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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:methylumi.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings methylumi_2.36.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/methylumi.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methylumi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methylumi’ version ‘2.36.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'Biobase', 'scales', 'reshape2', 'ggplot2', 'matrixStats',
'FDb.InfiniumMethylation.hg19', 'minfi'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘methylumi’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 10.7Mb
sub-directories of 1Mb or more:
R 2.0Mb
data 6.8Mb
extdata 1.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘Biobase’ ‘minfi’ ‘lattice’ ‘matrixStats’
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 dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
‘FDb.InfiniumMethylation.hg19’ ‘ggplot2’ ‘matrixStats’ ‘minfi’
‘reshape2’ ‘scales’
Please remove these calls from your code.
'library' or 'require' calls in package code:
‘Biostrings’ ‘MASS’ ‘lumi’ ‘parallel’ ‘rtracklayer’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘graphics’
All declared Imports should be used.
Packages in Depends field not imported from:
‘FDb.InfiniumMethylation.hg19’ ‘ggplot2’ ‘matrixStats’ ‘methods’
‘reshape2’ ‘scales’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
':::' call which should be '::': ‘lumi:::produceMethylationGEOSubmissionFile’
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
‘Biobase:::unsafeSetSlot’ ‘genefilter:::.findCentralMap’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getBarcodes: warning in list.files(path = path, patt = "idat"): partial
argument match of 'patt' to 'pattern'
coerce,RangedSummarizedExperiment-GenomicMethylSet: warning in
assays(from, withDim = F): partial argument match of 'withDim' to
'withDimnames'
.getFinalReportBlock: no visible global function definition for
‘read.table’
.mclapply: no visible global function definition for ‘mclapply’
.parallel : <anonymous>: no visible global function definition for
‘ecdf’
.readOldMethylationFile: no visible global function definition for
‘read.delim’
CSVtoDF: no visible global function definition for ‘read.csv’
SEtoGRset: no visible global function definition for ‘GenomicRatioSet’
beta.mme: no visible global function definition for ‘weighted.mean’
beta.transform: no visible global function definition for
‘weighted.mean’
cy3: no visible global function definition for ‘addColorChannelInfo’
cy5: no visible global function definition for ‘addColorChannelInfo’
gamma.get.xcs: no visible global function definition for
‘gamma.integral’
gamma.get.xs : <anonymous>: no visible global function definition for
‘gamma.mle’
gamma.get.xs : <anonymous>: no visible global function definition for
‘gamma.integral’
gamma.signal: no visible global function definition for
‘gamma.integral’
gammaM.get.xcs : <anonymous>: no visible binding for global variable
‘offset’
gammaM.get.xs : <anonymous>: no visible global function definition for
‘gamma.mode’
gammaM.get.xs : <anonymous>: no visible global function definition for
‘gamma.mle’
getAssayDataNameSubstitutions: no visible global function definition
for ‘read.table’
getMethylationBeadMappers : <anonymous>: no visible global function
definition for ‘data’
getMethylationBeadMappers : <anonymous>: no visible binding for global
variable ‘hm27.controls’
getMethylationBeadMappers : <anonymous>: no visible binding for global
variable ‘hm450.controls’
getMethylationBeadMappers : <anonymous>: no visible binding for global
variable ‘hm27.ordering’
getMethylationBeadMappers : <anonymous>: no visible binding for global
variable ‘hm450.ordering’
getPlatform: no visible global function definition for ‘features’
getPlatform: no visible binding for global variable
‘FDb.InfiniumMethylation.hg19’
getPlatform: no visible global function definition for ‘data’
getPlatform: no visible global function definition for ‘DNAStringSet’
illumina.get.xs: no visible global function definition for
‘colQuantiles’
median.get.xs: no visible global function definition for ‘colMedians’
methylumi.bgcorr: no visible binding for global variable
‘IlluminaHumanMethylation27kCOLORCHANNEL’
methylumi.bgcorr: no visible binding for global variable
‘IlluminaHumanMethylation450kCOLORCHANNEL’
methylumi.diagnostics: no visible binding for global variable
‘IlluminaHumanMethylation27kCOLORCHANNEL’
methylumi.diagnostics: no visible binding for global variable
‘IlluminaHumanMethylation450kCOLORCHANNEL’
methylumi.diagnostics: no visible global function definition for ‘par’
methylumi.diagnostics: no visible global function definition for
‘colorRampPalette’
methylumi.diagnostics: no visible global function definition for
‘lines’
methylumi.diagnostics: no visible global function definition for
‘title’
methylumi.diagnostics: no visible global function definition for
‘plot.density’
methylumi.diagnostics: no visible global function definition for
‘abline’
methylumiCSV: no visible global function definition for
‘DFsToNChannelSet’
methylumiR: no visible global function definition for ‘capture.output’
methylumiToMinfi: no visible global function definition for
‘RGChannelSet’
normalizeMethyLumiSet: no visible global function definition for
‘capture.output’
normexp.get.xs: no visible global function definition for ‘huber’
normexp.get.xs: no visible global function definition for ‘colSds’
normexp.signal: no visible global function definition for ‘dnorm’
normexp.signal: no visible global function definition for ‘pnorm’
plotNegOob: no visible global function definition for ‘par’
plotNegOob : <anonymous>: no visible global function definition for
‘melt’
plotNegOob: no visible global function definition for ‘ggplot’
plotNegOob: no visible global function definition for ‘aes’
plotNegOob: no visible binding for global variable ‘intensity’
plotNegOob: no visible binding for global variable ‘channel.probes’
plotNegOob: no visible global function definition for ‘geom_histogram’
plotNegOob: no visible binding for global variable ‘..density..’
plotNegOob: no visible global function definition for
‘position_identity’
plotNegOob: no visible global function definition for ‘facet_grid’
plotNegOob: no visible global function definition for
‘scale_x_continuous’
plotNegOob: no visible global function definition for
‘scale_y_continuous’
plotNegOob: no visible global function definition for
‘scale_fill_manual’
plotNegOob: no visible global function definition for ‘opts’
plotNegOob: no visible global function definition for ‘theme_bw’
psummary: no visible global function definition for ‘p.adjust’
qc.probe.plot: no visible global function definition for ‘log_trans’
qc.probe.plot: no visible global function definition for ‘melt’
qc.probe.plot: no visible binding for global variable ‘variable’
qc.probe.plot: no visible binding for global variable ‘value’
qc.probe.plot: no visible global function definition for ‘coord_flip’
qc.probe.plot: no visible global function definition for
‘scale_x_continuous’
qc.probe.plot: no visible global function definition for
‘scale_y_discrete’
qc.probe.plot: no visible global function definition for ‘facet_grid’
qc.probe.plot: no visible global function definition for
‘scale_colour_manual’
qc.probe.plot: no visible global function definition for
‘scale_shape_manual’
qc.probe.plot: no visible global function definition for ‘theme_bw’
[,MethyLumiM-ANY-ANY-ANY: no visible global function definition for
‘packageDescription’
coerce,MethyLumiM-MethylSet: no visible global function definition for
‘MethylSet’
coerce,MethyLumiM-MethylSet: no visible global function definition for
‘packageVersion’
coerce,MethyLumiSet-MethylSet: no visible global function definition
for ‘MethylSet’
coerce,MethyLumiSet-MethylSet: no visible global function definition
for ‘packageVersion’
coerce,RangedSummarizedExperiment-GenomicMethylSet: no visible global
function definition for ‘GenomicMethylSet’
coerce,eSet-MethyLumiM: no visible global function definition for
‘capture.output’
coerce,eSet-MethyLumiM: no visible global function definition for
‘packageDescription’
combine27k450k,MethyLumiSet-MethyLumiSet: no visible global function
definition for ‘subsetCommonProbes’
combine,MethyLumiM-MethyLumiM: no visible global function definition
for ‘capture.output’
combine,MethyLumiM-MethyLumiM: no visible global function definition
for ‘packageDescription’
corplot,MethyLumiSet: no visible global function definition for
‘hclust’
corplot,MethyLumiSet: no visible global function definition for
‘as.dist’
getProbesByChannel,methylData : <anonymous>: no visible binding for
global variable ‘allele’
hist,MethyLumiQC: no visible global function definition for ‘par’
hist,MethyLumiSet: no visible global function definition for ‘par’
initialize,MethyLumiQC: ... may be used in an incorrect context:
‘assayDataNew(...)’
intensities.IB,MethyLumiSet-character: no visible binding for global
variable ‘IlluminaHumanMethylation27kCOLORCHANNEL’
intensities.IB,MethyLumiSet-character: no visible binding for global
variable ‘IlluminaHumanMethylation450kCOLORCHANNEL’
intensities.M,MethyLumiSet-character: no visible binding for global
variable ‘IlluminaHumanMethylation27kCOLORCHANNEL’
intensities.M,MethyLumiSet-character: no visible binding for global
variable ‘IlluminaHumanMethylation450kCOLORCHANNEL’
intensities.OOB.allelic,MethyLumiSet-character-character: no visible
binding for global variable ‘IlluminaHumanMethylation27kCOLORCHANNEL’
intensities.OOB.allelic,MethyLumiSet-character-character: no visible
binding for global variable
‘IlluminaHumanMethylation450kCOLORCHANNEL’
intensities.OOB,MethyLumiSet-character: no visible binding for global
variable ‘IlluminaHumanMethylation27kCOLORCHANNEL’
intensities.OOB,MethyLumiSet-character: no visible binding for global
variable ‘IlluminaHumanMethylation450kCOLORCHANNEL’
intensities.U,MethyLumiSet-character: no visible binding for global
variable ‘IlluminaHumanMethylation27kCOLORCHANNEL’
intensities.U,MethyLumiSet-character: no visible binding for global
variable ‘IlluminaHumanMethylation450kCOLORCHANNEL’
pairs,MethyLumiSet : upperPanel: no visible global function definition
for ‘points’
pairs,MethyLumiSet : upperPanel: no visible global function definition
for ‘abline’
pairs,MethyLumiSet : lowerPanel: no visible global function definition
for ‘par’
pairs,MethyLumiSet : lowerPanel: no visible global function definition
for ‘text’
pairs,MethyLumiSet : diagPanel: no visible global function definition
for ‘par’
pairs,MethyLumiSet : diagPanel: no visible global function definition
for ‘rect’
pairs,MethyLumiSet: no visible global function definition for ‘par’
plotNAs,methylData: no visible binding for global variable ‘index’
plotNAs,methylData: no visible binding for global variable ‘dropouts’
plotProbeNAs,methylData: no visible binding for global variable ‘mu’
plotProbeNAs,methylData: no visible binding for global variable ‘drops’
plotSampleIntensities,MethyLumiSet: no visible global function
definition for ‘lines’
plotSampleIntensities,MethyLumiSet: no visible global function
definition for ‘box’
plotSampleIntensities,MethyLumiSet: no visible global function
definition for ‘axis’
pval.detect<-,methylData-numeric : <anonymous> : <anonymous>: no
visible global function definition for ‘ecdf’
pval.detect<-,methylData-numeric: no visible global function definition
for ‘rowMins’
Undefined global functions or variables:
..density.. DFsToNChannelSet DNAStringSet
FDb.InfiniumMethylation.hg19 GenomicMethylSet GenomicRatioSet
IlluminaHumanMethylation27kCOLORCHANNEL
IlluminaHumanMethylation450kCOLORCHANNEL MethylSet RGChannelSet
abline addColorChannelInfo aes allele as.dist axis box capture.output
channel.probes colMedians colQuantiles colSds colorRampPalette
coord_flip data dnorm dropouts drops ecdf facet_grid features
gamma.integral gamma.mle gamma.mode geom_histogram ggplot hclust
hm27.controls hm27.ordering hm450.controls hm450.ordering huber index
intensity lines log_trans mclapply melt mu offset opts p.adjust
packageDescription packageVersion par plot.density pnorm points
position_identity read.csv read.delim read.table rect rowMins
scale_colour_manual scale_fill_manual scale_shape_manual
scale_x_continuous scale_y_continuous scale_y_discrete
subsetCommonProbes text theme_bw title value variable weighted.mean
Consider adding
importFrom("grDevices", "colorRampPalette")
importFrom("graphics", "abline", "axis", "box", "lines", "par",
"points", "rect", "text", "title")
importFrom("stats", "as.dist", "dnorm", "ecdf", "hclust", "offset",
"p.adjust", "pnorm", "weighted.mean")
importFrom("utils", "capture.output", "data", "packageDescription",
"packageVersion", "read.csv", "read.delim", "read.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: estimateM.Rd:34-36: Dropping empty section \seealso
prepare_Rd: estimateM.Rd:37-39: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘IDATsToMatrices’ ‘IDATtoMatrix’ ‘tcgaPipeline’
Undocumented S4 methods:
generic '[' and siglist 'MethyLumiM,ANY,ANY,ANY'
generic '[' and siglist 'MethyLumiSet,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... WARNING
Files not of a type allowed in a ‘data’ directory:
‘5318317007_A_Grn.idat’ ‘5318317007_A_Red.idat’
‘5318317007_B_Grn.idat’ ‘5318317007_B_Red.idat’
‘5318317007_C_Grn.idat’ ‘5318317007_C_Red.idat’
Please use e.g. ‘inst/extdata’ for non-R data files
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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: 2 WARNINGs, 7 NOTEs
See
‘/Users/biocbuild/bbs-3.12-bioc/meat/methylumi.Rcheck/00check.log’
for details.
