Package: flowQ

Version: 1.16.0

Command: rm -rf flowQ.buildbin-libdir && mkdir flowQ.buildbin-libdir && E:\biocbld\bbs-2.10-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowQ.buildbin-libdir flowQ_1.16.0.tar.gz >flowQ-install.out 2>&1 && E:\biocbld\bbs-2.10-bioc\R\bin\R.exe CMD check --library=flowQ.buildbin-libdir --install="check:flowQ-install.out" --force-multiarch --no-vignettes --timings flowQ_1.16.0.tar.gz && mv flowQ.buildbin-libdir/* flowQ.Rcheck/ && rmdir flowQ.buildbin-libdir

StartedAt: 2012-09-24 00:37:55 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 00:43:41 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 346.1 seconds

RetCode: 1

Status:  ERROR

CheckDir: flowQ.Rcheck

Warnings: NA

* using log directory 'E:/biocbld/bbs-2.10-bioc/meat/flowQ.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowQ/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowQ' version '1.16.0'
* 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 'flowQ' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
copyGraphs: warning in dir.create(relBase, rec = TRUE): partial
  argument match of 'rec' to 'recursive'
normalizeSets: warning in normalization(normFun = function(x,
  parameters, ...) warpSet(x, parameters, peakNr = peaks, ...),
  parameters = as.character(cellType), arguments = list(grouping =
  NULL), normalizationId = "Norm"): partial argument match of 'normFun'
  to 'normFunction'
writeQAReport: warning in dir.create(file.path(outdir, "images"), rec =
  TRUE): partial argument match of 'rec' to 'recursive'
evaluateProcess: multiple local function definitions for 'efun' with
  different formal arguments
qaProcess.2DStatsPlot: no visible binding for global variable 'Aliquot'
qaProcess.DensityPlot: no visible binding for global variable 'Aliquot'
qaProcess.ECDFPlot: no visible binding for global variable 'Aliquot'
* checking Rd files ... NOTE
prepare_Rd: normalizeSets.Rd:44-51: Dropping empty section \examples
* 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 installed files from 'inst/doc' ... NOTE
The following directories should probably not be installed:
  'images'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'flowQ-Ex.R' failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: qaProcess.KLDistPlot
> ### Title: Creates a QA process for comparisons of KL Distances across
> ###   multiple samples
> ### Aliases: qaProcess.KLDistPlot
> ### Keywords: dynamic
> 
> ### ** Examples
> 
> data(qData)
> dest <- tempdir()
> resKLdist <- qaProcess.KLDistPlot(qData, dyes=c("SSC-A","FSC-A"),
+                outdir=dest, alpha=0.05, pdf=TRUE)
creating summary plots.............Warning: running command 'C:\Windows\system32\cmd.exe /c identify "E:/biocbld/bbs-2.10-bioc/tmpdir/Rtmp8o6Uek/images/NXj4M36onD/summary.pdf"' had status 5
Error in strsplit(iInf, " ")[[1]] : subscript out of bounds
Calls: qaProcess.KLDistPlot ... qaGraph -> new -> initialize -> initialize -> .local
Execution halted
** running examples for arch 'x64' ... OK

install for i386

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

install for x64

* installing *source* package 'flowQ' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowQ' as flowQ_1.16.0.zip

* DONE (flowQ)