Package: aroma.light

Version: 1.28.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch aroma.light_1.28.0.tar.gz

StartedAt: 2013-03-24 22:33:04 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 22:34:22 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 78.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: aroma.light.Rcheck

Warnings: 2

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/aroma.light.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.28.0'
* 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 ... WARNING
Found the following significant warnings:
  Warning: unable to re-encode '901.CalibrationAndNormalization.R' line(s) 28,67,162
  Warning: unable to re-encode 'normalizeCurveFit.matrix.R' line(s) 112
See '/Users/biocbuild/bbs-2.11-bioc/meat/aroma.light.Rcheck/00install.out' for details.
* 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 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 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 ... OK
* checking examples ... WARNING
checking a package with encoding  'latin1'  in an ASCII locale

 OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
normalizeAffine.matrix   15.537  0.506  16.107
normalizeCurveFit.matrix 15.491  0.461  15.979
* checking PDF version of manual ... OK

WARNING: There were 2 warnings.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/aroma.light.Rcheck/00check.log'
for details.

* installing *source* package 'aroma.light' ...
** R
Warning: unable to re-encode '901.CalibrationAndNormalization.R' line(s) 28,67,162
Warning: unable to re-encode 'normalizeCurveFit.matrix.R' line(s) 112
** 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	0.002	0.008
backtransformPrincipalCurve.matrix	0.701	0.035	0.739
calibrateMultiscan.matrix	0.001	0.000	0.000
callNaiveGenotypes.numeric	0.617	0.099	0.727
distanceBetweenLines	0.018	0.003	0.020
findPeaksAndValleys.density	0.057	0.012	0.069
fitPrincipalCurve.matrix	0.485	0.044	0.535
fitXYCurve.matrix	0.075	0.008	0.085
iwpca.matrix	0.013	0.002	0.015
likelihood.smooth.spline	0.173	0.020	0.194
medianPolish.matrix	0.006	0.001	0.006
normalizeAffine.matrix	15.537	0.506	16.107
normalizeCurveFit.matrix	15.491	0.461	15.979
normalizeDifferencesToAverage.list	0.290	0.028	0.326
normalizeFragmentLength	0.977	0.073	1.071
normalizeQuantileRank.list	0.262	0.084	0.354
normalizeQuantileRank.matrix	0.097	0.044	0.144
normalizeQuantileSpline.matrix	1.933	0.281	2.345
normalizeTumorBoost.numeric	0.216	0.038	0.275
robustSmoothSpline	0.099	0.011	0.117
sampleCorrelations.matrix	0.627	0.004	0.632
sampleTuples	0.001	0.001	0.001
wpca.matrix	0.025	0.006	0.031