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author | markd <markd@pkgsrc.org> | 2008-10-14 07:38:26 +0000 |
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committer | markd <markd@pkgsrc.org> | 2008-10-14 07:38:26 +0000 |
commit | 2a3185ac70b9ad5cf8cc9dc2aa26f9446d12bbe8 (patch) | |
tree | 0437b06fb8aa69c3ba84861b36b8805057530a9b /math | |
parent | c90557575b82fd5f654324ee5e0c3370e992e6f7 (diff) | |
download | pkgsrc-2a3185ac70b9ad5cf8cc9dc2aa26f9446d12bbe8.tar.gz |
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
Diffstat (limited to 'math')
-rw-r--r-- | math/R-genetics/Makefile | 6 | ||||
-rw-r--r-- | math/R-genetics/distinfo | 8 |
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 |