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BioC 3.3: CHECK report for MassArray on moscato2

This page was generated on 2016-10-13 12:49:17 -0700 (Thu, 13 Oct 2016).

Package 661/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MassArray 1.24.0
Reid F. Thompson
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/MassArray
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  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MassArray
Version: 1.24.0
Command: rm -rf MassArray.buildbin-libdir MassArray.Rcheck && mkdir MassArray.buildbin-libdir MassArray.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MassArray.buildbin-libdir MassArray_1.24.0.tar.gz >MassArray.Rcheck\00install.out 2>&1 && cp MassArray.Rcheck\00install.out MassArray-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=MassArray.buildbin-libdir --install="check:MassArray-install.out" --force-multiarch --no-vignettes --timings MassArray_1.24.0.tar.gz
StartedAt: 2016-10-13 05:49:37 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 05:51:20 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 102.5 seconds
RetCode: 0
Status:  OK  
CheckDir: MassArray.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MassArray.buildbin-libdir MassArray.Rcheck && mkdir MassArray.buildbin-libdir MassArray.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MassArray.buildbin-libdir MassArray_1.24.0.tar.gz >MassArray.Rcheck\00install.out 2>&1 && cp MassArray.Rcheck\00install.out MassArray-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=MassArray.buildbin-libdir --install="check:MassArray-install.out" --force-multiarch --no-vignettes --timings MassArray_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/MassArray.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MassArray/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MassArray' version '1.24.0'
* 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 whether package 'MassArray' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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'
$<-,MassArrayData: no visible global function definition for 'slot<-'
$<-,MassArrayFragment: no visible global function definition for
  'slot<-'
$<-,MassArrayPeak: no visible global function definition for 'slot<-'
$<-,MassArraySpectrum: no visible global function definition for
  'slot<-'
initialize,MassArrayData: no visible global function definition for
  'read.table'
Undefined global functions or variables:
  read.table slot<-
Consider adding
  importFrom("methods", "slot<-")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
evaluateSNPs 19.46   0.01   19.47
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
evaluateSNPs 21.98      0   21.99
* 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

Status: 2 NOTEs
See
  'E:/biocbld/bbs-3.3-bioc/meat/MassArray.Rcheck/00check.log'
for details.


MassArray.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'MassArray' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MassArray' as MassArray_1.24.0.zip
* DONE (MassArray)

MassArray.Rcheck/examples_i386/MassArray-Ex.timings:

nameusersystemelapsed
MassArray.example.data0.030.020.05
MassArrayData-class000
MassArrayFragment-class000
MassArrayPeak-class000
MassArraySpectrum-class0.020.000.01
ampliconPrediction1.030.001.03
analyzeCpGs0.090.000.10
bisConvert000
calcMW0.020.000.01
calcMeth000
calcPercentAdduct0.030.000.03
calcPercentConversion0.030.000.03
combine0.360.000.36
convControl0.020.000.02
countCGs000
createWiggle0.020.000.02
estimatePrimerDimer0.090.000.09
evaluateSNPs19.46 0.0119.47
expandSequence000
findCollisions000
findFragments000
findPeaks000
identifySNPs0.010.000.02
inSilicoFragmentation000
isAssayable000
numCollisions0.020.000.01
plot.MassArrayData0.010.000.02
position0.020.000.01
revComplement000
rnaDigest0.020.000.02
samples000
sum.MassArraySpectrum0.150.000.16

MassArray.Rcheck/examples_x64/MassArray-Ex.timings:

nameusersystemelapsed
MassArray.example.data0.030.000.03
MassArrayData-class000
MassArrayFragment-class000
MassArrayPeak-class000
MassArraySpectrum-class000
ampliconPrediction1.310.011.32
analyzeCpGs0.110.000.11
bisConvert000
calcMW000
calcMeth0.020.000.01
calcPercentAdduct0.040.000.05
calcPercentConversion0.040.000.03
combine0.490.000.50
convControl0.040.000.03
countCGs000
createWiggle0.010.000.02
estimatePrimerDimer0.050.000.04
evaluateSNPs21.98 0.0021.99
expandSequence000
findCollisions000
findFragments0.010.000.01
findPeaks000
identifySNPs0.020.000.02
inSilicoFragmentation0.020.000.01
isAssayable000
numCollisions000
plot.MassArrayData0.030.000.03
position0.010.000.02
revComplement000
rnaDigest000
samples000
sum.MassArraySpectrum0.220.000.22