Package: a4Base

Version: 1.2.1

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch a4Base_1.2.1.tar.gz

StartedAt: 2012-01-09 01:31:43 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 01:35:48 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 244.3 seconds

RetCode: 1

Status:  ERROR

CheckDir: a4Base.Rcheck

Warnings: NA

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/a4Base.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 'a4Base/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'a4Base' version '1.2.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  'gridSVG' 'JavaGD'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'a4Base' 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 ... NOTE
plotLogRatio: no visible global function definition for 'JavaGD'
plotLogRatio: no visible global function definition for 'grid.garnish'
plotLogRatio: no visible global function definition for
  'grid.hyperlink'
plotLogRatio: no visible global function definition for 'grid.script'
plotLogRatio: no visible global function definition for 'gridToSVG'
* 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 ... NOTE
'library' or 'require' call not declared from: 'nlcv'
* 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 'a4Base-Ex.R' failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotLogRatio
> ### Title: Plot a summary gene expression graph
> ### Aliases: plotLogRatio
> ### Keywords: hplot
> 
> ### ** Examples
> 
> if (require(ALL)){
+   data(ALL, package = "ALL")
+   ALL <- addGeneInfo(ALL)
+   ALL$BTtype <- as.factor(substr(ALL$BT,0,1))
+   ALL2 <- ALL[,ALL$BT != 'T1']  # omit subtype T1 as it only contains one sample
+   ALL2$BTtype <- as.factor(substr(ALL2$BT,0,1)) # create a vector with only T and B
+ 
+   # Test for differential expression between B and T cells
+   tTestResult <- tTest(ALL, "BTtype", probe2gene = FALSE)
+   topGenes <- rownames(tTestResult)[1:20]
+ 
+   # plot the log ratios versus subtype B of the top genes 
+   LogRatioALL <- computeLogRatio(ALL2, reference=list(var='BT',level='B'))
+   a <- plotLogRatio(e=LogRatioALL[topGenes,],openFile=FALSE, tooltipvalues=FALSE, device='X11',
+       colorsColumnsBy=c('BTtype'), main = 'Top 20 genes most differentially between T- and B-cells',
+       orderBy = list(rows = "hclust"), probe2gene = TRUE)
+ }
Loading required package: ALL
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db
Warning in x11(width = 3 + (nc * exp.width), height = nr * exp.height, ...) :
  Unable to open window
Warning in x11(width = 3 + (nc * exp.width), height = nr * exp.height, ...) :
  opening device failed
Error in x11(width = 3 + (nc * exp.width), height = nr * exp.height, ...) : 
  unable to start windows() device
Calls: plotLogRatio -> x11
Execution halted

* installing *source* package 'a4Base' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'head' when loading 'utils'
Warning: replacing previous import 'tail' when loading 'utils'
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Warning messages:
1: replacing previous import 'head' when loading 'utils' 
2: replacing previous import 'tail' when loading 'utils' 

* DONE (a4Base)

name	user	system	elapsed
a4palette	0.03	0.00	0.03
addQuantilesColors	3.81	0.05	3.89
boxPlot	3.82	0.09	3.90
combineTwoExpressionSet	0	0	0
computeLogRatio	10.86	0.11	11.72
createExpressionSet	0.32	0.00	0.33
filterVarInt	3.13	0.07	3.20
heatmap.expressionSet	0	0	0
histPvalue	3.57	0.06	3.67
histpvalueplotter	3.93	0.06	3.99
lassoReg	3.70	0.05	3.76
logReg	3.67	0.12	3.83
nlcvTT	1.67	0.03	1.75
plot1gene	3.67	0.11	3.78
plotComb2Samples	3.55	0.24	3.83
plotCombMultSamples	4.25	0.51	4.78
plotCombination2genes	3.45	0.02	3.53