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This page was generated on 2022-04-13 12:07:21 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 tokay2


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 1782/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
shinyMethyl 1.30.0  (landing page)
Jean-Philippe Fortin
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/shinyMethyl
git_branch: RELEASE_3_14
git_last_commit: a6b9628
git_last_commit_date: 2021-10-26 12:14:34 -0400 (Tue, 26 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: shinyMethyl
Version: 1.30.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:shinyMethyl.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings shinyMethyl_1.30.0.tar.gz
StartedAt: 2022-04-13 02:53:26 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 03:03:18 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 592.5 seconds
RetCode: 0
Status:   OK  
CheckDir: shinyMethyl.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:shinyMethyl.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings shinyMethyl_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/shinyMethyl.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'shinyMethyl/DESCRIPTION' ... OK
* this is package 'shinyMethyl' version '1.30.0'
* 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
* 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
shinySummarize-methods 33.4   2.66   36.06
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
shinySummarize-methods 36.33   1.53   37.86
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/shinyMethyl.Rcheck/00check.log'
for details.



Installation output

shinyMethyl.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/shinyMethyl_1.30.0.tar.gz && rm -rf shinyMethyl.buildbin-libdir && mkdir shinyMethyl.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=shinyMethyl.buildbin-libdir shinyMethyl_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL shinyMethyl_1.30.0.zip && rm shinyMethyl_1.30.0.tar.gz shinyMethyl_1.30.0.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
 13 9042k   13 1216k    0     0  1543k      0  0:00:05 --:--:--  0:00:05 1543k
 42 9042k   42 3821k    0     0  2135k      0  0:00:04  0:00:01  0:00:03 2135k
 81 9042k   81 7327k    0     0  2651k      0  0:00:03  0:00:02  0:00:01 2651k
100 9042k  100 9042k    0     0  2850k      0  0:00:03  0:00:03 --:--:-- 2851k

install for i386

* installing *source* package 'shinyMethyl' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'shinyMethyl'
    finding HTML links ... done
    runShinyMethyl                          html  
    shinyMethyl-package                     html  
    shinyMethylSet-class                    html  
    finding level-2 HTML links ... done

    shinySummarize-methods                  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 'shinyMethyl' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'shinyMethyl' as shinyMethyl_1.30.0.zip
* DONE (shinyMethyl)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'shinyMethyl' successfully unpacked and MD5 sums checked

Tests output

shinyMethyl.Rcheck/tests_i386/runTests.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, 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 1.5-9.5 	 2022-03-01
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 -- Wed Apr 13 03:02:19 2022 
*********************************************** 
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 
  45.56    3.73   49.31 

shinyMethyl.Rcheck/tests_x64/runTests.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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, 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 1.5-9.5 	 2022-03-01
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 -- Wed Apr 13 03:03:11 2022 
*********************************************** 
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 
  49.31    2.14   51.46 

Example timings

shinyMethyl.Rcheck/examples_i386/shinyMethyl-Ex.timings

nameusersystemelapsed
runShinyMethyl000
shinyMethylSet-class000
shinySummarize-methods33.40 2.6636.06

shinyMethyl.Rcheck/examples_x64/shinyMethyl-Ex.timings

nameusersystemelapsed
runShinyMethyl000
shinyMethylSet-class000
shinySummarize-methods36.33 1.5337.86