BioC 3.1: CHECK report for aroma.light on petty

Package: aroma.light

Version: 2.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings aroma.light_2.4.0.tar.gz

StartedAt: 2015-10-08 21:28:50 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 21:31:17 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 146.9 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 aroma.light_2.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/aroma.light.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘2.4.0’
* 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 ... [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 ... 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 ... [43s/43s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
normalizeAffine   17.543  0.072  17.649
normalizeCurveFit 17.539  0.066  17.637
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘backtransformAffine.matrix.R’ [1s/1s]
  Running ‘backtransformPrincipalCurve.matrix.R’ [1s/1s]
  Running ‘callNaiveGenotypes.R’ [2s/2s]
  Running ‘distanceBetweenLines.R’ [1s/1s]
  Running ‘findPeaksAndValleys.R’ [1s/1s]
  Running ‘fitPrincipalCurve.matrix.R’ [1s/1s]
  Running ‘fitXYCurve.matrix.R’ [1s/1s]
  Running ‘iwpca.matrix.R’ [1s/1s]
  Running ‘likelihood.smooth.spline.R’ [1s/1s]
  Running ‘medianPolish.matrix.R’ [1s/1s]
  Running ‘normalizeAffine.matrix.R’ [5s/5s]
  Running ‘normalizeCurveFit.matrix.R’ [18s/19s]
  Running ‘normalizeDifferencesToAverage.R’ [1s/1s]
  Running ‘normalizeFragmentLength-ex1.R’ [1s/1s]
  Running ‘normalizeFragmentLength-ex2.R’ [2s/2s]
  Running ‘normalizeQuantileRank.list.R’ [1s/1s]
  Running ‘normalizeQuantileRank.matrix.R’ [1s/1s]
  Running ‘normalizeQuantileSpline.matrix.R’ [2s/2s]
  Running ‘normalizeTumorBoost,flavors.R’ [1s/2s]
  Running ‘normalizeTumorBoost.R’ [1s/1s]
  Running ‘robustSmoothSpline.R’ [1s/2s]
  Running ‘sampleCorrelations.matrix.R’ [2s/2s]
  Running ‘sampleTuples.R’ [1s/1s]
  Running ‘wpca.matrix.R’ [1s/1s]
  Running ‘wpca2.matrix.R’ [1s/1s]
 [49s/52s] OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.1-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	0.009	0.002	0.010
backtransformPrincipalCurve	0.692	0.014	0.732
calibrateMultiscan	0.001	0.000	0.000
callNaiveGenotypes	0.592	0.012	0.606
distanceBetweenLines	0.070	0.001	0.071
findPeaksAndValleys	0.092	0.002	0.095
fitPrincipalCurve	0.398	0.013	0.413
fitXYCurve	0.101	0.005	0.109
iwpca	0.062	0.001	0.063
likelihood.smooth.spline	0.186	0.003	0.191
medianPolish	0.010	0.001	0.030
normalizeAffine	17.543	0.072	17.649
normalizeCurveFit	17.539	0.066	17.637
normalizeDifferencesToAverage	0.307	0.014	0.346
normalizeFragmentLength	0.987	0.028	1.170
normalizeQuantileRank	0.250	0.010	0.287
normalizeQuantileRank.matrix	0.131	0.002	0.144
normalizeQuantileSpline	1.119	0.024	1.176
normalizeTumorBoost	0.347	0.014	0.374
robustSmoothSpline	0.149	0.010	0.184
sampleCorrelations	0.733	0.002	0.735
sampleTuples	0.002	0.000	0.002
wpca	0.058	0.003	0.063