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 3.1: CHECK report for aroma.light on zin2

This page was generated on 2015-10-09 09:23:09 -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: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings aroma.light_2.4.0.tar.gz
StartedAt: 2015-10-08 22:31:27 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 22:32:44 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 76.3 seconds
RetCode: 0
Status:  OK 
CheckDir: aroma.light.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings aroma.light_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/aroma.light.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘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 ... [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 ... [27s/27s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
normalizeAffine   11.959  0.020  11.989
normalizeCurveFit 11.189  0.016  11.215
* 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’ [3s/3s]
  Running ‘normalizeCurveFit.matrix.R’ [11s/11s]
  Running ‘normalizeDifferencesToAverage.R’ [0s/0s]
  Running ‘normalizeFragmentLength-ex1.R’ [1s/1s]
  Running ‘normalizeFragmentLength-ex2.R’ [1s/1s]
  Running ‘normalizeQuantileRank.list.R’ [1s/1s]
  Running ‘normalizeQuantileRank.matrix.R’ [0s/0s]
  Running ‘normalizeQuantileSpline.matrix.R’ [1s/1s]
  Running ‘normalizeTumorBoost,flavors.R’ [1s/1s]
  Running ‘normalizeTumorBoost.R’ [0s/0s]
  Running ‘robustSmoothSpline.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]
 [27s/27s] OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/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
backtransformAffine0.0050.0000.005
backtransformPrincipalCurve0.4050.0070.422
calibrateMultiscan0.0010.0000.000
callNaiveGenotypes0.3850.0000.385
distanceBetweenLines0.0190.0000.020
findPeaksAndValleys0.0470.0000.047
fitPrincipalCurve0.2710.0080.279
fitXYCurve0.0590.0000.059
iwpca0.0160.0000.016
likelihood.smooth.spline0.1140.0000.114
medianPolish0.0060.0000.006
normalizeAffine11.959 0.02011.989
normalizeCurveFit11.189 0.01611.215
normalizeDifferencesToAverage0.1770.0000.178
normalizeFragmentLength0.6380.0120.650
normalizeQuantileRank0.1980.0000.198
normalizeQuantileRank.matrix0.0570.0000.057
normalizeQuantileSpline0.5930.0120.605
normalizeTumorBoost0.160.000.16
robustSmoothSpline0.050.000.05
sampleCorrelations0.4710.0000.471
sampleTuples0.0010.0000.001
wpca0.0270.0000.026