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BioC 3.0: CHECK report for yaqcaffy on perceval

This page was generated on 2015-04-10 09:53:42 -0700 (Fri, 10 Apr 2015).

Package 932/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
yaqcaffy 1.26.0
Laurent Gatto
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/yaqcaffy
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: yaqcaffy
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch yaqcaffy_1.26.0.tar.gz
StartedAt: 2015-04-10 07:38:58 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 07:44:20 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 322.4 seconds
RetCode: 0
Status:  OK 
CheckDir: yaqcaffy.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch yaqcaffy_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/yaqcaffy.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘yaqcaffy/DESCRIPTION’ ... OK
* this is package ‘yaqcaffy’ 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘yaqcaffy’ can be installed ... [20s/23s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘MAQCsubsetAFX’ ‘tcltk’ ‘tcltk2’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘simpleaffy:::.bg.stats’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.isHgu133plus2: no visible global function definition for ‘cdfName’
getBio: no visible global function definition for ‘featureNames’
getDeg: no visible global function definition for ‘cleancdfname’
getDeg: no visible global function definition for ‘cdfName’
getDeg: no visible global function definition for ‘featureNames’
getQcdefData: no visible global function definition for ‘cleancdfname’
getSpk: no visible global function definition for ‘featureNames’
probeSelectionInterface: no visible global function definition for
  ‘tkmessageBox’
probeSelectionInterface: no visible global function definition for
  ‘tktoplevel’
probeSelectionInterface: no visible global function definition for
  ‘tkframe’
probeSelectionInterface: no visible global function definition for
  ‘tkwm.title’
probeSelectionInterface: no visible global function definition for
  ‘tk2notebook’
probeSelectionInterface: no visible global function definition for
  ‘tkpack’
probeSelectionInterface: no visible global function definition for
  ‘tk2notetab’
probeSelectionInterface: no visible global function definition for
  ‘featureNames’
probeSelectionInterface: no visible global function definition for
  ‘tclVar’
probeSelectionInterface: no visible global function definition for
  ‘ttkcombobox’
probeSelectionInterface: no visible global function definition for
  ‘tklabel’
probeSelectionInterface: no visible global function definition for
  ‘tk2button’
probeSelectionInterface : <anonymous>: no visible global function
  definition for ‘tclvalue’
probeSelectionInterface : <anonymous>: no visible global function
  definition for ‘tkdestroy’
probeSelectionInterface: no visible global function definition for
  ‘tkgrid’
reprodPlot: no visible global function definition for ‘exprs’
reprodPlot: no visible global function definition for ‘gcrma’
reprodPlot: no visible global function definition for ‘mas5’
reprodPlot: no visible global function definition for ‘rma’
reprodPlot: no visible global function definition for ‘sampleNames’
yaqc.affy.affybatch: no visible global function definition for
  ‘package.version’
yaqc.affy.affybatch: no visible global function definition for
  ‘experimentData’
yaqc.affy.affybatch : <anonymous>: no visible global function
  definition for ‘exprs’
yaqc.affy.affybatch: no visible global function definition for
  ‘sampleNames’
yaqc.affy.exprSet: no visible global function definition for
  ‘package.version’
yaqc.affy.exprSet : <anonymous>: no visible global function definition
  for ‘exprs’
yaqc.summary: no visible global function definition for ‘xtable’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [137s/137s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
getOutliers 67.089  1.577  68.800
getAllInt   19.148  0.494  19.656
getQCRatios 11.710  0.644  12.354
yaqc.affy   11.419  0.571  11.990
yaqc.plot   11.000  0.509  11.509
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/yaqcaffy.Rcheck/00check.log’
for details.

yaqcaffy.Rcheck/00install.out:

* installing *source* package ‘yaqcaffy’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘summary’ from package ‘base’ in package ‘yaqcaffy’
Creating a generic function for ‘merge’ from package ‘base’ in package ‘yaqcaffy’
Creating a generic function for ‘identical’ from package ‘base’ in package ‘yaqcaffy’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (yaqcaffy)

yaqcaffy.Rcheck/yaqcaffy-Ex.timings:

nameusersystemelapsed
YaqcControlProbes-class0.0030.0010.004
getAllInt19.148 0.49419.656
getBioProbes0.7600.0220.783
getOutliers67.089 1.57768.800
getQCRatios11.710 0.64412.354
getRatioProbes1.6810.0591.740
getSpikeProbes1.1530.0261.179
probeSelectionInterface0.0010.0000.001
reprodPlot0.0010.0000.001
yaqc.affy11.419 0.57111.990
yaqc.plot11.000 0.50911.509