BioC 3.0: CHECK report for aroma.light on zin1

Package: aroma.light

Version: 2.2.1

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings aroma.light_2.2.1.tar.gz

StartedAt: 2015-04-09 21:36:12 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 21:37:06 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 54.5 seconds

RetCode: 0

Status:  OK

CheckDir: aroma.light.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings aroma.light_2.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/aroma.light.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘2.2.1’
* 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 ... [2s/2s] 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 ... [29s/29s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
normalizeCurveFit 12.169  0.012  12.264
normalizeAffine   11.944  0.000  11.999
* checking PDF version of manual ... OK
* DONE

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-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	0.008	0.000	0.006
backtransformPrincipalCurve	0.520	0.012	0.573
calibrateMultiscan	0	0	0
callNaiveGenotypes	0.468	0.004	0.491
distanceBetweenLines	0.028	0.000	0.030
findPeaksAndValleys	0.052	0.000	0.053
fitPrincipalCurve	0.324	0.008	0.332
fitXYCurve	0.056	0.000	0.059
iwpca	0.024	0.000	0.024
likelihood.smooth.spline	0.128	0.000	0.128
medianPolish	0.008	0.000	0.014
normalizeAffine	11.944	0.000	11.999
normalizeCurveFit	12.169	0.012	12.264
normalizeDifferencesToAverage	0.196	0.004	0.201
normalizeFragmentLength	0.720	0.000	0.728
normalizeQuantileRank	0.244	0.004	0.249
normalizeQuantileRank.matrix	0.076	0.000	0.078
normalizeQuantileSpline	0.900	0.000	0.938
normalizeTumorBoost	0.184	0.004	0.190
robustSmoothSpline	0.060	0.000	0.059
sampleCorrelations	0.432	0.000	0.432
sampleTuples	0.000	0.000	0.002
wpca	0.028	0.000	0.030