Back to the "Multiple platform build/check report"[A] B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.3: CHECK report for aroma.light on oaxaca

This page was generated on 2016-10-13 12:56:08 -0700 (Thu, 13 Oct 2016).

Package 54/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
aroma.light 3.2.0
Henrik Bengtsson
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/aroma.light
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
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
oaxaca 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: 3.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings aroma.light_3.2.0.tar.gz
StartedAt: 2016-10-12 23:19:05 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 23:20:30 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 84.7 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_3.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/aroma.light.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘aroma.light/DESCRIPTION’ ... OK
* this is package ‘aroma.light’ version ‘3.2.0’
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
normalizeCurveFit 9.013   0.05   9.094
normalizeAffine   8.844   0.06   8.923
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘backtransformAffine.matrix.R’
  Running ‘backtransformPrincipalCurve.matrix.R’
  Running ‘callNaiveGenotypes.R’
  Running ‘distanceBetweenLines.R’
  Running ‘findPeaksAndValleys.R’
  Running ‘fitPrincipalCurve.matrix.R’
  Running ‘fitXYCurve.matrix.R’
  Running ‘iwpca.matrix.R’
  Running ‘likelihood.smooth.spline.R’
  Running ‘medianPolish.matrix.R’
  Running ‘normalizeAffine.matrix.R’
  Running ‘normalizeAverage.list.R’
  Running ‘normalizeAverage.matrix.R’
  Running ‘normalizeCurveFit.matrix.R’
  Running ‘normalizeDifferencesToAverage.R’
  Running ‘normalizeFragmentLength-ex1.R’
  Running ‘normalizeFragmentLength-ex2.R’
  Running ‘normalizeQuantileRank.list.R’
  Running ‘normalizeQuantileRank.matrix.R’
  Running ‘normalizeQuantileSpline.matrix.R’
  Running ‘normalizeTumorBoost,flavors.R’
  Running ‘normalizeTumorBoost.R’
  Running ‘robustSmoothSpline.R’
  Running ‘rowAverages.matrix.R’
  Running ‘sampleCorrelations.matrix.R’
  Running ‘sampleTuples.R’
  Running ‘wpca.matrix.R’
  Running ‘wpca2.matrix.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-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
backtransformAffine0.0050.0010.006
backtransformPrincipalCurve0.4200.0130.493
calibrateMultiscan0.0000.0000.001
callNaiveGenotypes0.3840.0080.393
distanceBetweenLines0.0420.0010.043
findPeaksAndValleys0.0430.0020.062
fitPrincipalCurve0.2990.0100.311
fitXYCurve0.0500.0010.054
iwpca0.0330.0000.034
likelihood.smooth.spline0.0900.0030.094
medianPolish0.0070.0000.020
normalizeAffine8.8440.0608.923
normalizeCurveFit9.0130.0509.094
normalizeDifferencesToAverage0.2040.0080.228
normalizeFragmentLength0.5700.0200.598
normalizeQuantileRank0.1700.0060.186
normalizeQuantileRank.matrix0.0590.0010.061
normalizeQuantileSpline0.6830.0100.694
normalizeTumorBoost0.1830.0080.195
robustSmoothSpline0.0480.0030.055
sampleCorrelations0.4580.0060.465
sampleTuples0.0010.0000.002
wpca0.0340.0030.037