BioC 3.3: CHECK report for aroma.light on morelia

Package: aroma.light

Version: 3.1.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings aroma.light_3.1.1.tar.gz

StartedAt: 2016-04-20 23:19:31 -0700 (Wed, 20 Apr 2016)

EndedAt: 2016-04-20 23:20:54 -0700 (Wed, 20 Apr 2016)

EllapsedTime: 82.5 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_3.1.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/aroma.light.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘3.1.1’
* 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 ... [2s/2s] 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 ... [20s/20s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
normalizeCurveFit 8.312  0.050   8.374
normalizeAffine   7.679  0.032   7.906
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘backtransformAffine.matrix.R’ [0s/0s]
  Running ‘backtransformPrincipalCurve.matrix.R’ [1s/1s]
  Running ‘callNaiveGenotypes.R’ [1s/1s]
  Running ‘distanceBetweenLines.R’ [0s/0s]
  Running ‘findPeaksAndValleys.R’ [1s/1s]
  Running ‘fitPrincipalCurve.matrix.R’ [1s/1s]
  Running ‘fitXYCurve.matrix.R’ [1s/1s]
  Running ‘iwpca.matrix.R’ [0s/0s]
  Running ‘likelihood.smooth.spline.R’ [1s/1s]
  Running ‘medianPolish.matrix.R’ [0s/0s]
  Running ‘normalizeAffine.matrix.R’ [4s/4s]
  Running ‘normalizeAverage.list.R’ [1s/1s]
  Running ‘normalizeAverage.matrix.R’ [1s/1s]
  Running ‘normalizeCurveFit.matrix.R’ [10s/10s]
  Running ‘normalizeDifferencesToAverage.R’ [1s/1s]
  Running ‘normalizeFragmentLength-ex1.R’ [1s/1s]
  Running ‘normalizeFragmentLength-ex2.R’ [1s/1s]
  Running ‘normalizeQuantileRank.list.R’ [1s/1s]
  Running ‘normalizeQuantileRank.matrix.R’ [1s/1s]
  Running ‘normalizeQuantileSpline.matrix.R’ [1s/1s]
  Running ‘normalizeTumorBoost,flavors.R’ [1s/1s]
  Running ‘normalizeTumorBoost.R’ [1s/1s]
  Running ‘robustSmoothSpline.R’ [1s/1s]
  Running ‘rowAverages.matrix.R’ [0s/0s]
  Running ‘sampleCorrelations.matrix.R’ [1s/1s]
  Running ‘sampleTuples.R’ [0s/0s]
  Running ‘wpca.matrix.R’ [0s/0s]
  Running ‘wpca2.matrix.R’ [0s/0s]
 [30s/31s] OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-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	0.004	0.001	0.004
backtransformPrincipalCurve	0.361	0.010	0.371
calibrateMultiscan	0	0	0
callNaiveGenotypes	0.300	0.009	0.310
distanceBetweenLines	0.040	0.001	0.042
findPeaksAndValleys	0.034	0.001	0.037
fitPrincipalCurve	0.226	0.007	0.245
fitXYCurve	0.039	0.001	0.046
iwpca	0.021	0.000	0.021
likelihood.smooth.spline	0.081	0.002	0.099
medianPolish	0.004	0.000	0.024
normalizeAffine	7.679	0.032	7.906
normalizeCurveFit	8.312	0.050	8.374
normalizeDifferencesToAverage	0.180	0.007	0.245
normalizeFragmentLength	0.494	0.015	0.522
normalizeQuantileRank	0.188	0.006	0.217
normalizeQuantileRank.matrix	0.055	0.003	0.061
normalizeQuantileSpline	0.597	0.016	0.613
normalizeTumorBoost	0.132	0.005	0.141
robustSmoothSpline	0.039	0.003	0.096
sampleCorrelations	0.272	0.001	0.273
sampleTuples	0.001	0.001	0.001
wpca	0.035	0.002	0.038