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This page was generated on 2022-01-26 13:06:54 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for methylumi on tokay2


To the developers/maintainers of the methylumi package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methylumi.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1129/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylumi 2.40.1  (landing page)
Sean Davis
Snapshot Date: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/methylumi
git_branch: RELEASE_3_14
git_last_commit: 2110392
git_last_commit_date: 2021-10-30 09:58:54 -0500 (Sat, 30 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: methylumi
Version: 2.40.1
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methylumi.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings methylumi_2.40.1.tar.gz
StartedAt: 2022-01-25 22:49:31 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 22:56:35 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 423.9 seconds
RetCode: 0
Status:   OK  
CheckDir: methylumi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methylumi.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings methylumi_2.40.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/methylumi.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '2.40.1'
* package encoding: UTF-8
* 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 ... OK
* checking installed package size ... NOTE
  installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    data      2.7Mb
    extdata   5.8Mb
* 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 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 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 ... 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 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: 7 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/methylumi.Rcheck/00check.log'
for details.



Installation output

methylumi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/methylumi_2.40.1.tar.gz && rm -rf methylumi.buildbin-libdir && mkdir methylumi.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=methylumi.buildbin-libdir methylumi_2.40.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL methylumi_2.40.1.zip && rm methylumi_2.40.1.tar.gz methylumi_2.40.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 23 5616k   23 1343k    0     0  3199k      0  0:00:01 --:--:--  0:00:01 3198k
100 5616k  100 5616k    0     0  5794k      0 --:--:-- --:--:-- --:--:-- 5796k

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  
    IDATsToMatrices                         html  
    IDATtoMatrix                            html  
    MethyLumi-class                         html  
    finding level-2 HTML links ... done

    MethyLumiM-class                        html  
    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  
    tcgaPipeline                            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_2.40.1.zip
* DONE (methylumi)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'methylumi' successfully unpacked and MD5 sums checked

Tests output


Example timings

methylumi.Rcheck/examples_i386/methylumi-Ex.timings

nameusersystemelapsed
CpGs1.380.051.42
MethyLumi-class0.400.160.60
MethyLumiM-class000
MethyLumiQC-class000
MethyLumiSet-class000
extractBarcodeAndPosition000
getAssayDataNameSubstitutions0.010.000.02
methylData-class000
methylumIDAT000
methylumiR0.170.090.26
mldat0.110.000.11
normalizeMethyLumiSet0.350.050.39
plotSampleIntensities0.110.010.13
qcplot0.200.030.23
varFilter0.440.020.45

methylumi.Rcheck/examples_x64/methylumi-Ex.timings

nameusersystemelapsed
CpGs0.590.030.62
MethyLumi-class0.650.000.65
MethyLumiM-class000
MethyLumiQC-class000
MethyLumiSet-class0.000.010.02
extractBarcodeAndPosition000
getAssayDataNameSubstitutions000
methylData-class000
methylumIDAT000
methylumiR0.350.000.35
mldat0.090.020.10
normalizeMethyLumiSet0.440.050.49
plotSampleIntensities0.080.010.09
qcplot0.230.020.25
varFilter0.390.010.41