Sean Davis
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/methylumi |
| git_branch: master |
| git_last_commit: 80d9b99 |
| git_last_commit_date: 2021-10-27 03:30:10 -0400 (Wed, 27 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:00 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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. |
| Package 1134/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| methylumi 2.41.1 (landing page) Sean Davis
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: methylumi |
| Version: 2.41.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:methylumi.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings methylumi_2.41.1.tar.gz |
| StartedAt: 2022-03-17 19:33:28 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:38:11 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 282.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: methylumi.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:methylumi.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings methylumi_2.41.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/methylumi.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '2.41.1'
* 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 10.4Mb
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
* 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 ... 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
'D:/biocbuild/bbs-3.15-bioc/meat/methylumi.Rcheck/00check.log'
for details.
methylumi.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL methylumi
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* 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
* DONE (methylumi)
Making 'packages.html' ... done
methylumi.Rcheck/methylumi-Ex.timings
| name | user | system | elapsed | |
| CpGs | 0.60 | 0.05 | 0.64 | |
| MethyLumi-class | 0.47 | 0.00 | 0.47 | |
| MethyLumiM-class | 0 | 0 | 0 | |
| MethyLumiQC-class | 0 | 0 | 0 | |
| MethyLumiSet-class | 0 | 0 | 0 | |
| extractBarcodeAndPosition | 0.00 | 0.01 | 0.01 | |
| getAssayDataNameSubstitutions | 0 | 0 | 0 | |
| methylData-class | 0 | 0 | 0 | |
| methylumIDAT | 0 | 0 | 0 | |
| methylumiR | 0.22 | 0.00 | 0.22 | |
| mldat | 0.06 | 0.00 | 0.07 | |
| normalizeMethyLumiSet | 0.25 | 0.02 | 0.26 | |
| plotSampleIntensities | 0.07 | 0.00 | 0.06 | |
| qcplot | 0.22 | 0.01 | 0.24 | |
| varFilter | 0.32 | 0.02 | 0.34 | |