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This page was generated on 2021-05-06 12:36:47 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the shinyMethyl package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1695/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
shinyMethyl 1.26.0 (landing page) Jean-Philippe Fortin
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: shinyMethyl |
Version: 1.26.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:shinyMethyl.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings shinyMethyl_1.26.0.tar.gz |
StartedAt: 2021-05-06 06:11:47 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 06:19:12 -0400 (Thu, 06 May 2021) |
EllapsedTime: 445.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: shinyMethyl.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:shinyMethyl.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings shinyMethyl_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/shinyMethyl.Rcheck’ * using R version 4.0.5 (2021-03-31) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘shinyMethyl/DESCRIPTION’ ... OK * this is package ‘shinyMethyl’ version ‘1.26.0’ * 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 for sufficient/correct file permissions ... 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 35.184 1.437 36.671 * 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 ‘/Users/biocbuild/bbs-3.12-bioc/meat/shinyMethyl.Rcheck/00check.log’ for details.
shinyMethyl.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL shinyMethyl ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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)
shinyMethyl.Rcheck/tests/runTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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 Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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, 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 object is masked from 'package:base': expand.grid Loading required package: IRanges 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: locfit locfit 1.5-9.4 2020-03-24 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 -- Thu May 6 06:19:06 2021 *********************************************** 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 54.392 2.220 58.148
shinyMethyl.Rcheck/shinyMethyl-Ex.timings
name | user | system | elapsed | |
runShinyMethyl | 0.000 | 0.001 | 0.001 | |
shinyMethylSet-class | 0.001 | 0.001 | 0.002 | |
shinySummarize-methods | 35.184 | 1.437 | 36.671 | |