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Package 7/609HostnameOS / ArchBUILDCHECKBUILD BIN
ABarray 1.26.0
Yongming Andrew Sun
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/ABarray
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: ABarray
Version: 1.26.0
Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings ABarray_1.26.0.tar.gz
StartedAt: 2013-03-24 22:54:03 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 22:54:55 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 51.5 seconds
RetCode: 0
Status:  OK 
CheckDir: ABarray.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/ABarray.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ABarray/DESCRIPTION’ ... OK
* this is package ‘ABarray’ version ‘1.26.0’
* 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 ‘ABarray’ 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 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
* 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 ... 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
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/ABarray.Rcheck/00check.log’
for details.

ABarray.Rcheck/00install.out:

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

* DONE (ABarray)

ABarray.Rcheck/ABarray-Ex.timings:

nameusersystemelapsed
ABarray000
ABarrayGUI000
concord000
doANOVA000
doLPE000
doPlotEset0.0000.0000.001
doPlotFCT000
drawVennDiagram000
icpPlot0.0000.0000.001
imputeFlag000
lpe.fdr.BH0.0000.0000.001
mamaplot000
mvaPair2000
panel.cor000
panel.scatter000
rgcolorsfunc0.0000.0000.002
scaleColorBar0.0000.0000.001