GeneticsDesign 1.5.0
Weiliang Qiu
| Snapshot Date: 2008-04-09 00:13:10 -0700 (Wed, 09 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneticsDesign | | Last Changed Rev: 29703 / Revision: 30951 | | Last Changed Date: 2008-01-25 12:40:16 -0800 (Fri, 25 Jan 2008) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | ERROR | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | ERROR | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | ERROR | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ ERROR ] | OK |
| pelham | Mac OS X Leopard (10.5.1) / i386 | OK | ERROR | OK |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.2-bioc/meat/GeneticsDesign.Rcheck'
* using R version 2.7.0 Under development (unstable) (2008-03-10 r44730)
* 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 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 R.css in E:/biocbld/bbs-2.2-bioc/meat/GeneticsDesign.Rcheck
---------- Making package GeneticsDesign ------------
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
installing R files
installing inst files
installing man source files
installing indices
installing help
Note: removing empty section \details
Note: removing empty section \details
>>> Building/Updating help pages for package 'GeneticsDesign'
Formats: text html latex example chm
GPC text html latex example chm
gregorius text html latex example chm
power.casectlr text html latex example chm
power.genotype.conti text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.2-bioc\meat\GeneticsDesign.Rcheck\00_pkg_src\GeneticsDesign\chm\GeneticsDesign.chm
Compile time: 0 minutes, 0 seconds
5 Topics
10 Local links
0 Internet links
1 Graphic
Created e:\biocbld\bbs-2.2-bioc\meat\GeneticsDesign.Rcheck\00_pkg_src\GeneticsDesign\chm\GeneticsDesign.chm, 26,999 bytes
Compression decreased file by 27 bytes.
adding MD5 sums
* DONE (GeneticsDesign)