Back to the "Multiple platform build/check report"[A] B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

Package 49/658HostnameOS / ArchBUILDCHECKBUILD BIN
ArrayTools 1.19.0
Arthur Li
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ArrayTools
Last Changed Rev: 70052 / Revision: 74774
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / 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: 1.19.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ArrayTools_1.19.0.tar.gz
StartedAt: 2013-03-25 01:14:46 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 01:16:51 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 125.1 seconds
RetCode: 0
Status:  OK 
CheckDir: ArrayTools.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ArrayTools.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ArrayTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ArrayTools' version '1.19.0'
* 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 for sufficient/correct file permissions ... OK
* checking whether package 'ArrayTools' can be installed ... [8s/8s] 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
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [21s/21s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
preProcess3prime 6.933  0.258   7.200
geneFilter       5.035  0.148   5.189
* 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
  '/Users/biocbuild/bbs-2.12-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
Output2HTML0.2230.0300.262
QC0.0120.0070.020
Sort0.1640.0170.182
contrastMatrix-class0.0920.0260.123
createExpressionSet0.1090.0080.117
createGSEAFiles0.0700.0060.076
createIndex0.5870.0330.621
createIngenuityFile0.1590.0140.175
designMatrix-class0.0540.0180.071
eSetExample0.0140.0070.022
exprsExample0.0130.0090.027
geneFilter5.0350.1485.189
interactionResult-class0.3570.0290.386
pDataExample0.0110.0060.018
postInteraction0.5810.0260.608
preProcess3prime6.9330.2587.200
preProcessGeneST0.0230.0080.031
qa3prime0.0120.0070.019
qaGeneST0.0300.0130.043
regress0.1520.0140.167
regressResult-class0.1600.0190.179
selectSigGene0.1610.0160.181
selectSigGeneInt0.4690.0250.494