------------------

- Fix bug in makeGenotypes that caused it to ignore the 'sep' argument
  when determining which columns contain genotypes & add a corresponing
  regression test


genetics 1.3.3 - 2007-04-29
---------------------------

- Correct 'obsolete' use of '$'.  R no longer permits '$' to be used
  to extract named elements from vectors (just lists).

- Remove the power.casectl() function, which was based on invalid
  assumpations.  It has been marked depreciated.  Please use the
  functions in the Bioconductor package 'GeneticsDesign' instead.

genetics 1.3.2 - 2007-11-20
---------------------------

- Fix bug in handling of assignment of NA value(s) to elements of an
  existing genotype object.

- Fix warning messages from R CMD CHECK

- Correct documentation error by swapping definitions of kp and alpha
  arguments of power.casectl().

genetics 1.3.1
--------------

- fixes in genotypeOrder to ensure all genotype/haplotype combinations
  are used.

- genotypeOrder<- is now exported

genetics 1.3.0
--------------

- A note is now displayed on startup:

  The R-Genetics project has developed an set of enhanced genetics
  packages that will shortly replace 'genetics'. Please visit the
  project homepage at http://rgenetics.org for more information.

- binsearch() has been moved to the gtools package

- New function groupGenotype to create groups/levels based on genotype
  names

- Added some internal utility functions
  (.genotype2Haplotype, .genotype2Allele, and .matchGenotype)

- Genotype class gets additional slot genotypeOrder (and genotype()
  function gets additional argument with the same name) in order to enable
  predefined order of genotypes in other functions e.g. summary

- Added order, sort and %in% methods for genotype and haplotype classes.

- Fixed genotype() with allow.partial.missing=FALSE when 'alleles' argument
  is passed

- There is no more warning in genotype() if 'a1' or 'a2' have NA value(s)
  and 'alleles'' argument is specified, since NA is NA anyway

- Fixed documentation of power.casectrl()

- added gtools to Depends as needed by expectedGenotypes(); the latter now
  gives sorted genotypes according to order of given alleles

- print.HWE.test() wasn't displaying the observed vs expected genotype
  frequency table.  Fixed.

genetics 1.2.1
--------------

- Update Greg's email address

- Fixed a bug in function allele.number, as pointed out by Chris
  Wallace

2 files changed, 7 insertions, 7 deletions

diff --git a/math/R-genetics/Makefile b/math/R-genetics/Makefile
index a1e8e9287d0..9dc5b70b8ca 100644
--- a/math/R-genetics/Makefile
+++ b/math/R-genetics/Makefile
@@ -1,15 +1,15 @@
-# $NetBSD: Makefile,v 1.3 2006/07/02 13:19:53 markd Exp $
+# $NetBSD: Makefile,v 1.4 2008/10/14 07:38:26 markd Exp $
 #
 
 CATEGORIES=	math
 MASTER_SITES=	${MASTER_SITE_R_CRAN:=contrib/}
 
 MAINTAINER=	mchittur@cs.nmsu.edu
-HOMEPAGE=	${R_HOMEPAGE_BASE}/genetics.html
+HOMEPAGE=	${R_HOMEPAGE_BASE}/genetics/
 COMMENT=	Classes and methods for handling genetic data
 
 R_PKGNAME=	genetics
-R_PKGVER=	1.2.0
+R_PKGVER=	1.3.4
 
 DEPENDS+=	R-combinat>=0.0.6:../../math/R-combinat
 DEPENDS+=	R-gdata>=2.1.2:../../math/R-gdata
diff --git a/math/R-genetics/distinfo b/math/R-genetics/distinfo
index c7598b55504..a1656ed08d6 100644
--- a/math/R-genetics/distinfo
+++ b/math/R-genetics/distinfo
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.2 2006/07/02 13:19:53 markd Exp $
+$NetBSD: distinfo,v 1.3 2008/10/14 07:38:26 markd Exp $
 
-SHA1 (R/genetics_1.2.0.tar.gz) = 99d1f421cc8cfc48a45ec305ed24d336372d7661
-RMD160 (R/genetics_1.2.0.tar.gz) = 34522aa05594bb0e1b205dd44c1c9d0a48c82f49
-Size (R/genetics_1.2.0.tar.gz) = 202026 bytes
+SHA1 (R/genetics_1.3.4.tar.gz) = 7693c3523ec81b382866ca52c6e53a6c4614c9f5
+RMD160 (R/genetics_1.3.4.tar.gz) = eb46aad4aff41b48e31b2b5d60a0d34cd08af06d
+Size (R/genetics_1.3.4.tar.gz) = 235317 bytes