BioC 2.14: CHECK report for yaqcaffy on petty

Package: yaqcaffy

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch yaqcaffy_1.24.0.tar.gz

StartedAt: 2014-10-08 00:41:04 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:46:50 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 345.3 seconds

RetCode: 0

Status:  OK

CheckDir: yaqcaffy.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch yaqcaffy_1.24.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/yaqcaffy.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.24.0’
* 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 ... [22s/25s] 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
Unexported object imported by a ':::' call: ‘simpleaffy:::.bg.stats’
  See the note in ?`:::` about the use of this operator.
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 files in ‘vignettes’ ... OK
* checking examples ... [138s/138s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
getOutliers 64.931  1.379  66.392
getAllInt   19.776  0.456  20.270
yaqc.affy   12.409  0.490  12.905
yaqc.plot   12.319  0.493  12.814
getQCRatios 12.063  0.505  12.569
* 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 was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-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	0.003	0.001	0.004
getAllInt	19.776	0.456	20.270
getBioProbes	1.161	0.030	1.190
getOutliers	64.931	1.379	66.392
getQCRatios	12.063	0.505	12.569
getRatioProbes	1.801	0.031	1.832
getSpikeProbes	1.354	0.023	1.378
probeSelectionInterface	0.001	0.000	0.001
reprodPlot	0.001	0.000	0.001
yaqc.affy	12.409	0.490	12.905
yaqc.plot	12.319	0.493	12.814