Package: GeneticsDesign

Version: 1.5.0

Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check GeneticsDesign_1.5.0.tar.gz

StartedAt: 2008-04-09 07:48:23 -0700 (Wed, 09 Apr 2008)

EndedAt: 2008-04-09 07:48:58 -0700 (Wed, 09 Apr 2008)

EllapsedTime: 34.6 seconds

RetCode: 1

Status: ERROR

CheckDir: GeneticsDesign.Rcheck

Warnings: NA

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.2-bioc/meat/GeneticsDesign.Rcheck'
* using R version 2.7.0 beta (2008-04-07 r45159)
* using session charset: ISO8859-1
* checking for file 'GeneticsDesign/DESCRIPTION' ... OK
* this is package 'GeneticsDesign' version '1.5.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GeneticsDesign' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating GeneticsDesign-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'GeneticsDesign-Ex.R' failed.
The error most likely occurred in:

> ### * power.casectlr
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: power.casectrl
> ### Title: Power for case-control genetics study
> ### Aliases: power.casectrl
> ### Keywords: design
> 
> ### ** Examples
> 
> 
> # single calc
> power.casectrl(p=0.1, N=50, gamma=1.1, kp=.1, alpha=5e-2, minh='r')
Warning: 'power.casectrl' is deprecated.
Use 'GPC', 'GeneticPower.Quantitative.Factor', or 'GeneticPower.Quantitative.Numeric' instead.
See help("Deprecated")
> 
> # for a range of sample sizes
> power.casectrl(p=0.1, N=c(25,50,100,200,500), gamma=1.1, kp=.1,
+               alpha=5e-2, minh='r')
Warning: 'power.casectrl' is deprecated.
Use 'GPC', 'GeneticPower.Quantitative.Factor', or 'GeneticPower.Quantitative.Numeric' instead.
See help("Deprecated")
> 
> # create a power table
> fun <- function(p)
+   power.casectrl(p=p, N=seq(100,1000,by=100), gamma=1.1, kp=.1,
+                 alpha=5e-2, minh='recessive')
> 
> m <- sapply( X=seq(0.1,0.9, by=0.1), fun )
Warning: 'power.casectrl' is deprecated.
Use 'GPC', 'GeneticPower.Quantitative.Factor', or 'GeneticPower.Quantitative.Numeric' instead.
See help("Deprecated")
Warning: 'power.casectrl' is deprecated.
Use 'GPC', 'GeneticPower.Quantitative.Factor', or 'GeneticPower.Quantitative.Numeric' instead.
See help("Deprecated")
Warning: 'power.casectrl' is deprecated.
Use 'GPC', 'GeneticPower.Quantitative.Factor', or 'GeneticPower.Quantitative.Numeric' instead.
See help("Deprecated")
Warning: 'power.casectrl' is deprecated.
Use 'GPC', 'GeneticPower.Quantitative.Factor', or 'GeneticPower.Quantitative.Numeric' instead.
See help("Deprecated")
Warning: 'power.casectrl' is deprecated.
Use 'GPC', 'GeneticPower.Quantitative.Factor', or 'GeneticPower.Quantitative.Numeric' instead.
See help("Deprecated")
Warning: 'power.casectrl' is deprecated.
Use 'GPC', 'GeneticPower.Quantitative.Factor', or 'GeneticPower.Quantitative.Numeric' instead.
See help("Deprecated")
Warning: 'power.casectrl' is deprecated.
Use 'GPC', 'GeneticPower.Quantitative.Factor', or 'GeneticPower.Quantitative.Numeric' instead.
See help("Deprecated")
Warning: 'power.casectrl' is deprecated.
Use 'GPC', 'GeneticPower.Quantitative.Factor', or 'GeneticPower.Quantitative.Numeric' instead.
See help("Deprecated")
Warning: 'power.casectrl' is deprecated.
Use 'GPC', 'GeneticPower.Quantitative.Factor', or 'GeneticPower.Quantitative.Numeric' instead.
See help("Deprecated")
> colnames(m) <- seq(0.1,0.9, by=0.1)
Error in `colnames<-`(`*tmp*`, value = c(0.1, 0.2, 0.3, 0.4, 0.5, 0.6,  : 
  attempt to set colnames on object with less than two dimensions
Execution halted

* Installing *source* package 'GeneticsDesign' ...
** R
** inst
** help
Note: removing empty section \details
 >>> Building/Updating help pages for package 'GeneticsDesign'
     Formats: text html latex example 
  GPC                               text    html    latex   example
  gregorius                         text    html    latex   example
  power.casectlr                    text    html    latex   example
  power.genotype.conti              text    html    latex   example
** building package indices ...
* DONE (GeneticsDesign)