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 Wallacediff -r1.3 -r1.4 pkgsrc/math/R-genetics/Makefile
(markd)
@@ -1,19 +1,19 @@ | @@ -1,19 +1,19 @@ | |||
1 | # $NetBSD: Makefile,v 1.3 2006/07/02 13:19:53 markd Exp $ | 1 | # $NetBSD: Makefile,v 1.4 2008/10/14 07:38:26 markd Exp $ | |
2 | # | 2 | # | |
3 | 3 | |||
4 | CATEGORIES= math | 4 | CATEGORIES= math | |
5 | MASTER_SITES= ${MASTER_SITE_R_CRAN:=contrib/} | 5 | MASTER_SITES= ${MASTER_SITE_R_CRAN:=contrib/} | |
6 | 6 | |||
7 | MAINTAINER= mchittur@cs.nmsu.edu | 7 | MAINTAINER= mchittur@cs.nmsu.edu | |
8 | HOMEPAGE= ${R_HOMEPAGE_BASE}/genetics.html | 8 | HOMEPAGE= ${R_HOMEPAGE_BASE}/genetics/ | |
9 | COMMENT= Classes and methods for handling genetic data | 9 | COMMENT= Classes and methods for handling genetic data | |
10 | 10 | |||
11 | R_PKGNAME= genetics | 11 | R_PKGNAME= genetics | |
12 | R_PKGVER= 1.2.0 | 12 | R_PKGVER= 1.3.4 | |
13 | 13 | |||
14 | DEPENDS+= R-combinat>=0.0.6:../../math/R-combinat | 14 | DEPENDS+= R-combinat>=0.0.6:../../math/R-combinat | |
15 | DEPENDS+= R-gdata>=2.1.2:../../math/R-gdata | 15 | DEPENDS+= R-gdata>=2.1.2:../../math/R-gdata | |
16 | DEPENDS+= R-mvtnorm>=0.7.2:../../math/R-mvtnorm | 16 | DEPENDS+= R-mvtnorm>=0.7.2:../../math/R-mvtnorm | |
17 | 17 | |||
18 | .include "../../math/R/Makefile.extension" | 18 | .include "../../math/R/Makefile.extension" | |
19 | .include "../../mk/bsd.pkg.mk" | 19 | .include "../../mk/bsd.pkg.mk" |
@@ -1,5 +1,5 @@ | @@ -1,5 +1,5 @@ | |||
1 | $NetBSD: distinfo,v 1.2 2006/07/02 13:19:53 markd Exp $ | 1 | $NetBSD: distinfo,v 1.3 2008/10/14 07:38:26 markd Exp $ | |
2 | 2 | |||
3 | SHA1 (R/genetics_1.2.0.tar.gz) = 99d1f421cc8cfc48a45ec305ed24d336372d7661 | 3 | SHA1 (R/genetics_1.3.4.tar.gz) = 7693c3523ec81b382866ca52c6e53a6c4614c9f5 | |
4 | RMD160 (R/genetics_1.2.0.tar.gz) = 34522aa05594bb0e1b205dd44c1c9d0a48c82f49 | 4 | RMD160 (R/genetics_1.3.4.tar.gz) = eb46aad4aff41b48e31b2b5d60a0d34cd08af06d | |
5 | Size (R/genetics_1.2.0.tar.gz) = 202026 bytes | 5 | Size (R/genetics_1.3.4.tar.gz) = 235317 bytes |