BioC 3.6: CHECK report for aroma.light on veracruz1

Package: aroma.light

Version: 3.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings aroma.light_3.7.0.tar.gz

StartedAt: 2017-08-15 23:57:50 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 23:59:30 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 99.9 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_3.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/aroma.light.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘aroma.light/DESCRIPTION’ ... OK
* this is package ‘aroma.light’ version ‘3.7.0’
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
normalizeAffine   8.548  0.060   8.863
normalizeCurveFit 8.323  0.048   8.621
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘backtransformAffine.matrix.R’
  Running ‘backtransformPrincipalCurve.matrix.R’
  Running ‘callNaiveGenotypes.R’
  Running ‘distanceBetweenLines.R’
  Running ‘findPeaksAndValleys.R’
  Running ‘fitPrincipalCurve.matrix.R’
  Running ‘fitXYCurve.matrix.R’
  Running ‘iwpca.matrix.R’
  Running ‘likelihood.smooth.spline.R’
  Running ‘medianPolish.matrix.R’
  Running ‘normalizeAffine.matrix.R’
  Running ‘normalizeAverage.list.R’
  Running ‘normalizeAverage.matrix.R’
  Running ‘normalizeCurveFit.matrix.R’
  Running ‘normalizeDifferencesToAverage.R’
  Running ‘normalizeFragmentLength-ex1.R’
  Running ‘normalizeFragmentLength-ex2.R’
  Running ‘normalizeQuantileRank.list.R’
  Running ‘normalizeQuantileRank.matrix.R’
  Running ‘normalizeQuantileSpline.matrix.R’
  Running ‘normalizeTumorBoost,flavors.R’
  Running ‘normalizeTumorBoost.R’
  Running ‘robustSmoothSpline.R’
  Running ‘rowAverages.matrix.R’
  Running ‘sampleCorrelations.matrix.R’
  Running ‘sampleTuples.R’
  Running ‘wpca.matrix.R’
  Running ‘wpca2.matrix.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.6-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	0.051	0.002	0.052
backtransformPrincipalCurve	0.544	0.016	0.575
calibrateMultiscan	0.001	0.000	0.000
callNaiveGenotypes	0.830	0.012	0.878
distanceBetweenLines	0.131	0.002	0.150
findPeaksAndValleys	0.039	0.002	0.041
fitPrincipalCurve	0.664	0.007	0.703
fitXYCurve	0.055	0.002	0.058
iwpca	0.100	0.001	0.103
likelihood.smooth.spline	0.142	0.002	0.150
medianPolish	0.007	0.001	0.007
normalizeAffine	8.548	0.060	8.863
normalizeCurveFit	8.323	0.048	8.621
normalizeDifferencesToAverage	0.191	0.007	0.202
normalizeFragmentLength	0.711	0.017	0.764
normalizeQuantileRank	0.215	0.005	0.231
normalizeQuantileRank.matrix	0.087	0.002	0.093
normalizeQuantileSpline	1.248	0.016	1.305
normalizeTumorBoost	0.253	0.008	0.279
robustSmoothSpline	0.093	0.003	0.097
sampleCorrelations	0.363	0.001	0.372
sampleTuples	0.012	0.001	0.013
wpca	0.081	0.002	0.085