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: 2015-10-27 05:28:08 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:30:05 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 117.7 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 ... [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 ... [36s/37s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
normalizeCurveFit 15.280  0.052  15.336
normalizeAffine   15.054  0.038  15.103
* 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/44s] 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	0.507	0.010	0.556
calibrateMultiscan	0.000	0.000	0.001
callNaiveGenotypes	0.426	0.011	0.437
distanceBetweenLines	0.054	0.001	0.055
findPeaksAndValleys	0.093	0.005	0.109
fitPrincipalCurve	0.361	0.012	0.652
fitXYCurve	0.071	0.002	0.107
iwpca	0.039	0.001	0.040
likelihood.smooth.spline	0.127	0.003	0.155
medianPolish	0.007	0.001	0.015
normalizeAffine	15.054	0.038	15.103
normalizeCurveFit	15.280	0.052	15.336
normalizeDifferencesToAverage	0.255	0.012	0.297
normalizeFragmentLength	0.764	0.022	0.793
normalizeQuantileRank	0.215	0.008	0.234
normalizeQuantileRank.matrix	0.119	0.003	0.135
normalizeQuantileSpline	0.817	0.027	0.962
normalizeTumorBoost	0.259	0.009	0.272
robustSmoothSpline	0.095	0.004	0.127
sampleCorrelations	0.603	0.003	0.606
sampleTuples	0.002	0.001	0.002
wpca	0.042	0.002	0.045