Package: aroma.light

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch aroma.light_1.20.0.tar.gz

StartedAt: 2011-10-20 13:26:10 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 13:28:24 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 134.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: aroma.light.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/aroma.light.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'aroma.light/DESCRIPTION' ... OK
* this is package 'aroma.light' version '1.20.0'
* package encoding: latin1
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 ... 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 ... NOTE
'library' or 'require' call not declared from: R.basic
* checking examples ... WARNING
checking a package with encoding  'latin1'  in an ASCII locale

 OK
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  '/Users/biocbuild/bbs-2.8-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
Warning messages:
1: In value[[3L]](cond) :
  Multiple installations of package 'aroma.light' was found. Using the first. Paths to all installations: /Users/biocbuild/bbs-2.8-bioc/meat/aroma.light.Rcheck, /Library/Frameworks/R.framework/Versions/2.13/Resources/library
2: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible 

* DONE (aroma.light)

name	user	system	elapsed
backtransformAffine.matrix	0.008	0.001	0.011
backtransformPrincipalCurve.matrix	1.067	0.026	1.337
calibrateMultiscan.matrix	0	0	0
callNaiveGenotypes.numeric	0.775	0.104	0.914
distanceBetweenLines	0.025	0.002	0.028
findPeaksAndValleys.density	0.070	0.015	0.096
fitPrincipalCurve.matrix	0.745	0.018	0.770
fitXYCurve.matrix	0.096	0.003	0.102
iwpca.matrix	0.018	0.002	0.023
likelihood.smooth.spline	0.306	0.019	0.333
medianPolish.matrix	0.009	0.001	0.010
normalizeAffine.matrix	28.423	0.535	30.075
normalizeCurveFit.matrix	28.389	0.508	29.643
normalizeDifferencesToAverage.list	0.027	0.002	0.029
normalizeFragmentLength	1.386	0.048	1.441
normalizeQuantileRank.list	0.203	0.059	0.263
normalizeQuantileRank.matrix	0.133	0.034	0.170
normalizeQuantileSpline.matrix	2.679	0.222	2.948
normalizeTumorBoost.numeric	0.176	0.023	0.213
robustSmoothSpline	0.083	0.003	0.102
sampleCorrelations.matrix	0.217	0.005	0.247
sampleTuples	0.002	0.000	0.001
weightedMedian	5.781	0.463	6.373
wpca.matrix	0.112	0.006	0.118