BioC 2.12: CHECK report for aroma.light on george2

Package: aroma.light

Version: 1.30.5

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings aroma.light_1.30.5.tar.gz

StartedAt: 2013-10-09 00:10:02 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 00:11:39 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 97.6 seconds

RetCode: 0

Status:  OK

CheckDir: aroma.light.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/aroma.light.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘aroma.light/DESCRIPTION’ ... OK
* this is package ‘aroma.light’ version ‘1.30.5’
* 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 for hidden files and directories ... NOTE
Found the following hidden files and directories:
  inst/rsp/.rspPlugins
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘aroma.light’ can be installed ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... 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 ... [53s/53s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
normalizeAffine.matrix   21.009  0.012  21.284
normalizeCurveFit.matrix 20.929  0.024  21.085
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.12-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	0.124	0.008	0.162
backtransformPrincipalCurve.matrix	1.088	0.036	1.196
calibrateMultiscan.matrix	0.008	0.000	0.006
callNaiveGenotypes.numeric	1.004	0.016	1.091
distanceBetweenLines	0.088	0.004	0.093
findPeaksAndValleys.density	0.132	0.000	0.132
fitPrincipalCurve.matrix	0.756	0.016	0.776
fitXYCurve.matrix	0.136	0.004	0.138
iwpca.matrix	0.200	0.000	0.199
likelihood.smooth.spline	0.296	0.004	0.300
medianPolish.matrix	0.04	0.00	0.04
normalizeAffine.matrix	21.009	0.012	21.284
normalizeCurveFit.matrix	20.929	0.024	21.085
normalizeDifferencesToAverage.list	0.320	0.008	0.328
normalizeFragmentLength	1.269	0.024	1.296
normalizeQuantileRank.list	0.396	0.004	0.401
normalizeQuantileRank.matrix	0.116	0.004	0.123
normalizeQuantileSpline.matrix	1.804	0.004	1.813
normalizeTumorBoost.numeric	0.268	0.008	0.274
robustSmoothSpline	0.124	0.004	0.125
sampleCorrelations.matrix	0.820	0.000	0.821
sampleTuples	0.020	0.000	0.021
wpca.matrix	0.256	0.004	0.263