dyebias 1.9.2
Philip Lijnzaad
| Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/dyebias | | Last Changed Rev: 53114 / Revision: 53255 | | Last Changed Date: 2011-02-23 08:48:36 -0800 (Wed, 23 Feb 2011) |
| lamb2 | Linux (openSUSE 11.2) / x86_64 | OK | ERROR | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | ERROR | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | ERROR | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | ERROR | OK |
| petty | Mac OS X Snow Leopard (10.6.4) / i386 | OK | [ ERROR ] | OK |
* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/dyebias.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'dyebias/DESCRIPTION' ... OK
* this is package 'dyebias' version '1.9.2'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'dyebias' 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 ... NOTE
Found the following CITATION file(s) in a non-standard place:
inst/doc/CITATION
Most likely inst/CITATION should be used instead.
* 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 ... NOTE
dyebias.apply.correction: no visible global function definition for
'maR<-'
dyebias.apply.correction: no visible global function definition for
'maG<-'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... ERROR
Running examples in 'dyebias-Ex.R' failed
The error most likely occurred in:
> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dyebias.monotonicity
> ### Title: Calculate the degree of monotonicity of the dye bias across the
> ### slides. DEPRACATED
> ### Aliases: dyebias.monotonicity
> ### Keywords: misc htest
>
> ### ** Examples
>
> ## Not run:
> ##D options(stringsAsFactors = FALSE)
> ##D
> ##D library(dyebias)
> ##D library(dyebiasexamples)
> ##D data(data.raw)
> ##D data(data.norm)
> ##D
> ##D ### obtain estimate for the iGSDBs:
> ##D iGSDBs.estimated <- dyebias.estimate.iGSDBs(data.norm,
> ##D is.balanced=TRUE,
> ##D verbose=FALSE)
> ##D
> ##D ### choose the estimators and which spots to correct:
> ##D estimator.subset <- dyebias.umcu.proper.estimators(maInfo(maGnames(data.norm)))
> ##D
> ##D application.subset <- maW(data.norm) == 1 &
> ##D dyebias.application.subset(data.raw=data.raw, use.background=TRUE)
> ##D
> ##D ### do the correction:
> ##D correction <- dyebias.apply.correction(data.norm=data.norm,
> ##D iGSDBs = iGSDBs.estimated,
> ##D estimator.subset=estimator.subset,
> ##D application.subset = application.subset,
> ##D verbose=FALSE)
> ##D
> ## End(Not run)
>
> cat("monotonicity before correction")
monotonicity before correction> monotonicity <- dyebias.monotonicity(data=data.norm,
+ iGSDBs=iGSDBs.estimated,
+ order=NULL)
Warning in dyebias.monotonicity(data = data.norm, iGSDBs = iGSDBs.estimated, :
dyebias.monotonicity: this function has been depracated
Warning in .monotonicity(data, iGSDBs, dyebias.percentile, order) :
.monotonicity: this function has been depracated
Error: object 'iGSDBs.estimated' not found
Execution halted
* installing *source* package 'dyebias' ...
** R
** inst
** preparing package for lazy loading
Loading required package: limma
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (dyebias)