Package: aroma.light

Version: 1.24.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings aroma.light_1.24.0.tar.gz

StartedAt: 2012-03-31 23:37:13 -0700 (Sat, 31 Mar 2012)

EndedAt: 2012-03-31 23:38:11 -0700 (Sat, 31 Mar 2012)

EllapsedTime: 57.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: aroma.light.Rcheck

Warnings: 1

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/aroma.light.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* 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 ... OK
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  '/loc/home/hpages/test-puck5/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	0.004	0.000	0.004
backtransformPrincipalCurve.matrix	0.492	0.000	0.508
calibrateMultiscan.matrix	0	0	0
callNaiveGenotypes.numeric	0.488	0.000	0.505
distanceBetweenLines	0.012	0.000	0.016
findPeaksAndValleys.density	0.076	0.000	0.074
fitPrincipalCurve.matrix	0.364	0.012	0.400
fitXYCurve.matrix	0.060	0.000	0.063
iwpca.matrix	0.008	0.004	0.014
likelihood.smooth.spline	0.136	0.004	0.138
medianPolish.matrix	0.008	0.000	0.006
normalizeAffine.matrix	12.580	0.000	12.593
normalizeCurveFit.matrix	12.909	0.020	12.938
normalizeDifferencesToAverage.list	0.188	0.000	0.188
normalizeFragmentLength	0.616	0.004	0.621
normalizeQuantileRank.list	0.192	0.004	0.194
normalizeQuantileRank.matrix	0.056	0.000	0.058
normalizeQuantileSpline.matrix	1.064	0.004	1.069
normalizeTumorBoost.numeric	0.192	0.000	0.212
robustSmoothSpline	0.068	0.000	0.070
sampleCorrelations.matrix	0.108	0.000	0.108
sampleTuples	0.000	0.000	0.001
weightedMedian	3.185	0.036	3.219
wpca.matrix	0.016	0.004	0.025