BioC 2.12: CHECK report for ABarray on moscato2

Package: ABarray

Version: 1.28.0

Command: rm -rf ABarray.buildbin-libdir && mkdir ABarray.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ABarray.buildbin-libdir ABarray_1.28.0.tar.gz >ABarray-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=ABarray.buildbin-libdir --install="check:ABarray-install.out" --force-multiarch --no-vignettes --timings ABarray_1.28.0.tar.gz && mv ABarray.buildbin-libdir/* ABarray.Rcheck/ && rmdir ABarray.buildbin-libdir

StartedAt: 2013-10-09 00:48:34 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 00:50:01 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 87.5 seconds

RetCode: 0

Status:  OK

CheckDir: ABarray.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/ABarray.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ABarray/DESCRIPTION' ... OK
* this is package 'ABarray' version '1.28.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'ABarray' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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
ABarray: warning in read.table(dataFile, header = TRUE, sep = sep, nrow
  = 5000, colClasses = colRead): partial argument match of 'nrow' to
  'nrows'
ABarray: warning in read.table(dataFile, header = TRUE, sep = sep, nrow
  = 36000, colClasses = colRead, as.is = TRUE, check.names = FALSE,
  comment.char = "", na.string = c("NA", "MultipleValues", "Multiple
  Values")): partial argument match of 'na.string' to 'na.strings'
ABarray: warning in read.table(dataFile, header = TRUE, sep = sep, nrow
  = 36000, colClasses = colRead, as.is = TRUE, check.names = FALSE,
  comment.char = "", na.string = c("NA", "MultipleValues", "Multiple
  Values")): partial argument match of 'nrow' to 'nrows'
ABarray: warning in read.table(dataFile, header = TRUE, sep = sep, nrow
  = 36000, colClasses = colRead, check.names = FALSE, comment.char =
  "", na.string = c("NA", "MultipleValues", "Multiple Values")):
  partial argument match of 'na.string' to 'na.strings'
ABarray: warning in read.table(dataFile, header = TRUE, sep = sep, nrow
  = 36000, colClasses = colRead, check.names = FALSE, comment.char =
  "", na.string = c("NA", "MultipleValues", "Multiple Values")):
  partial argument match of 'nrow' to 'nrows'
ABarray: warning in dir.create(dataDir, showWarning = FALSE): partial
  argument match of 'showWarning' to 'showWarnings'
ABarray: warning in dir.create(pdfDir, showWarning = FALSE): partial
  argument match of 'showWarning' to 'showWarnings'
ABarray: warning in dir.create(jpgDir, showWarning = FALSE): partial
  argument match of 'showWarning' to 'showWarnings'
doLPE: warning in dir.create(dataDir, showWarning = FALSE): partial
  argument match of 'showWarning' to 'showWarnings'
doPlotEset: warning in dir.create(dataDir, showWarning = FALSE):
  partial argument match of 'showWarning' to 'showWarnings'
doPlotEset: warning in dir.create(pdfDir, showWarning = FALSE): partial
  argument match of 'showWarning' to 'showWarnings'
doPlotEset: warning in dir.create(jpgDir, showWarning = FALSE): partial
  argument match of 'showWarning' to 'showWarnings'
doPlotFCT: warning in dir.create(dataDir, showWarning = FALSE): partial
  argument match of 'showWarning' to 'showWarnings'
doPlotFCT: warning in dir.create(pdfDir, showWarning = FALSE): partial
  argument match of 'showWarning' to 'showWarnings'
doPlotFCT: warning in dir.create(jpgDir, showWarning = FALSE): partial
  argument match of 'showWarning' to 'showWarnings'
icpPlot: warning in jpeg(file = paste(jpgDir, fname, "_Heatmap.jpg",
  sep = ""), width = fWidth, height = fHeight): partial argument match
  of 'file' to 'filename'
ABarray: no visible binding for global variable 'colSn'
ABarrayGUI : getImputeFunc: no visible binding for global variable
  'knnRbtn'
getPantherMap: no visible binding for global variable 'panther'
* checking Rd files ... NOTE
prepare_Rd: ABarrayGUI.Rd:12-13: Dropping empty section \arguments
prepare_Rd: calcsn.Rd:26-28: Dropping empty section \examples
prepare_Rd: cvv.Rd:22-24: Dropping empty section \examples
prepare_Rd: cvvPlot.Rd:24-26: Dropping empty section \examples
prepare_Rd: doVennDiagram.Rd:33-36: Dropping empty section \examples
prepare_Rd: getMemberEset.Rd:23-25: Dropping empty section \examples
prepare_Rd: getPantherMap.Rd:24-26: Dropping empty section \examples
prepare_Rd: hclusterPlot.Rd:27-29: Dropping empty section \examples
prepare_Rd: matrixPlot.Rd:32-34: Dropping empty section \examples
prepare_Rd: qnNormalize.Rd:52-54: Dropping empty section \examples
prepare_Rd: savejpg.Rd:26-28: Dropping empty section \examples
prepare_Rd: snSummary.Rd:22-25: 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 installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... [2s] OK
** running examples for arch 'x64' ... [2s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  'E:/biocbld/bbs-2.12-bioc/meat/ABarray.Rcheck/00check.log'
for details.

install for i386

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

install for x64

* installing *source* package 'ABarray' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ABarray' as ABarray_1.28.0.zip
* DONE (ABarray)