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BioC 3.1: CHECK report for aroma.light on petty

This page was generated on 2015-10-09 09:33:05 -0700 (Fri, 09 Oct 2015).

Package 50/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
aroma.light 2.4.0
Henrik Bengtsson
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/aroma.light
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: aroma.light
Version: 2.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings aroma.light_2.4.0.tar.gz
StartedAt: 2015-10-08 21:28:50 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 21:31:17 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 146.9 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 aroma.light_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/aroma.light.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘2.4.0’
* 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 ... [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 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 ... [43s/43s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
normalizeAffine   17.543  0.072  17.649
normalizeCurveFit 17.539  0.066  17.637
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘backtransformAffine.matrix.R’ [1s/1s]
  Running ‘backtransformPrincipalCurve.matrix.R’ [1s/1s]
  Running ‘callNaiveGenotypes.R’ [2s/2s]
  Running ‘distanceBetweenLines.R’ [1s/1s]
  Running ‘findPeaksAndValleys.R’ [1s/1s]
  Running ‘fitPrincipalCurve.matrix.R’ [1s/1s]
  Running ‘fitXYCurve.matrix.R’ [1s/1s]
  Running ‘iwpca.matrix.R’ [1s/1s]
  Running ‘likelihood.smooth.spline.R’ [1s/1s]
  Running ‘medianPolish.matrix.R’ [1s/1s]
  Running ‘normalizeAffine.matrix.R’ [5s/5s]
  Running ‘normalizeCurveFit.matrix.R’ [18s/19s]
  Running ‘normalizeDifferencesToAverage.R’ [1s/1s]
  Running ‘normalizeFragmentLength-ex1.R’ [1s/1s]
  Running ‘normalizeFragmentLength-ex2.R’ [2s/2s]
  Running ‘normalizeQuantileRank.list.R’ [1s/1s]
  Running ‘normalizeQuantileRank.matrix.R’ [1s/1s]
  Running ‘normalizeQuantileSpline.matrix.R’ [2s/2s]
  Running ‘normalizeTumorBoost,flavors.R’ [1s/2s]
  Running ‘normalizeTumorBoost.R’ [1s/1s]
  Running ‘robustSmoothSpline.R’ [1s/2s]
  Running ‘sampleCorrelations.matrix.R’ [2s/2s]
  Running ‘sampleTuples.R’ [1s/1s]
  Running ‘wpca.matrix.R’ [1s/1s]
  Running ‘wpca2.matrix.R’ [1s/1s]
 [49s/52s] OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.1-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
backtransformAffine0.0090.0020.010
backtransformPrincipalCurve0.6920.0140.732
calibrateMultiscan0.0010.0000.000
callNaiveGenotypes0.5920.0120.606
distanceBetweenLines0.0700.0010.071
findPeaksAndValleys0.0920.0020.095
fitPrincipalCurve0.3980.0130.413
fitXYCurve0.1010.0050.109
iwpca0.0620.0010.063
likelihood.smooth.spline0.1860.0030.191
medianPolish0.0100.0010.030
normalizeAffine17.543 0.07217.649
normalizeCurveFit17.539 0.06617.637
normalizeDifferencesToAverage0.3070.0140.346
normalizeFragmentLength0.9870.0281.170
normalizeQuantileRank0.2500.0100.287
normalizeQuantileRank.matrix0.1310.0020.144
normalizeQuantileSpline1.1190.0241.176
normalizeTumorBoost0.3470.0140.374
robustSmoothSpline0.1490.0100.184
sampleCorrelations0.7330.0020.735
sampleTuples0.0020.0000.002
wpca0.0580.0030.063