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Package 116/436HostnameOS / ArchBUILDCHECKBUILD BIN
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 

Summary

Package: dyebias
Version: 1.9.2
Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings dyebias_1.9.2.tar.gz
StartedAt: 2011-02-24 19:14:52 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 19:15:50 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 57.8 seconds
RetCode: 1
Status:  ERROR 
CheckDir: dyebias.Rcheck
Warnings: NA

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/dyebias.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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

dyebias.Rcheck/00install.out:

* 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)

dyebias.Rcheck/dyebias-Ex.timings:

nameusersystemelapsed
dyebias.application.subset9.5880.1409.838
dyebias.apply.correction10.465 0.08810.599
dyebias.boxplot10.700 0.08410.795
dyebias.estimate.iGSDBs2.8130.0082.819