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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Repitools_1.22.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/Repitools.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Repitools/DESCRIPTION’ ... OK
* this is package ‘Repitools’ version ‘1.22.0’
* 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 ‘Repitools’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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
.cpgBoxplots: no visible global function definition for ‘pdf’
.cpgBoxplots: no visible global function definition for ‘par’
.cpgBoxplots: no visible global function definition for ‘dev.off’
.diracBetaDirac: no visible global function definition for ‘dbeta’
.doBiasPlot: no visible global function definition for ‘plot’
.doBiasPlot: no visible global function definition for ‘lines’
.doBiasPlot: no visible global function definition for ‘lowess’
.doChrPlot: no visible global function definition for ‘plot’
.doChrPlot: no visible global function definition for ‘points’
.doChrPlot: no visible global function definition for ‘abline’
.drawSegs : <anonymous>: no visible global function definition for
‘lines’
.makeClusters : clusterScores: no visible global function definition
for ‘embed’
.makeClusters : clusterScores: no visible global function definition
for ‘filter’
.methylEstbeta: no visible global function definition for ‘qnorm’
.mydmarginal: no visible global function definition for ‘dbeta’
.mydmarginalDBD: no visible global function definition for ‘dbeta’
.plotFreqs: no visible global function definition for ‘layout’
.plotFreqs : <anonymous>: no visible global function definition for
‘matplot’
.plotFreqs : <anonymous>: no visible global function definition for
‘abline’
.plotFreqs : <anonymous>: no visible global function definition for
‘legend’
determineOffset: no visible global function definition for ‘par’
determineOffset: no visible global function definition for ‘grid’
determineOffset: no visible global function definition for ‘abline’
determineOffset: no visible global function definition for ‘text’
getSampleOffsets: no visible global function definition for ‘grid’
getSampleOffsets: no visible global function definition for ‘abline’
loadPairFile: no visible global function definition for ‘read.table’
plotQdnaByCN: no visible global function definition for ‘layout’
plotQdnaByCN: no visible global function definition for ‘grid’
plotQdnaByCN: no visible global function definition for ‘abline’
plotQdnaByCN: no visible global function definition for ‘plot’
processNDF: no visible global function definition for ‘read.table’
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
definition for ‘nbrOfArrays’
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
definition for ‘extract’
.blocksStats,AffymetrixCelSet-GRanges: no visible binding for global
variable ‘verbose’
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
definition for ‘getCdf’
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
definition for ‘extractMatrix’
.blocksStats,GRangesList-GRanges: no visible global function definition
for ‘p.adjust’
.blocksStats,matrix-GRanges: no visible global function definition for
‘t.test’
.blocksStats,matrix-GRanges: no visible global function definition for
‘pt’
.blocksStats,matrix-GRanges: no visible global function definition for
‘p.adjust’
.featureScores,AffymetrixCelSet-GRanges: no visible global function
definition for ‘getCdf’
.featureScores,AffymetrixCelSet-GRanges: no visible binding for global
variable ‘verbose’
.featureScores,AffymetrixCelSet-GRanges: no visible global function
definition for ‘extractMatrix’
GCadjustCopy,GRanges-matrix-GCAdjustParams : <anonymous>: no visible
global function definition for ‘lm’
GCadjustCopy,GRanges-matrix-GCAdjustParams : <anonymous>: no visible
global function definition for ‘predict’
GCbiasPlots,AdjustedCopyEstimate: no visible global function definition
for ‘par’
GCbiasPlots,AdjustedCopyEstimate : <anonymous>: no visible global
function definition for ‘abline’
binPlots,ScoresList: no visible global function definition for ‘par’
binPlots,ScoresList : <anonymous>: no visible global function
definition for ‘layout’
binPlots,ScoresList : <anonymous>: no visible global function
definition for ‘par’
binPlots,ScoresList : <anonymous>: no visible global function
definition for ‘matplot’
binPlots,ScoresList : <anonymous>: no visible global function
definition for ‘plot.new’
binPlots,ScoresList : <anonymous>: no visible global function
definition for ‘legend’
binPlots,ScoresList : <anonymous>: no visible global function
definition for ‘mtext’
binPlots,ScoresList : <anonymous>: no visible global function
definition for ‘axis’
binPlots,ScoresList : <anonymous>: no visible global function
definition for ‘plot’
binPlots,ScoresList : <anonymous>: no visible global function
definition for ‘plot.window’
binPlots,ScoresList : <anonymous>: no visible global function
definition for ‘text’
binPlots,ScoresList : <anonymous>: no visible global function
definition for ‘title’
binPlots,ScoresList : <anonymous>: no visible global function
definition for ‘persp’
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
definition for ‘par’
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
definition for ‘matplot’
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
definition for ‘axis’
checkProbes,GRanges-GRanges : <anonymous> : <anonymous>: no visible
global function definition for ‘matlines’
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
definition for ‘plot’
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
definition for ‘text’
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
definition for ‘mtext’
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
definition for ‘abline’
chromosomeCNplots,AdjustedCopyEstimate: no visible global function
definition for ‘par’
chromosomeCNplots,CopyEstimate : <anonymous>: no visible global
function definition for ‘str’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
function definition for ‘layout’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
function definition for ‘par’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
function definition for ‘plot.new’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
function definition for ‘legend’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
function definition for ‘matplot’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
function definition for ‘axis’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
function definition for ‘mtext’
clusterPlots,ClusteredScoresList: no visible global function definition
for ‘par’
clusterPlots,ClusteredScoresList: no visible global function definition
for ‘layout’
clusterPlots,ClusteredScoresList: no visible global function definition
for ‘matplot’
clusterPlots,ClusteredScoresList: no visible global function definition
for ‘axis’
clusterPlots,ClusteredScoresList: no visible global function definition
for ‘mtext’
clusterPlots,ClusteredScoresList: no visible global function definition
for ‘title’
clusterPlots,ClusteredScoresList: no visible global function definition
for ‘plot.new’
clusterPlots,ClusteredScoresList: no visible global function definition
for ‘plot.window’
clusterPlots,ClusteredScoresList: no visible global function definition
for ‘text’
clusterPlots,ClusteredScoresList: no visible global function definition
for ‘bxp’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
function definition for ‘rect’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
function definition for ‘abline’
clusterPlots,ClusteredScoresList: no visible global function definition
for ‘plot’
clusterPlots,ScoresList: no visible global function definition for
‘kmeans’
cpgBoxplots,AffymetrixCelSet: no visible binding for global variable
‘Arguments’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘pushState’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘popState’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘nbrOfArrays’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘getCdf’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘getMainCdf’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘nbrOfUnits’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘indexOf’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘enter’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘getCellIndices’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘exit’
cpgBoxplots,AffymetrixCelSet: no visible binding for global variable
‘AromaCellSequenceFile’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘getChipType’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘countBases’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘extract’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘getNames’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘extractMatrix’
cpgBoxplots,AffymetrixCelSet: no visible binding for global variable
‘AromaCellCpgFile’
cpgBoxplots,matrix: no visible binding for global variable ‘Arguments’
cpgBoxplots,matrix: no visible global function definition for
‘pushState’
cpgBoxplots,matrix: no visible global function definition for
‘popState’
cpgBoxplots,matrix: no visible global function definition for ‘enter’
cpgBoxplots,matrix: no visible global function definition for ‘exit’
cpgDensityCalc,GRanges-BSgenome: no visible global function definition
for ‘DNAString’
cpgDensityPlot,GRangesList: no visible global function definition for
‘rainbow’
cpgDensityPlot,GRangesList: no visible global function definition for
‘plot’
cpgDensityPlot,GRangesList: no visible global function definition for
‘lines’
cpgDensityPlot,GRangesList: no visible global function definition for
‘legend’
enrichmentPlot,GRangesList: no visible global function definition for
‘rainbow’
enrichmentPlot,GRangesList: no visible global function definition for
‘plot’
enrichmentPlot,GRangesList: no visible global function definition for
‘lines’
enrichmentPlot,GRangesList: no visible global function definition for
‘legend’
genQC,SequenceQCSet: no visible global function definition for
‘matplot’
genQC,SequenceQCSet: no visible global function definition for ‘legend’
genQC,SequenceQCSet: no visible global function definition for ‘par’
genQC,SequenceQCSet: no visible global function definition for ‘layout’
genQC,SequenceQCSet : <anonymous>: no visible global function
definition for ‘par’
genQC,SequenceQCSet : <anonymous>: no visible global function
definition for ‘matplot’
genQC,SequenceQCSet : <anonymous>: no visible global function
definition for ‘abline’
genQC,SequenceQCSet : <anonymous>: no visible global function
definition for ‘plot.new’
genQC,SequenceQCSet : <anonymous>: no visible global function
definition for ‘legend’
genQC,SequenceQCSet : <anonymous>: no visible global function
definition for ‘barplot’
genQC,SequenceQCSet : <anonymous>: no visible global function
definition for ‘axis’
getProbePositionsDf,AffymetrixCdfFile: no visible global function
definition for ‘getCellIndices’
getProbePositionsDf,AffymetrixCdfFile: no visible binding for global
variable ‘AromaCellPositionFile’
getProbePositionsDf,AffymetrixCdfFile: no visible global function
definition for ‘getChipType’
plotClusters,GRanges : <anonymous>: no visible global function
definition for ‘par’
plotClusters,GRanges : <anonymous>: no visible global function
definition for ‘plot’
plotClusters,GRanges : <anonymous>: no visible global function
definition for ‘title’
plotClusters,GRanges : <anonymous>: no visible global function
definition for ‘mtext’
plotClusters,GRanges : <anonymous>: no visible global function
definition for ‘axis’
profilePlots,ScoresList: no visible global function definition for
‘rainbow’
profilePlots,ScoresList : <anonymous>: no visible global function
definition for ‘matplot’
profilePlots,ScoresList : <anonymous>: no visible global function
definition for ‘polygon’
profilePlots,ScoresList : <anonymous>: no visible global function
definition for ‘legend’
regionStats,AffymetrixCelSet: no visible global function definition for
‘getCdf’
regionStats,AffymetrixCelSet: no visible global function definition for
‘getCellIndices’
regionStats,AffymetrixCelSet: no visible global function definition for
‘nbrOfArrays’
regionStats,AffymetrixCelSet: no visible binding for global variable
‘AromaCellPositionFile’
regionStats,AffymetrixCelSet: no visible global function definition for
‘getChipType’
regionStats,AffymetrixCelSet: no visible global function definition for
‘extract’
regionStats,AffymetrixCelSet: no visible global function definition for
‘extractMatrix’
sequenceCalc,GRanges-BSgenome : <anonymous>: no visible global function
definition for ‘matchPattern’
writeWig,AffymetrixCelSet: no visible global function definition for
‘getNames’
writeWig,AffymetrixCelSet: no visible global function definition for
‘extract’
writeWig,AffymetrixCelSet: no visible global function definition for
‘getCdf’
writeWig,AffymetrixCelSet: no visible global function definition for
‘extractMatrix’
Undefined global functions or variables:
Arguments AromaCellCpgFile AromaCellPositionFile
AromaCellSequenceFile DNAString abline axis barplot bxp countBases
dbeta dev.off embed enter exit extract extractMatrix filter getCdf
getCellIndices getChipType getMainCdf getNames grid indexOf kmeans
layout legend lines lm lowess matchPattern matlines matplot mtext
nbrOfArrays nbrOfUnits p.adjust par pdf persp plot plot.new
plot.window points polygon popState predict pt pushState qnorm
rainbow read.table rect str t.test text title verbose
Consider adding
importFrom("grDevices", "dev.off", "pdf", "rainbow")
importFrom("graphics", "abline", "axis", "barplot", "bxp", "grid",
"layout", "legend", "lines", "matlines", "matplot", "mtext",
"par", "persp", "plot", "plot.new", "plot.window", "points",
"polygon", "rect", "text", "title")
importFrom("stats", "dbeta", "embed", "filter", "kmeans", "lm",
"lowess", "p.adjust", "predict", "pt", "qnorm", "t.test")
importFrom("utils", "read.table", "str")
to your NAMESPACE file.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
methylEst 63.092 4.444 22.022
empBayes 26.836 3.716 16.381
cpgDensityCalc 9.992 1.352 11.776
sequenceCalc 9.412 0.756 10.171
BayMethList-class 9.452 0.112 9.655
gcContentCalc 5.140 0.108 5.826
determineOffset 4.904 0.272 5.179
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘tests.R’
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: 1 NOTE
See
‘/home/biocbuild/bbs-3.5-bioc/meat/Repitools.Rcheck/00check.log’
for details.
