Package: aroma.light

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch aroma.light_1.22.0.tar.gz

StartedAt: 2012-03-23 23:20:08 -0700 (Fri, 23 Mar 2012)

EndedAt: 2012-03-23 23:22:10 -0700 (Fri, 23 Mar 2012)

EllapsedTime: 121.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: aroma.light.Rcheck

Warnings: 2

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/aroma.light.Rcheck'
* using R version 2.14.2 (2012-02-29)
* 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 '1.22.0'
* 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 ... 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
  Warning: unable to re-encode 'weightedMedian.R' line(s) 104
See '/Users/biocbuild/bbs-2.9-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 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 ... WARNING
checking a package with encoding  'latin1'  in an ASCII locale

 OK
* checking PDF version of manual ... OK

WARNING: There were 2 warnings, see
  '/Users/biocbuild/bbs-2.9-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
Warning: unable to re-encode 'weightedMedian.R' line(s) 104
** 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	0.005	0.001	0.007
backtransformPrincipalCurve.matrix	0.952	0.031	1.001
calibrateMultiscan.matrix	0	0	0
callNaiveGenotypes.numeric	0.720	0.103	0.833
distanceBetweenLines	0.026	0.002	0.028
findPeaksAndValleys.density	0.086	0.016	0.101
fitPrincipalCurve.matrix	0.689	0.032	0.724
fitXYCurve.matrix	0.116	0.007	0.123
iwpca.matrix	0.018	0.002	0.020
likelihood.smooth.spline	0.259	0.022	0.282
medianPolish.matrix	0.009	0.000	0.009
normalizeAffine.matrix	27.875	0.500	28.554
normalizeCurveFit.matrix	27.978	0.525	28.530
normalizeDifferencesToAverage.list	0.384	0.023	0.407
normalizeFragmentLength	1.495	0.067	1.565
normalizeQuantileRank.list	0.344	0.068	0.412
normalizeQuantileRank.matrix	0.149	0.035	0.189
normalizeQuantileSpline.matrix	2.035	0.230	2.277
normalizeTumorBoost.numeric	0.352	0.030	0.383
robustSmoothSpline	0.136	0.008	0.166
sampleCorrelations.matrix	0.197	0.003	0.200
sampleTuples	0.001	0.000	0.002
weightedMedian	5.607	0.446	6.062
wpca.matrix	0.037	0.004	0.041