Package: mBPCR

Version: 1.8.0

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch mBPCR_1.8.0.tar.gz

StartedAt: 2012-01-09 04:09:34 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 04:11:46 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 131.8 seconds

RetCode: 1

Status:  ERROR

CheckDir: mBPCR.Rcheck

Warnings: NA

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/mBPCR.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'mBPCR/DESCRIPTION' ... OK
* this is package 'mBPCR' version '1.8.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'mBPCR' can be installed ... OK
* checking installed package size ... 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 package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... ERROR
Running examples in 'mBPCR-Ex.R' failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotEstProfile
> ### Title: Plot the estimated profile of copy number data
> ### Aliases: plotEstProfile
> ### Keywords: hplot print
> 
> ### ** Examples
> 
> ##import the 10K data of cell line REC
> data(rec10k)
> ##estimation of chromosomes 3 and 5
> results <- estProfileWithMBPCR(rec10k$SNPname, rec10k$Chromosome, rec10k$PhysicalPosition, rec10k$log2ratio, chrToBeAnalyzed=c(3,5), maxProbeNumber=2000)
Estimation of global  parameters
Estimation of the profile of chromosome 3
Computation of log(A^0)
Computation of left and right recursions
Determination of PC Regression
Estimation of the profile of chromosome 5
Computation of log(A^0)
Computation of left and right recursions
Determination of PC Regression
> ##plot the corresponding estimated profiles
> plotEstProfile(sampleName='rec10k', rec10k$Chromosome, rec10k$PhysicalPosition, rec10k$log2ratio, chrToBePlotted=c(3,5), results$estPC, maxProbeNumber=2000)
Warning in x11() : Unable to open window
Warning in x11() : opening device failed
Error in x11() : unable to start windows() device
Calls: plotEstProfile -> x11
Execution halted

* installing *source* package 'mBPCR' ...
** R
** data
**  moving datasets to lazyload DB
** inst
** preparing package for lazy loading
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
Welcome to SNPchip version 1.18.1
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'mBPCR.Rnw' 
** testing if installed package can be loaded
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
Welcome to SNPchip version 1.18.1

* DONE (mBPCR)

name	user	system	elapsed
computeMBPCR	6.52	0.00	6.51
estGlobParam	0.01	0.00	0.02
estProfileWithMBPCR	11.93	0.00	11.98
estProfileWithMBPCRforOligoSnpSet	0	0	0
importCNData	0.07	0.01	0.10
logAdd	0	0	0