Package: aroma.light

Version: 1.22.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings aroma.light_1.22.0.tar.gz

StartedAt: 2012-03-23 23:09:17 -0700 (Fri, 23 Mar 2012)

EndedAt: 2012-03-23 23:10:32 -0700 (Fri, 23 Mar 2012)

EllapsedTime: 74.5 seconds

RetCode: 0

Status:  OK

CheckDir: aroma.light.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/aroma.light.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-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 ‘1.22.0’
* 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 whether package ‘aroma.light’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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 ... NOTE
File ‘aroma.light/R/zzz.R’:
  .onAttach calls:
    require("R.oo")

Package startup functions should not change the search path.
See section ‘Good practice’ in ?.onAttach.

* 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 ... NOTE
‘library’ or ‘require’ call not declared from: ‘R.basic’
* checking examples ... OK
* checking PDF version of manual ... OK

* 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.matrix	0.004	0.000	0.004
backtransformPrincipalCurve.matrix	0.664	0.008	0.676
calibrateMultiscan.matrix	0	0	0
callNaiveGenotypes.numeric	0.652	0.016	0.713
distanceBetweenLines	0.028	0.000	0.023
findPeaksAndValleys.density	0.064	0.004	0.069
fitPrincipalCurve.matrix	0.464	0.012	0.477
fitXYCurve.matrix	0.076	0.000	0.075
iwpca.matrix	0.020	0.000	0.018
likelihood.smooth.spline	0.244	0.004	0.248
medianPolish.matrix	0.008	0.000	0.006
normalizeAffine.matrix	17.777	0.012	17.872
normalizeCurveFit.matrix	17.673	0.020	17.723
normalizeDifferencesToAverage.list	0.220	0.012	0.231
normalizeFragmentLength	0.908	0.008	0.916
normalizeQuantileRank.list	0.228	0.008	0.235
normalizeQuantileRank.matrix	0.092	0.000	0.090
normalizeQuantileSpline.matrix	1.880	0.004	1.952
normalizeTumorBoost.numeric	0.256	0.008	0.263
robustSmoothSpline	0.072	0.000	0.073
sampleCorrelations.matrix	0.212	0.000	0.210
sampleTuples	0.000	0.000	0.001
weightedMedian	4.916	0.092	5.011
wpca.matrix	0.028	0.000	0.025