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BioC 2.14: CHECK report for aroma.light on zin2

This page was generated on 2014-10-08 08:48:01 -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: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings aroma.light_2.0.0.tar.gz
StartedAt: 2014-10-07 21:46:45 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 21:47:36 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 50.6 seconds
RetCode: 0
Status:  OK 
CheckDir: aroma.light.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings aroma.light_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/aroma.light.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘2.0.0’
* 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 ... [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 ... 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 ... [28s/28s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
normalizeCurveFit 11.441  0.008  11.475
normalizeAffine   11.284  0.004  11.306
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/home/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
backtransformAffine0.0040.0000.006
backtransformPrincipalCurve0.4520.0000.462
calibrateMultiscan000
callNaiveGenotypes0.6040.0080.616
distanceBetweenLines0.0280.0000.027
findPeaksAndValleys0.0520.0000.052
fitPrincipalCurve0.3560.0040.361
fitXYCurve0.0560.0000.069
iwpca0.0200.0000.021
likelihood.smooth.spline0.1160.0040.121
medianPolish0.0040.0000.006
normalizeAffine11.284 0.00411.306
normalizeCurveFit11.441 0.00811.475
normalizeDifferencesToAverage0.1960.0000.197
normalizeFragmentLength0.7040.0120.715
normalizeQuantileRank0.1880.0000.186
normalizeQuantileRank.matrix0.0720.0000.070
normalizeQuantileSpline0.8400.0040.847
normalizeTumorBoost0.1640.0120.180
robustSmoothSpline0.0560.0000.058
sampleCorrelations0.4240.0000.426
sampleTuples0.0040.0000.002
wpca0.0280.0000.029