Package: methVisual

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch methVisual_1.9.0.tar.gz

StartedAt: 2012-06-21 01:38:11 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 01:40:33 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 142.4 seconds

RetCode: 1

Status:  ERROR

CheckDir: methVisual.Rcheck

Warnings: NA

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/methVisual.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'methVisual/DESCRIPTION' ... OK
* this is package 'methVisual' version '1.9.0'
* 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 'methVisual' can be installed ... OK
* checking installed package size ... 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 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... ERROR
Running examples in 'methVisual-Ex.R' failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: readBisulfFASTA
> ### Title: Read multiple FASTA file
> ### Aliases: readBisulfFASTA
> ### Keywords: graphs
> 
> ### ** Examples
> 
> ## In order to use the following example 
> ## make sure that you have writing permission under R.home()
> ## directory. If you do not have permission choose your own path. 
> dir.create(file.path(R.home(component="home"),"/BiqAnalyzer")) 
Warning in dir.create(file.path(R.home(component = "home"), "/BiqAnalyzer")) :
  '/Library/Frameworks/R.framework/Versions/2.15/Resources//BiqAnalyzer' already exists
> makeLocalExpDir(dataPath="/examples/BiqAnalyzer",
+ 	localDir=file.path(R.home(component="home"),"/BiqAnalyzer"))
[1] "seq_A.fasta"
[1] "seq_B.fasta"
[1] "seq_C.fasta"
[1] "seq_D.fasta"
[1] "seq_E.fasta"
[1] "seq_F.fasta"
[1] "seq_G.fasta"
[1] "seq_H.fasta"
[1] "seq_I.fasta"
[1] "seq_J.fasta"
          FILE
1  seq_A.fasta
2  seq_B.fasta
3  seq_C.fasta
4  seq_D.fasta
5  seq_E.fasta
6  seq_F.fasta
7  seq_G.fasta
8  seq_H.fasta
9  seq_I.fasta
10 seq_J.fasta
                                                                   PATH
1  /Library/Frameworks/R.framework/Versions/2.15/Resources//BiqAnalyzer
2  /Library/Frameworks/R.framework/Versions/2.15/Resources//BiqAnalyzer
3  /Library/Frameworks/R.framework/Versions/2.15/Resources//BiqAnalyzer
4  /Library/Frameworks/R.framework/Versions/2.15/Resources//BiqAnalyzer
5  /Library/Frameworks/R.framework/Versions/2.15/Resources//BiqAnalyzer
6  /Library/Frameworks/R.framework/Versions/2.15/Resources//BiqAnalyzer
7  /Library/Frameworks/R.framework/Versions/2.15/Resources//BiqAnalyzer
8  /Library/Frameworks/R.framework/Versions/2.15/Resources//BiqAnalyzer
9  /Library/Frameworks/R.framework/Versions/2.15/Resources//BiqAnalyzer
10 /Library/Frameworks/R.framework/Versions/2.15/Resources//BiqAnalyzer
> 
> 	readBisulfFASTA(sFileName=file.path(R.home(component="home"),"/BiqAnalyzer/multiFASTA.fasta"), sDirName= file.path(R.home(component="home"),"/BiqAnalyzer/"))
Error: 'readFASTA' is defunct.
Use 'readDNAStringSet' instead.
See help("Defunct")
Execution halted

* installing *source* package 'methVisual' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'methVisual.Rnw' 
** testing if installed package can be loaded

* DONE (methVisual)

name	user	system	elapsed
Cooccurrence	0.716	0.027	0.758
MethAlignNW	1.784	0.070	2.057
MethDataInput	0.056	0.022	0.107
MethLollipops	0.015	0.003	0.023
MethylQC	1.475	0.067	1.610
cgInAlign	0.003	0.001	0.005
cgMethFinder	0.001	0.000	0.001
coversionGenom	0	0	0
findNonAligned	0.003	0.002	0.005
heatMapMeth	0.102	0.007	0.109
makeDataMethGFF	0.205	0.010	0.249
makeLocalExpDir	0.041	0.018	0.066
makeTabFilePath	0.006	0.003	0.067
matrixSNP	0.331	0.011	0.352
methCA	0.019	0.004	0.138
methData	0.002	0.000	0.003
methFisherTest	0.034	0.002	0.037
methWhitneyUTest	0.007	0.001	0.010
plotAbsMethyl	0.004	0.002	0.006
plotMatrixSNP	0.714	0.016	0.752