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pkgsrc/math/R-genetics/Makefile

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Updated to genetics v1.3.6, added LICENSE (commented) and updated MAINTAINER.
2012-04-15 18:54:17 +02:00
# $NetBSD: Makefile,v 1.5 2012/04/15 16:54:17 brook Exp $
Imported R-genetics from pkgsrc-wip. Classes and methods for handling genetic data. Includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium, ...
2005-11-04 09:13:15 +01:00
#
Update to version 1.2.0, add correct dependencies. Fixes build problem seen in bulk builds.
2006-07-02 15:19:53 +02:00
CATEGORIES= math
MASTER_SITES= ${MASTER_SITE_R_CRAN:=contrib/}
Imported R-genetics from pkgsrc-wip. Classes and methods for handling genetic data. Includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium, ...
2005-11-04 09:13:15 +01:00
Updated to genetics v1.3.6, added LICENSE (commented) and updated MAINTAINER.
2012-04-15 18:54:17 +02:00
MAINTAINER= pkgsrc-users@NetBSD.org
Update R-genetics to 1.3.4 genetics 1.3.4 - 2008-08-20 --------------------------- - Fix bug in makeGenotypes that caused it to ignore the 'sep' argument when determining which columns contain genotypes & add a corresponing regression test genetics 1.3.3 - 2007-04-29 --------------------------- - Correct 'obsolete' use of '$'. 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
2008-10-14 09:38:26 +02:00
HOMEPAGE= ${R_HOMEPAGE_BASE}/genetics/
Update to version 1.2.0, add correct dependencies. Fixes build problem seen in bulk builds.
2006-07-02 15:19:53 +02:00
COMMENT= Classes and methods for handling genetic data
Updated to genetics v1.3.6, added LICENSE (commented) and updated MAINTAINER.
2012-04-15 18:54:17 +02:00
# LICENSE= GPL (gnu-gpl-v?)
Imported R-genetics from pkgsrc-wip. Classes and methods for handling genetic data. Includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium, ...
2005-11-04 09:13:15 +01:00
Update to version 1.2.0, add correct dependencies. Fixes build problem seen in bulk builds.
2006-07-02 15:19:53 +02:00
R_PKGNAME= genetics
Updated to genetics v1.3.6, added LICENSE (commented) and updated MAINTAINER.
2012-04-15 18:54:17 +02:00
R_PKGVER= 1.3.6
Update to version 1.2.0, add correct dependencies. Fixes build problem seen in bulk builds.
2006-07-02 15:19:53 +02:00
Updated to genetics v1.3.6, added LICENSE (commented) and updated MAINTAINER.
2012-04-15 18:54:17 +02:00
DEPENDS+= R-combinat>=0.0.8:../../math/R-combinat
DEPENDS+= R-gdata>=2.8.2:../../math/R-gdata
DEPENDS+= R-gtools>=2.6.2:../../math/R-gtools
DEPENDS+= R-mvtnorm>=0.9.9992:../../math/R-mvtnorm
Imported R-genetics from pkgsrc-wip. Classes and methods for handling genetic data. Includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium, ...
2005-11-04 09:13:15 +01:00
.include "../../math/R/Makefile.extension"
.include "../../mk/bsd.pkg.mk"
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