BioC 3.2: CHECK report for aroma.light on linux1.bioconductor.org

Package: aroma.light

Version: 3.0.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings aroma.light_3.0.0.tar.gz

StartedAt: 2015-10-27 01:03:59 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 01:05:14 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 74.7 seconds

RetCode: 0

Status:  OK

CheckDir: aroma.light.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings aroma.light_3.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/aroma.light.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ... [1s/1s] 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 ... [24s/24s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
normalizeCurveFit 10.878  0.008  10.891
normalizeAffine    8.776  0.004   8.783
* 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’ [0s/0s]
  Running ‘normalizeAverage.matrix.R’ [0s/0s]
  Running ‘normalizeCurveFit.matrix.R’ [10s/10s]
  Running ‘normalizeDifferencesToAverage.R’ [0s/0s]
  Running ‘normalizeFragmentLength-ex1.R’ [1s/1s]
  Running ‘normalizeFragmentLength-ex2.R’ [1s/1s]
  Running ‘normalizeQuantileRank.list.R’ [0s/0s]
  Running ‘normalizeQuantileRank.matrix.R’ [0s/0s]
  Running ‘normalizeQuantileSpline.matrix.R’ [1s/1s]
  Running ‘normalizeTumorBoost,flavors.R’ [1s/1s]
  Running ‘normalizeTumorBoost.R’ [0s/0s]
  Running ‘robustSmoothSpline.R’ [0s/0s]
  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]
 [26s/26s] OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/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	0.006
backtransformPrincipalCurve	0.323	0.007	0.332
calibrateMultiscan	0	0	0
callNaiveGenotypes	0.333	0.016	0.349
distanceBetweenLines	0.016	0.000	0.015
findPeaksAndValleys	0.041	0.000	0.041
fitPrincipalCurve	0.233	0.004	0.238
fitXYCurve	0.044	0.000	0.044
iwpca	0.012	0.000	0.012
likelihood.smooth.spline	0.084	0.000	0.086
medianPolish	0.004	0.000	0.005
normalizeAffine	8.776	0.004	8.783
normalizeCurveFit	10.878	0.008	10.891
normalizeDifferencesToAverage	0.167	0.008	0.175
normalizeFragmentLength	0.649	0.028	0.678
normalizeQuantileRank	0.213	0.008	0.222
normalizeQuantileRank.matrix	0.074	0.000	0.074
normalizeQuantileSpline	0.979	0.008	0.988
normalizeTumorBoost	0.211	0.000	0.211
robustSmoothSpline	0.063	0.004	0.068
sampleCorrelations	0.416	0.000	0.421
sampleTuples	0.000	0.004	0.001
wpca	0.016	0.000	0.018