BioC 3.1: CHECK report for aroma.light on zin2

Package: aroma.light

Version: 2.4.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings aroma.light_2.4.0.tar.gz

StartedAt: 2015-10-08 22:31:27 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 22:32:44 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 76.3 seconds

RetCode: 0

Status:  OK

CheckDir: aroma.light.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings aroma.light_2.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-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 ‘2.4.0’
* 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/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 ... [27s/27s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
normalizeAffine   11.959  0.020  11.989
normalizeCurveFit 11.189  0.016  11.215
* 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’ [0s/0s]
  Running ‘fitPrincipalCurve.matrix.R’ [1s/1s]
  Running ‘fitXYCurve.matrix.R’ [0s/0s]
  Running ‘iwpca.matrix.R’ [0s/0s]
  Running ‘likelihood.smooth.spline.R’ [0s/0s]
  Running ‘medianPolish.matrix.R’ [0s/0s]
  Running ‘normalizeAffine.matrix.R’ [3s/3s]
  Running ‘normalizeCurveFit.matrix.R’ [11s/11s]
  Running ‘normalizeDifferencesToAverage.R’ [0s/0s]
  Running ‘normalizeFragmentLength-ex1.R’ [1s/1s]
  Running ‘normalizeFragmentLength-ex2.R’ [1s/1s]
  Running ‘normalizeQuantileRank.list.R’ [1s/1s]
  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 ‘sampleCorrelations.matrix.R’ [1s/1s]
  Running ‘sampleTuples.R’ [0s/0s]
  Running ‘wpca.matrix.R’ [0s/0s]
  Running ‘wpca2.matrix.R’ [0s/0s]
 [27s/27s] OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.1-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	0.005	0.000	0.005
backtransformPrincipalCurve	0.405	0.007	0.422
calibrateMultiscan	0.001	0.000	0.000
callNaiveGenotypes	0.385	0.000	0.385
distanceBetweenLines	0.019	0.000	0.020
findPeaksAndValleys	0.047	0.000	0.047
fitPrincipalCurve	0.271	0.008	0.279
fitXYCurve	0.059	0.000	0.059
iwpca	0.016	0.000	0.016
likelihood.smooth.spline	0.114	0.000	0.114
medianPolish	0.006	0.000	0.006
normalizeAffine	11.959	0.020	11.989
normalizeCurveFit	11.189	0.016	11.215
normalizeDifferencesToAverage	0.177	0.000	0.178
normalizeFragmentLength	0.638	0.012	0.650
normalizeQuantileRank	0.198	0.000	0.198
normalizeQuantileRank.matrix	0.057	0.000	0.057
normalizeQuantileSpline	0.593	0.012	0.605
normalizeTumorBoost	0.16	0.00	0.16
robustSmoothSpline	0.05	0.00	0.05
sampleCorrelations	0.471	0.000	0.471
sampleTuples	0.001	0.000	0.001
wpca	0.027	0.000	0.026