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Package 45/553HostnameOS / ArchBUILDCHECKBUILD BIN
ArrayTools 1.16.0
Arthur Li
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/ArrayTools
Last Changed Rev: 64678 / Revision: 69725
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: ArrayTools
Version: 1.16.0
Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings ArrayTools_1.16.0.tar.gz
StartedAt: 2012-09-23 23:25:54 -0700 (Sun, 23 Sep 2012)
EndedAt: 2012-09-23 23:27:21 -0700 (Sun, 23 Sep 2012)
EllapsedTime: 87.2 seconds
RetCode: 0
Status:  OK 
CheckDir: ArrayTools.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/ArrayTools.Rcheck’
* using R version 2.15.1 (2012-06-22)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ArrayTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ArrayTools’ 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 ‘ArrayTools’ 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 ... NOTE
qa3prime : emptyPlot: warning in png(file = figureName): partial
  argument match of 'file' to 'filename'
qa3prime: warning in png(file = figure2): partial argument match of
  'file' to 'filename'
qa3prime: warning in png(file = figure6): partial argument match of
  'file' to 'filename'
qa3prime: warning in plotAffyRNAdeg(deg, col = rainbow(nchip)): partial
  argument match of 'col' to 'cols'
qa3prime: warning in png(file = figure8): partial argument match of
  'file' to 'filename'
qa3prime: warning in png(file = figure9): partial argument match of
  'file' to 'filename'
preProcessGeneST: no visible binding for global variable
  ‘hugene10stCONTROL’
preProcessGeneST: no visible binding for global variable
  ‘mogene10stCONTROL’
regress: no visible global function definition for ‘permute.1’
* 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 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 was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/ArrayTools.Rcheck/00check.log’
for details.

ArrayTools.Rcheck/00install.out:

* installing *source* package ‘ArrayTools’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘summary’ from package ‘base’ in package ‘ArrayTools’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘ArrayTools.Rnw’ 
** testing if installed package can be loaded

* DONE (ArrayTools)

ArrayTools.Rcheck/ArrayTools-Ex.timings:

nameusersystemelapsed
Output2HTML0.2320.0040.236
QC0.0040.0000.002
Sort0.0880.0000.089
contrastMatrix-class0.0400.0000.041
createExpressionSet0.0840.0000.090
createGSEAFiles0.0040.0000.003
createIndex0.4280.0000.429
createIngenuityFile0.0760.0040.078
designMatrix-class0.0120.0000.014
eSetExample0.0000.0000.004
exprsExample0.0000.0000.003
geneFilter3.7440.0483.839
interactionResult-class0.4760.0120.499
pDataExample0.0040.0000.002
postInteraction0.2320.0000.237
preProcess3prime6.7400.1246.976
preProcessGeneST0.0120.0040.014
qa3prime0.0000.0000.001
qaGeneST0.0160.0000.013
regress0.0840.0040.090
regressResult-class0.1080.0120.120
selectSigGene0.1160.0040.125
selectSigGeneInt0.3000.0000.322