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BioC 3.1: CHECK report for codelink on morelia

This page was generated on 2015-10-09 09:38:13 -0700 (Fri, 09 Oct 2015).

Package 196/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
codelink 1.36.0
Diego Diez
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/codelink
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: codelink
Version: 1.36.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings codelink_1.36.0.tar.gz
StartedAt: 2015-10-09 00:32:09 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 00:34:04 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 115.7 seconds
RetCode: 0
Status:  OK 
CheckDir: codelink.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings codelink_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/codelink.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘codelink/DESCRIPTION’ ... OK
* this is package ‘codelink’ version ‘1.36.0’
* 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 ‘codelink’ can be installed ... [15s/15s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... NOTE
'library' or 'require' call to ‘genefilter’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Codelink2CodelinkSet: no visible global function definition for
  ‘phenoData<-’
Codelink2CodelinkSet: no visible global function definition for
  ‘featureData<-’
Codelink2CodelinkSet: no visible global function definition for
  ‘experimentData’
Codelink2CodelinkSet: no visible global function definition for
  ‘experimentData<-’
Codelink2eSet: no visible global function definition for
  ‘featureNames<-’
Codelink2eSet: no visible global function definition for
  ‘sampleNames<-’
Codelink2eSet: no visible global function definition for
  ‘experimentData’
Codelink2eSet: no visible global function definition for
  ‘experimentData<-’
averageProbes,CodelinkSet: no visible global function definition for
  ‘sampleNames’
averageProbes,CodelinkSet: no visible global function definition for
  ‘pData’
averageProbes,CodelinkSet: no visible global function definition for
  ‘featureData’
averageProbes,CodelinkSet: no visible global function definition for
  ‘varMetadata’
averageProbes,CodelinkSet: no visible global function definition for
  ‘featureNames<-’
averageProbes,CodelinkSet: no visible global function definition for
  ‘phenoData’
codCorrect,CodelinkSet: no visible global function definition for
  ‘assayDataElement<-’
codCorrect,CodelinkSet: no visible global function definition for
  ‘experimentData’
codCorrect,CodelinkSet: no visible global function definition for
  ‘experimentData<-’
codPlotDensity,CodelinkSet : .local: no visible global function
  definition for ‘sampleNames’
codPlotImage,CodelinkSet : .local: no visible global function
  definition for ‘sampleNames’
codPlotMA,CodelinkSet : .local: no visible global function definition
  for ‘sampleNames’
codPlotMA,MArrayLM : .local: no visible global function definition for
  ‘plotma’
codPlotScatter,CodelinkSet : .local: no visible global function
  definition for ‘sampleNames’
createFlagWeights,CodelinkSet: no visible global function definition
  for ‘sampleNames’
createFlagWeights,CodelinkSet: no visible global function definition
  for ‘featureNames’
createTypeWeights,CodelinkSet: no visible global function definition
  for ‘sampleNames’
createTypeWeights,CodelinkSet: no visible global function definition
  for ‘featureNames’
exprs,CodelinkSet: no visible global function definition for
  ‘assayDataElement’
filterSNR,matrix: no visible global function definition for
  ‘genefilter’
filterSNR,matrix: no visible global function definition for ‘filterfun’
getBkg,CodelinkSet: no visible global function definition for
  ‘assayDataElement’
getFlag,CodelinkSet: no visible global function definition for
  ‘assayDataElement’
getInfo,CodelinkSet: no visible global function definition for
  ‘experimentData’
getSNR,CodelinkSet: no visible global function definition for
  ‘assayDataElement’
getWeight,CodelinkSet: no visible global function definition for
  ‘assayDataElement’
logicalCol,CodelinkSet: no visible global function definition for
  ‘pData’
logicalCol,CodelinkSet: no visible global function definition for
  ‘featureData’
logicalRow,CodelinkSet: no visible global function definition for
  ‘pData’
logicalRow,CodelinkSet: no visible global function definition for
  ‘featureData’
meanSNR,CodelinkSet: no visible global function definition for ‘pData’
meanSNR,CodelinkSet: no visible global function definition for
  ‘featureData’
normalize,CodelinkSet : .local: no visible global function definition
  for ‘assayDataElement<-’
normalize,CodelinkSet : .local: no visible global function definition
  for ‘experimentData’
normalize,CodelinkSet : .local: no visible global function definition
  for ‘experimentData<-’
probeNames,CodelinkSet: no visible global function definition for
  ‘pData’
probeNames,CodelinkSet: no visible global function definition for
  ‘featureData’
probeNames,CodelinkSetUnique: no visible global function definition for
  ‘featureNames’
probeTypes,CodelinkSet: no visible global function definition for
  ‘pData’
probeTypes,CodelinkSet: no visible global function definition for
  ‘featureData’
writeCluster,CodelinkSet : .local: no visible global function
  definition for ‘sampleNames’
writeCluster,ExpressionSet : .local: no visible global function
  definition for ‘sampleNames’
writeCluster,ExpressionSet : .local: no visible global function
  definition for ‘featureNames’
writeCodelink,CodelinkSet: no visible global function definition for
  ‘sampleNames’
writeCodelink,CodelinkSet: no visible global function definition for
  ‘featureNames’
* 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 ... [7s/7s] OK
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/codelink.Rcheck/00check.log’
for details.


codelink.Rcheck/00install.out:

* installing *source* package ‘codelink’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
in method for ‘createWeights’ with signature ‘"CodelinkSet"’: no definition for class “CodelinkSet”
in method for ‘createFlagWeights’ with signature ‘"CodelinkSet"’: no definition for class “CodelinkSet”
in method for ‘createTypeWeights’ with signature ‘"CodelinkSet"’: no definition for class “CodelinkSet”
Creating a generic function for ‘summary’ from package ‘base’ in package ‘codelink’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (codelink)

codelink.Rcheck/codelink-Ex.timings:

nameusersystemelapsed
Codelink-class0.0000.0000.001
CodelinkSet-class000
CodelinkSetUnique-class0.0010.0000.000
arrayNew0.0010.0000.001
as.matrix.Codelink0.0010.0000.001
averageProbes0.0000.0000.001
bkgdCorrect0.7930.0930.888
createWeights0.9200.0330.954
cutCV0.0010.0000.001
dim.Codelink0.0010.0000.001
imageCodelink0.0010.0000.001
logCodelink0.0010.0000.001
mergeArray0.0010.0000.001
na2false0.0000.0000.001
normalize0.9060.0550.961
plotCorrelation0.0000.0010.001
plotDensities0.0000.0000.001
plotMA0.0000.0000.001
readCodelink0.0000.0010.001
readHeader0.0000.0000.001
readHeaderXLS0.0000.0000.001
writeCodelink000