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This page was generated on 2023-04-12 11:05:52 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 shinyMethyl on palomino4


To the developers/maintainers of the shinyMethyl package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/shinyMethyl.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1860/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
shinyMethyl 1.34.0  (landing page)
Jean-Philippe Fortin
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/shinyMethyl
git_branch: RELEASE_3_16
git_last_commit: fc4bc50
git_last_commit_date: 2022-11-01 11:09:56 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 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 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: shinyMethyl
Version: 1.34.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:shinyMethyl.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings shinyMethyl_1.34.0.tar.gz
StartedAt: 2023-04-11 05:59:28 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 06:06:14 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 406.1 seconds
RetCode: 0
Status:   OK  
CheckDir: shinyMethyl.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:shinyMethyl.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings shinyMethyl_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/shinyMethyl.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'shinyMethyl/DESCRIPTION' ... OK
* this is package 'shinyMethyl' version '1.34.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 'shinyMethyl' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addHoverDensity: no visible global function definition for 'lines'
addHoverPoints: no visible global function definition for 'points'
addHoverQC: no visible global function definition for 'points'
densitiesPlot: no visible global function definition for 'lines'
plotDesign450k: no visible global function definition for 'par'
plotDiscrepancyGenders: no visible global function definition for
  'legend'
plotInternalControls: no visible global function definition for 'grid'
plotInternalControls: no visible global function definition for
  'abline'
plotLegendDesign450k: no visible global function definition for
  'legend'
plotPCA: no visible global function definition for 'legend'
plotPCA: no visible global function definition for 'grid'
plotPlate: no visible global function definition for 'rect'
plotPredictedGender: no visible global function definition for 'abline'
plotQC: no visible global function definition for 'grid'
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
  assignment to 'mouse.click.indices'
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
  assignment to 'colorSet'
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
  assignment to 'genderCutoff'
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
  assignment to 'current.control.type'
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
  assignment to 'current.probe.type'
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
  assignment to 'current.density.type'
server.shinyMethyl : <anonymous> : set.palette: no visible global
  function definition for 'palette'
server.shinyMethyl : <anonymous>: no visible binding for global
  variable 'current.control.type'
server.shinyMethyl : <anonymous>: no visible binding for global
  variable 'mouse.click.indices'
server.shinyMethyl : <anonymous>: no visible binding for global
  variable 'current.probe.type'
server.shinyMethyl : <anonymous>: no visible binding for global
  variable 'current.density.type'
server.shinyMethyl : <anonymous> : content: no visible global function
  definition for 'write.csv'
server.shinyMethyl : <anonymous>: no visible global function definition
  for 'abline'
server.shinyMethyl : <anonymous>: no visible binding for global
  variable 'genderCutoff'
server.shinyMethyl : <anonymous>: no visible global function definition
  for 'complete.cases'
server.shinyMethyl : <anonymous>: no visible global function definition
  for 'lm'
server.shinyMethyl : <anonymous>: no visible global function definition
  for 'lines'
server.shinyMethyl : <anonymous>: no visible global function definition
  for 'legend'
ui.shinyMethyl: no visible binding for '<<-' assignment to
  'sampleColors'
shinySummarize,GenomicRatioSet: no visible global function definition
  for 'prcomp'
shinySummarize,RGChannelSet: no visible global function definition for
  'prcomp'
Undefined global functions or variables:
  abline complete.cases current.control.type current.density.type
  current.probe.type genderCutoff grid legend lines lm
  mouse.click.indices palette par points prcomp rect write.csv
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "grid", "legend", "lines", "par",
             "points", "rect")
  importFrom("stats", "complete.cases", "lm", "prcomp")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
* checking Rd files ... OK
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
shinySummarize-methods 40.3   0.75   41.47
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.R'
 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: 2 NOTEs
See
  'F:/biocbuild/bbs-3.16-bioc/meat/shinyMethyl.Rcheck/00check.log'
for details.



Installation output

shinyMethyl.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL shinyMethyl
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'shinyMethyl' ...
** using staged installation
** R
** 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 (shinyMethyl)

Tests output

shinyMethyl.Rcheck/tests/runTests.Rout


R version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("shinyMethyl") || stop("unable to load shinyMethyl")
Loading required package: shinyMethyl
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: shiny
Loading required package: minfi
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: locfit
locfit 1.5-9.7 	 2023-01-02
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: IlluminaHumanMethylation450kmanifest
[1] TRUE
> BiocGenerics:::testPackage("shinyMethyl")
Loading required package: minfiData
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
Loading required package: digest
[shinySummarize] Extracting Red and Green channels 
[shinySummarize] Raw preprocessing 
[shinySummarize] Mapping to genome 
[shinySummarize] Computing quantiles 
[shinySummarize] Computing principal components 


RUNIT TEST PROTOCOL -- Tue Apr 11 06:06:04 2023 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
shinyMethyl RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  53.12    2.00   55.14 

Example timings

shinyMethyl.Rcheck/shinyMethyl-Ex.timings

nameusersystemelapsed
runShinyMethyl000
shinyMethylSet-class000
shinySummarize-methods40.30 0.7541.47