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BioC 3.2: CHECK report for aroma.light on zin1

This page was generated on 2016-04-23 10:10:32 -0700 (Sat, 23 Apr 2016).

Package 53/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
aroma.light 3.0.0
Henrik Bengtsson
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/aroma.light
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (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: 3.0.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings aroma.light_3.0.0.tar.gz
StartedAt: 2016-04-22 22:10:29 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 22:11:48 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 79.3 seconds
RetCode: 0
Status:  OK 
CheckDir: aroma.light.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings aroma.light_3.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/aroma.light.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-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 ‘3.0.0’
* 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 ... [1s/1s] 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 11.797  0.023  11.853
normalizeAffine   11.479  0.028  11.514
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘backtransformAffine.matrix.R’ [0s/0s]
  Running ‘backtransformPrincipalCurve.matrix.R’ [1s/1s]
  Running ‘callNaiveGenotypes.R’ [1s/1s]
  Running ‘distanceBetweenLines.R’ [0s/0s]
  Running ‘findPeaksAndValleys.R’ [0s/0s]
  Running ‘fitPrincipalCurve.matrix.R’ [1s/1s]
  Running ‘fitXYCurve.matrix.R’ [0s/0s]
  Running ‘iwpca.matrix.R’ [0s/0s]
  Running ‘likelihood.smooth.spline.R’ [0s/0s]
  Running ‘medianPolish.matrix.R’ [0s/0s]
  Running ‘normalizeAffine.matrix.R’ [4s/4s]
  Running ‘normalizeAverage.list.R’ [0s/0s]
  Running ‘normalizeAverage.matrix.R’ [0s/0s]
  Running ‘normalizeCurveFit.matrix.R’ [12s/12s]
  Running ‘normalizeDifferencesToAverage.R’ [0s/0s]
  Running ‘normalizeFragmentLength-ex1.R’ [1s/1s]
  Running ‘normalizeFragmentLength-ex2.R’ [1s/1s]
  Running ‘normalizeQuantileRank.list.R’ [0s/0s]
  Running ‘normalizeQuantileRank.matrix.R’ [0s/0s]
  Running ‘normalizeQuantileSpline.matrix.R’ [1s/1s]
  Running ‘normalizeTumorBoost,flavors.R’ [1s/1s]
  Running ‘normalizeTumorBoost.R’ [1s/1s]
  Running ‘robustSmoothSpline.R’ [0s/0s]
  Running ‘rowAverages.matrix.R’ [0s/0s]
  Running ‘sampleCorrelations.matrix.R’ [1s/1s]
  Running ‘sampleTuples.R’ [0s/0s]
  Running ‘wpca.matrix.R’ [0s/0s]
  Running ‘wpca2.matrix.R’ [0s/0s]
 [30s/30s] OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.2-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
backtransformAffine0.0050.0000.005
backtransformPrincipalCurve0.4060.0080.424
calibrateMultiscan0.0000.0000.001
callNaiveGenotypes0.4320.0080.439
distanceBetweenLines0.0220.0000.022
findPeaksAndValleys0.0510.0000.051
fitPrincipalCurve0.2710.0000.271
fitXYCurve0.050.000.05
iwpca0.0140.0000.014
likelihood.smooth.spline0.1040.0000.108
medianPolish0.0060.0000.011
normalizeAffine11.479 0.02811.514
normalizeCurveFit11.797 0.02311.853
normalizeDifferencesToAverage0.1880.0000.188
normalizeFragmentLength0.6900.0080.698
normalizeQuantileRank0.1670.0000.167
normalizeQuantileRank.matrix0.0610.0000.060
normalizeQuantileSpline0.7460.0000.748
normalizeTumorBoost0.1670.0000.167
robustSmoothSpline0.0510.0000.051
sampleCorrelations0.4290.0000.429
sampleTuples0.0010.0000.001
wpca0.0220.0000.022