BioC 2.14: CHECK report for aroma.light on petty

Package: aroma.light

Version: 2.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch aroma.light_2.0.0.tar.gz

StartedAt: 2014-10-07 20:43:18 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 20:45:20 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 121.2 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_2.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/aroma.light.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 ‘aroma.light/DESCRIPTION’ ... OK
* this is package ‘aroma.light’ version ‘2.0.0’
* 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 ... [4s/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 ... OK
* 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 ... [54s/55s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
normalizeAffine   21.912  0.090  22.491
normalizeCurveFit 21.778  0.097  21.967
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-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	0.001	0.012
backtransformPrincipalCurve	0.987	0.016	1.014
calibrateMultiscan	0.001	0.000	0.001
callNaiveGenotypes	1.180	0.026	1.207
distanceBetweenLines	0.091	0.003	0.094
findPeaksAndValleys	0.079	0.002	0.081
fitPrincipalCurve	0.890	0.033	0.932
fitXYCurve	0.108	0.004	0.115
iwpca	0.066	0.003	0.069
likelihood.smooth.spline	0.247	0.006	0.282
medianPolish	0.013	0.001	0.014
normalizeAffine	21.912	0.090	22.491
normalizeCurveFit	21.778	0.097	21.967
normalizeDifferencesToAverage	0.357	0.019	0.379
normalizeFragmentLength	1.148	0.038	1.197
normalizeQuantileRank	0.381	0.009	0.400
normalizeQuantileRank.matrix	0.119	0.002	0.124
normalizeQuantileSpline	1.623	0.023	1.653
normalizeTumorBoost	0.408	0.021	0.434
robustSmoothSpline	0.147	0.008	0.159
sampleCorrelations	0.889	0.002	0.891
sampleTuples	0.003	0.001	0.003
wpca	0.075	0.006	0.082