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BioC 3.4: CHECK report for methylumi on malbec1

This page was generated on 2017-04-15 16:09:53 -0400 (Sat, 15 Apr 2017).

Package 762/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylumi 2.20.0
Sean Davis
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/methylumi
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: methylumi
Version: 2.20.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings methylumi_2.20.0.tar.gz
StartedAt: 2017-04-14 23:49:48 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:53:31 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 222.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: methylumi.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings methylumi_2.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/methylumi.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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 ‘2.20.0’
* 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 ... OK
* 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  9.7Mb
  sub-directories of 1Mb or more:
    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'
.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 data sets:
  ‘mset’
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 ... 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 ... OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
* 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 WARNING, 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/methylumi.Rcheck/00check.log’
for details.


methylumi.Rcheck/00install.out:

* installing *source* package ‘methylumi’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (methylumi)

methylumi.Rcheck/methylumi-Ex.timings:

nameusersystemelapsed
CpGs1.6840.0001.686
MethyLumi-class0.7960.0000.795
MethyLumiM-class0.0000.0000.001
MethyLumiQC-class0.0040.0000.001
MethyLumiSet-class0.0000.0000.001
extractBarcodeAndPosition0.0080.0000.007
getAssayDataNameSubstitutions0.0040.0000.002
methylData-class0.0000.0000.001
methylumIDAT000
methylumiR0.2240.0000.224
mldat0.0680.0000.066
normalizeMethyLumiSet0.3640.0040.370
plotSampleIntensities0.0800.0000.079
qcplot0.2200.0000.217
varFilter0.3400.0080.346