Package: aroma.light

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch aroma.light_1.24.0.tar.gz

StartedAt: 2012-09-23 23:16:15 -0700 (Sun, 23 Sep 2012)

EndedAt: 2012-09-23 23:17:42 -0700 (Sun, 23 Sep 2012)

EllapsedTime: 87.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: aroma.light.Rcheck

Warnings: 2

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/aroma.light.Rcheck'
* using R version 2.15.1 (2012-06-22)
* 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 '1.24.0'
* 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.

Found .Internal calls in the following functions:
  'medianPolish.matrix' 'sampleCorrelations.matrix'
  'weightedMedian.default'
with calls to .Internal functions
  'cor' 'order' 'psort' 'qsort'

Packages should not call .Internal(): it is not part of the API, for
use only by R itself and subject to change without notice.
* 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 ... WARNING
'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 were 2 warnings.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.10-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.matrix	0.006	0.001	0.007
backtransformPrincipalCurve.matrix	0.982	0.030	1.029
calibrateMultiscan.matrix	0	0	0
callNaiveGenotypes.numeric	0.591	0.071	0.664
distanceBetweenLines	0.016	0.003	0.019
findPeaksAndValleys.density	0.089	0.011	0.100
fitPrincipalCurve.matrix	0.445	0.025	0.472
fitXYCurve.matrix	0.079	0.005	0.084
iwpca.matrix	0.011	0.002	0.013
likelihood.smooth.spline	0.199	0.016	0.215
medianPolish.matrix	0.007	0.001	0.008
normalizeAffine.matrix	17.568	0.316	17.901
normalizeCurveFit.matrix	18.223	0.323	18.559
normalizeDifferencesToAverage.list	0.440	0.024	0.472
normalizeFragmentLength	1.340	0.071	1.413
normalizeQuantileRank.list	0.362	0.069	0.432
normalizeQuantileRank.matrix	0.135	0.034	0.170
normalizeQuantileSpline.matrix	2.266	0.221	2.489
normalizeTumorBoost.numeric	0.341	0.035	0.377
robustSmoothSpline	0.150	0.008	0.158
sampleCorrelations.matrix	0.244	0.002	0.246
sampleTuples	0.001	0.001	0.002
weightedMedian	6.395	0.451	6.851
wpca.matrix	0.037	0.005	0.042