BioC 2.13: CHECK report for yaqcaffy on perceval

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

* 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.

* 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)

name	user	system	elapsed
YaqcControlProbes-class	0.232	0.003	0.236
getAllInt	20.402	0.628	21.057
getBioProbes	0.797	0.028	0.825
getOutliers	62.659	1.527	64.294
getQCRatios	12.334	0.713	13.048
getRatioProbes	1.558	0.037	1.595
getSpikeProbes	1.211	0.048	1.260
probeSelectionInterface	0.002	0.004	0.006
reprodPlot	0.003	0.004	0.007
yaqc.affy	11.731	0.540	12.271
yaqc.plot	12.744	0.674	13.419