BioC 3.1: CHECK report for codelink on petty

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: 2015-10-08 22:14:23 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 22:17:17 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 174.0 seconds

RetCode: 0

Status: OK

CheckDir: codelink.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings codelink_1.36.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/codelink.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [22s/22s] 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 ... [10s/11s] 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.

* 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)

name	user	system	elapsed
Codelink-class	0.001	0.000	0.001
CodelinkSet-class	0.002	0.000	0.002
CodelinkSetUnique-class	0.001	0.000	0.002
arrayNew	0.001	0.000	0.001
as.matrix.Codelink	0.001	0.000	0.001
averageProbes	0.001	0.000	0.001
bkgdCorrect	1.058	0.040	1.099
createWeights	1.140	0.034	1.175
cutCV	0.001	0.000	0.002
dim.Codelink	0.001	0.000	0.001
imageCodelink	0.001	0.000	0.001
logCodelink	0.001	0.001	0.001
mergeArray	0.001	0.000	0.001
na2false	0.001	0.000	0.002
normalize	1.229	0.067	1.296
plotCorrelation	0.000	0.000	0.001
plotDensities	0	0	0
plotMA	0.000	0.000	0.001
readCodelink	0.000	0.000	0.001
readHeader	0.000	0.000	0.001
readHeaderXLS	0.000	0.000	0.001
writeCodelink	0.001	0.001	0.001

BioC 3.1: CHECK report for codelink on petty

Summary

Command output