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CHECK report for methylumi on tokay2

This page was generated on 2020-10-17 11:57:05 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE methylumi PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1066/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylumi 2.34.0
Sean Davis
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/methylumi
Branch: RELEASE_3_11
Last Commit: 8afacb9
Last Changed Date: 2020-04-27 14:19:25 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: methylumi
Version: 2.34.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methylumi.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings methylumi_2.34.0.tar.gz
StartedAt: 2020-10-17 05:59:07 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:08:28 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 560.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: methylumi.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methylumi.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings methylumi_2.34.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/methylumi.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'methylumi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'methylumi' version '2.34.0'
* 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 whether package 'methylumi' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpEDGnmz/R.INSTALL2a1c34ca726a/methylumi/man/MethyLumiM-class.Rd:41: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpEDGnmz/R.INSTALL2a1c34ca726a/methylumi/man/MethyLumiM-class.Rd:41: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpEDGnmz/R.INSTALL2a1c34ca726a/methylumi/man/MethyLumiM-class.Rd:53: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpEDGnmz/R.INSTALL2a1c34ca726a/methylumi/man/MethyLumiM-class.Rd:54: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpEDGnmz/R.INSTALL2a1c34ca726a/methylumi/man/MethyLumiM-class.Rd:55: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpEDGnmz/R.INSTALL2a1c34ca726a/methylumi/man/MethyLumiM-class.Rd:56: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpEDGnmz/R.INSTALL2a1c34ca726a/methylumi/man/MethyLumiM-class.Rd:57: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpEDGnmz/R.INSTALL2a1c34ca726a/methylumi/man/MethyLumiM-class.Rd:58: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpEDGnmz/R.INSTALL2a1c34ca726a/methylumi/man/MethyLumiM-class.Rd:70: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/methylumi.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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 WARNINGs, 7 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/methylumi.Rcheck/00check.log'
for details.

Installation output

methylumi.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/methylumi_2.34.0.tar.gz && rm -rf methylumi.buildbin-libdir && mkdir methylumi.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=methylumi.buildbin-libdir methylumi_2.34.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL methylumi_2.34.0.zip && rm methylumi_2.34.0.tar.gz methylumi_2.34.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 5614k  100 5614k    0     0  30.9M      0 --:--:-- --:--:-- --:--:-- 32.0M

install for i386

* installing *source* package 'methylumi' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'methylumi'
    finding HTML links ... done
    CpGs                                    html  
    MethyLumi-class                         html  
    finding level-2 HTML links ... done

    MethyLumiM-class                        html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpEDGnmz/R.INSTALL2a1c34ca726a/methylumi/man/MethyLumiM-class.Rd:41: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpEDGnmz/R.INSTALL2a1c34ca726a/methylumi/man/MethyLumiM-class.Rd:41: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpEDGnmz/R.INSTALL2a1c34ca726a/methylumi/man/MethyLumiM-class.Rd:53: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpEDGnmz/R.INSTALL2a1c34ca726a/methylumi/man/MethyLumiM-class.Rd:54: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpEDGnmz/R.INSTALL2a1c34ca726a/methylumi/man/MethyLumiM-class.Rd:55: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpEDGnmz/R.INSTALL2a1c34ca726a/methylumi/man/MethyLumiM-class.Rd:56: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpEDGnmz/R.INSTALL2a1c34ca726a/methylumi/man/MethyLumiM-class.Rd:57: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpEDGnmz/R.INSTALL2a1c34ca726a/methylumi/man/MethyLumiM-class.Rd:58: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpEDGnmz/R.INSTALL2a1c34ca726a/methylumi/man/MethyLumiM-class.Rd:70: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    MethyLumiQC-class                       html  
    MethyLumiSet-class                      html  
    estimateM                               html  
    extractBarcodeAndPosition               html  
    featureFilter                           html  
    generics                                html  
    getAssayDataNameSubstitutions           html  
    methylData-class                        html  
    methylumIDAT                            html  
    methylumi-package                       html  
    methylumiGenerics                       html  
    methylumiR                              html  
    mldat                                   html  
    normalizeMethyLumiSet                   html  
    plotSampleIntensities                   html  
    qcplot                                  html  
    stripBeadExtras                         html  
    varFilter                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'methylumi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'methylumi' as methylumi_2.34.0.zip
* DONE (methylumi)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'methylumi' successfully unpacked and MD5 sums checked

Tests output

Example timings

methylumi.Rcheck/examples_i386/methylumi-Ex.timings

nameusersystemelapsed
CpGs1.890.112.00
MethyLumi-class0.500.142.77
MethyLumiM-class000
MethyLumiQC-class000
MethyLumiSet-class000
extractBarcodeAndPosition0.000.010.02
getAssayDataNameSubstitutions000
methylData-class000
methylumIDAT000
methylumiR0.230.050.28
mldat0.110.000.11
normalizeMethyLumiSet0.370.120.50
plotSampleIntensities0.130.000.13
qcplot0.250.040.28
varFilter0.370.010.39

methylumi.Rcheck/examples_x64/methylumi-Ex.timings

nameusersystemelapsed
CpGs1.670.051.72
MethyLumi-class0.330.000.33
MethyLumiM-class000
MethyLumiQC-class000
MethyLumiSet-class000
extractBarcodeAndPosition000
getAssayDataNameSubstitutions000
methylData-class000
methylumIDAT000
methylumiR0.210.000.21
mldat0.060.020.07
normalizeMethyLumiSet0.390.000.39
plotSampleIntensities0.060.010.08
qcplot0.200.000.21
varFilter0.600.040.62