BioC 3.2: CHECK report for aroma.light on perceval

Package: aroma.light

Version: 3.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings aroma.light_3.0.0.tar.gz

StartedAt: 2015-11-10 02:11:46 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 02:13:42 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 115.6 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_3.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/aroma.light.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘3.0.0’
* 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 ... [2s/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 ... [36s/36s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
normalizeCurveFit 15.243  0.115  15.387
normalizeAffine   15.156  0.069  15.228
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘backtransformAffine.matrix.R’ [1s/1s]
  Running ‘backtransformPrincipalCurve.matrix.R’ [1s/1s]
  Running ‘callNaiveGenotypes.R’ [1s/1s]
  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’ [4s/4s]
  Running ‘normalizeAverage.list.R’ [1s/1s]
  Running ‘normalizeAverage.matrix.R’ [1s/1s]
  Running ‘normalizeCurveFit.matrix.R’ [16s/16s]
  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’ [2s/2s]
  Running ‘normalizeTumorBoost,flavors.R’ [1s/1s]
  Running ‘normalizeTumorBoost.R’ [1s/1s]
  Running ‘robustSmoothSpline.R’ [1s/1s]
  Running ‘rowAverages.matrix.R’ [1s/1s]
  Running ‘sampleCorrelations.matrix.R’ [1s/1s]
  Running ‘sampleTuples.R’ [1s/1s]
  Running ‘wpca.matrix.R’ [1s/1s]
  Running ‘wpca2.matrix.R’ [1s/1s]
 [42s/42s] OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-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	0.006	0.001	0.007
backtransformPrincipalCurve	0.511	0.012	0.579
calibrateMultiscan	0.001	0.000	0.000
callNaiveGenotypes	0.422	0.013	0.434
distanceBetweenLines	0.055	0.001	0.055
findPeaksAndValleys	0.089	0.005	0.113
fitPrincipalCurve	0.373	0.014	0.421
fitXYCurve	0.072	0.004	0.084
iwpca	0.039	0.001	0.041
likelihood.smooth.spline	0.127	0.003	0.136
medianPolish	0.007	0.001	0.032
normalizeAffine	15.156	0.069	15.228
normalizeCurveFit	15.243	0.115	15.387
normalizeDifferencesToAverage	0.252	0.011	0.314
normalizeFragmentLength	0.739	0.020	0.774
normalizeQuantileRank	0.208	0.007	0.225
normalizeQuantileRank.matrix	0.112	0.002	0.115
normalizeQuantileSpline	0.760	0.021	0.792
normalizeTumorBoost	0.259	0.008	0.272
robustSmoothSpline	0.093	0.004	0.110
sampleCorrelations	0.597	0.002	0.599
sampleTuples	0.002	0.000	0.002
wpca	0.041	0.002	0.048