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 3.0: CHECK report for MassArray on perceval

This page was generated on 2015-04-10 09:54:54 -0700 (Fri, 10 Apr 2015).

Package 511/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MassArray 1.18.0
Reid F. Thompson
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/MassArray
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: MassArray
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MassArray_1.18.0.tar.gz
StartedAt: 2015-04-10 03:17:39 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 03:18:51 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 71.3 seconds
RetCode: 0
Status:  OK 
CheckDir: MassArray.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MassArray_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/MassArray.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MassArray/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MassArray’ version ‘1.18.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MassArray’ can be installed ... [2s/4s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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 loading without being on the library search path ... 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 ... NOTE
calcMeth: warning in matrix(0, nr = 0, nc = N): partial argument match
  of 'nr' to 'nrow'
calcMeth: warning in matrix(0, nr = 0, nc = N): partial argument match
  of 'nc' to 'ncol'
calcMeth: warning in matrix(0, nr = num.SNRs, nc = N): partial argument
  match of 'nr' to 'nrow'
calcMeth: warning in matrix(0, nr = num.SNRs, nc = N): partial argument
  match of 'nc' to 'ncol'
calcMeth: warning in matrix(0, nr = num.missing, nc = N): partial
  argument match of 'nr' to 'nrow'
calcMeth: warning in matrix(0, nr = num.missing, nc = N): partial
  argument match of 'nc' to 'ncol'
calcMeth: warning in matrix(0, nr = length(na.coefs), nc = N): partial
  argument match of 'nr' to 'nrow'
calcMeth: warning in matrix(0, nr = length(na.coefs), nc = N): partial
  argument match of 'nc' to 'ncol'
calcMeth : optimizeCoefficients: warning in matrix(0, nr =
  num.fragments, nc = N): partial argument match of 'nr' to 'nrow'
calcMeth : optimizeCoefficients: warning in matrix(0, nr =
  num.fragments, nc = N): partial argument match of 'nc' to 'ncol'
calcMeth : optimizeCoefficients: warning in matrix(NA, nr =
  length(coefs) + 1, nc = length(coefs)): partial argument match of
  'nr' to 'nrow'
calcMeth : optimizeCoefficients: warning in matrix(NA, nr =
  length(coefs) + 1, nc = length(coefs)): partial argument match of
  'nc' to 'ncol'
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [30s/30s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
evaluateSNPs 25.835   0.05  25.927
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/MassArray.Rcheck/00check.log’
for details.

MassArray.Rcheck/00install.out:

* installing *source* package ‘MassArray’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MassArray)

MassArray.Rcheck/MassArray-Ex.timings:

nameusersystemelapsed
MassArray.example.data0.0370.0060.043
MassArrayData-class0.0020.0010.003
MassArrayFragment-class0.0020.0000.003
MassArrayPeak-class0.0020.0000.002
MassArraySpectrum-class0.0020.0000.002
ampliconPrediction1.6060.0131.619
analyzeCpGs0.2090.0030.218
bisConvert0.0010.0010.001
calcMW0.0020.0000.002
calcMeth0.0130.0010.014
calcPercentAdduct0.0500.0020.051
calcPercentConversion0.0420.0020.051
combine0.7180.0060.725
convControl0.0250.0020.027
countCGs0.0010.0000.001
createWiggle0.0150.0030.019
estimatePrimerDimer0.0610.0030.064
evaluateSNPs25.835 0.05025.927
expandSequence0.0010.0010.001
findCollisions0.0010.0000.000
findFragments0.0140.0010.016
findPeaks0.0010.0000.001
identifySNPs0.0300.0010.032
inSilicoFragmentation0.0120.0020.014
isAssayable0.0000.0010.000
numCollisions0.0010.0000.001
plot.MassArrayData0.0300.0020.040
position0.0080.0000.009
revComplement0.0010.0000.001
rnaDigest0.0110.0020.012
samples0.0150.0010.016
sum.MassArraySpectrum0.2700.0010.270