Back to Multiple platform build/check report for BioC 3.18:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2024-03-04 11:37:33 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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

Package 1235/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylumi 2.48.0  (landing page)
Sean Davis
Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024)
git_url: https://git.bioconductor.org/packages/methylumi
git_branch: RELEASE_3_18
git_last_commit: ce4c6e4
git_last_commit_date: 2023-10-24 09:41:58 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for methylumi on lconway


To the developers/maintainers of the methylumi package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: methylumi
Version: 2.48.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:methylumi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings methylumi_2.48.0.tar.gz
StartedAt: 2024-03-03 21:45:17 -0500 (Sun, 03 Mar 2024)
EndedAt: 2024-03-03 21:52:06 -0500 (Sun, 03 Mar 2024)
EllapsedTime: 409.1 seconds
RetCode: 0
Status:   OK  
CheckDir: methylumi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:methylumi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings methylumi_2.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/methylumi.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methylumi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methylumi’ version ‘2.48.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘methylumi’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 10.0Mb
  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
* 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
checkRd: (-1) extractBarcodeAndPosition.Rd:14: Escaped LaTeX specials: \_ \_
* 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 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: 7 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/methylumi.Rcheck/00check.log’
for details.



Installation output

methylumi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL methylumi
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘methylumi’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (methylumi)

Tests output


Example timings

methylumi.Rcheck/methylumi-Ex.timings

nameusersystemelapsed
CpGs0.5840.0280.623
MethyLumi-class0.4150.0260.451
MethyLumiM-class0.0010.0010.002
MethyLumiQC-class0.0010.0010.002
MethyLumiSet-class0.0010.0010.001
extractBarcodeAndPosition0.0020.0000.003
getAssayDataNameSubstitutions0.0030.0010.004
methylData-class0.0000.0000.001
methylumIDAT000
methylumiR0.2730.0140.294
mldat0.0680.0050.074
normalizeMethyLumiSet0.4700.0230.502
plotSampleIntensities0.0830.0050.090
qcplot0.2170.0080.226
varFilter0.4060.0190.428