BioC 3.0: CHECK report for aroma.light on oaxaca

Package: aroma.light

Version: 2.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch aroma.light_2.2.1.tar.gz

StartedAt: 2015-04-09 21:25:00 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 21:26:05 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 65.3 seconds

RetCode: 0

Status:  OK

CheckDir: aroma.light.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 aroma.light_2.2.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/aroma.light.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘aroma.light/DESCRIPTION’ ... OK
* this is package ‘aroma.light’ version ‘2.2.1’
* package encoding: latin1
* 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 ... NOTE
Found the following hidden files and directories:
  inst/rsp/.rspPlugins
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘aroma.light’ can be installed ... [3s/3s] 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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 examples ... [25s/25s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
normalizeCurveFit 9.696  0.048   9.879
normalizeAffine   9.456  0.044   9.602
* checking PDF version of manual ... OK
* DONE

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

* installing *source* package ‘aroma.light’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (aroma.light)

name	user	system	elapsed
backtransformAffine	0.007	0.001	0.008
backtransformPrincipalCurve	0.569	0.010	0.623
calibrateMultiscan	0	0	0
callNaiveGenotypes	0.432	0.008	0.441
distanceBetweenLines	0.037	0.001	0.038
findPeaksAndValleys	0.077	0.002	0.137
fitPrincipalCurve	0.338	0.012	0.361
fitXYCurve	0.058	0.002	0.062
iwpca	0.035	0.001	0.036
likelihood.smooth.spline	0.127	0.002	0.133
medianPolish	0.007	0.001	0.025
normalizeAffine	9.456	0.044	9.602
normalizeCurveFit	9.696	0.048	9.879
normalizeDifferencesToAverage	0.221	0.009	0.232
normalizeFragmentLength	0.650	0.022	0.679
normalizeQuantileRank	0.199	0.004	0.214
normalizeQuantileRank.matrix	0.069	0.001	0.071
normalizeQuantileSpline	0.956	0.021	0.979
normalizeTumorBoost	0.223	0.013	0.241
robustSmoothSpline	0.069	0.003	0.078
sampleCorrelations	0.541	0.004	0.547
sampleTuples	0.002	0.000	0.002
wpca	0.041	0.003	0.050