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BioC 2.14: CHECK report for aroma.light on petty

This page was generated on 2014-10-08 08:57:43 -0700 (Wed, 08 Oct 2014).

Package 47/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
aroma.light 2.0.0
Henrik Bengtsson
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/aroma.light
Last Changed Rev: 88849 / Revision: 95116
Last Changed Date: 2014-04-11 16:08:58 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: aroma.light
Version: 2.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch aroma.light_2.0.0.tar.gz
StartedAt: 2014-10-07 20:43:18 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 20:45:20 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 121.2 seconds
RetCode: 0
Status:  OK 
CheckDir: aroma.light.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch aroma.light_2.0.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/aroma.light.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘aroma.light/DESCRIPTION’ ... OK
* this is package ‘aroma.light’ version ‘2.0.0’
* 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 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 ... [4s/4s] 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 ... 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 ... [54s/55s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
normalizeAffine   21.912  0.090  22.491
normalizeCurveFit 21.778  0.097  21.967
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/aroma.light.Rcheck/00check.log’
for details.

aroma.light.Rcheck/00install.out:

* 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)

aroma.light.Rcheck/aroma.light-Ex.timings:

nameusersystemelapsed
backtransformAffine0.0110.0010.012
backtransformPrincipalCurve0.9870.0161.014
calibrateMultiscan0.0010.0000.001
callNaiveGenotypes1.1800.0261.207
distanceBetweenLines0.0910.0030.094
findPeaksAndValleys0.0790.0020.081
fitPrincipalCurve0.8900.0330.932
fitXYCurve0.1080.0040.115
iwpca0.0660.0030.069
likelihood.smooth.spline0.2470.0060.282
medianPolish0.0130.0010.014
normalizeAffine21.912 0.09022.491
normalizeCurveFit21.778 0.09721.967
normalizeDifferencesToAverage0.3570.0190.379
normalizeFragmentLength1.1480.0381.197
normalizeQuantileRank0.3810.0090.400
normalizeQuantileRank.matrix0.1190.0020.124
normalizeQuantileSpline1.6230.0231.653
normalizeTumorBoost0.4080.0210.434
robustSmoothSpline0.1470.0080.159
sampleCorrelations0.8890.0020.891
sampleTuples0.0030.0010.003
wpca0.0750.0060.082