BioC 3.0: CHECK report for aroma.light on perceval

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 22:45:07 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 22:46:30 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 83.3 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-darwin10.8.0 (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/4s] 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 ... [35s/36s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
normalizeCurveFit 14.168  0.081  14.270
normalizeAffine   13.944  0.068  14.069
* 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	0.011	0.002	0.012
backtransformPrincipalCurve	0.678	0.015	0.747
calibrateMultiscan	0.001	0.000	0.001
callNaiveGenotypes	0.528	0.014	0.542
distanceBetweenLines	0.055	0.002	0.058
findPeaksAndValleys	0.141	0.004	0.155
fitPrincipalCurve	0.469	0.030	0.536
fitXYCurve	0.072	0.004	0.094
iwpca	0.042	0.002	0.043
likelihood.smooth.spline	0.152	0.004	0.170
medianPolish	0.011	0.001	0.024
normalizeAffine	13.944	0.068	14.069
normalizeCurveFit	14.168	0.081	14.270
normalizeDifferencesToAverage	0.281	0.017	0.412
normalizeFragmentLength	0.863	0.034	0.950
normalizeQuantileRank	0.236	0.012	0.293
normalizeQuantileRank.matrix	0.093	0.004	0.109
normalizeQuantileSpline	1.181	0.027	1.219
normalizeTumorBoost	0.312	0.021	0.363
robustSmoothSpline	0.107	0.006	0.141
sampleCorrelations	0.648	0.007	0.655
sampleTuples	0.002	0.001	0.002
wpca	0.046	0.004	0.057