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BioC 2.13: CHECK report for yaqcaffy on perceval

This page was generated on 2014-04-05 09:52:01 -0700 (Sat, 05 Apr 2014).

Package 749/750HostnameOS / ArchBUILDCHECKBUILD BIN
yaqcaffy 1.22.0
Laurent Gatto
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/yaqcaffy
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: yaqcaffy
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch yaqcaffy_1.22.0.tar.gz
StartedAt: 2014-04-05 05:06:18 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 05:11:14 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 296.0 seconds
RetCode: 0
Status:  OK 
CheckDir: yaqcaffy.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/yaqcaffy.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.22.0’
* 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 ... [18s/19s] 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
Packages in Depends field not imported from:
  ‘methods’ ‘simpleaffy’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ‘:::’ call: ‘simpleaffy:::.bg.stats’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘getAlpha1’ ‘getAlpha2’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘yaqcaffy.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [135s/135s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
getOutliers 62.659  1.527  64.294
getAllInt   20.402  0.628  21.057
yaqc.plot   12.744  0.674  13.419
getQCRatios 12.334  0.713  13.048
yaqc.affy   11.731  0.540  12.271
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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-class0.2320.0030.236
getAllInt20.402 0.62821.057
getBioProbes0.7970.0280.825
getOutliers62.659 1.52764.294
getQCRatios12.334 0.71313.048
getRatioProbes1.5580.0371.595
getSpikeProbes1.2110.0481.260
probeSelectionInterface0.0020.0040.006
reprodPlot0.0030.0040.007
yaqc.affy11.731 0.54012.271
yaqc.plot12.744 0.67413.419