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 2.12: CHECK report for aroma.light on petty

This page was generated on 2013-10-09 09:39:32 -0700 (Wed, 09 Oct 2013).

Package 44/671HostnameOS / ArchBUILDCHECKBUILD BIN
aroma.light 1.30.5
Henrik Bengtsson
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/aroma.light
Last Changed Rev: 80825 / Revision: 81334
Last Changed Date: 2013-09-26 22:34:11 -0700 (Thu, 26 Sep 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ WARNINGS ] OK 

Summary

Package: aroma.light
Version: 1.30.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch aroma.light_1.30.5.tar.gz
StartedAt: 2013-10-08 21:35:39 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 21:37:32 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 113.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: aroma.light.Rcheck
Warnings: 1

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/aroma.light.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'aroma.light/DESCRIPTION' ... OK
* this is package 'aroma.light' version '1.30.5'
* 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 ... [4s/4s] 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 for unstated 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 ... WARNING
checking a package with encoding  'latin1'  in an ASCII locale

 [56s/57s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
normalizeCurveFit.matrix 22.676  0.129  23.065
normalizeAffine.matrix   22.412  0.118  22.662
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-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
backtransformAffine.matrix0.0890.0020.092
backtransformPrincipalCurve.matrix1.0790.0351.128
calibrateMultiscan.matrix0.0050.0010.005
callNaiveGenotypes.numeric0.9860.0251.012
distanceBetweenLines0.0610.0030.065
findPeaksAndValleys.density0.1010.0040.106
fitPrincipalCurve.matrix0.7450.0290.780
fitXYCurve.matrix0.1290.0070.139
iwpca.matrix0.0480.0040.052
likelihood.smooth.spline0.2720.0190.293
medianPolish.matrix0.0230.0030.026
normalizeAffine.matrix22.412 0.11822.662
normalizeCurveFit.matrix22.676 0.12923.065
normalizeDifferencesToAverage.list0.3810.0180.403
normalizeFragmentLength1.3340.0631.408
normalizeQuantileRank.list0.3470.0140.373
normalizeQuantileRank.matrix0.1920.0050.199
normalizeQuantileSpline.matrix1.7860.0311.818
normalizeTumorBoost.numeric0.2910.0190.315
robustSmoothSpline0.1420.0120.157
sampleCorrelations.matrix0.9460.0080.956
sampleTuples0.0090.0030.012
wpca.matrix0.1020.0240.127