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CHECK report for shinyMethyl on veracruz1

This page was generated on 2018-04-12 13:38:56 -0400 (Thu, 12 Apr 2018).

Package 1285/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
shinyMethyl 1.14.0
Jean-Philippe Fortin
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/shinyMethyl
Branch: RELEASE_3_6
Last Commit: 9be9cdd
Last Changed Date: 2017-10-30 12:40:18 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: shinyMethyl
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings shinyMethyl_1.14.0.tar.gz
StartedAt: 2018-04-12 09:33:17 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 09:39:12 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 354.9 seconds
RetCode: 0
Status:  OK 
CheckDir: shinyMethyl.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings shinyMethyl_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/shinyMethyl.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘shinyMethyl/DESCRIPTION’ ... OK
* this is package ‘shinyMethyl’ version ‘1.14.0’
* 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 loading without being on the library search path ... 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 ‘plot’
densitiesPlot: no visible global function definition for ‘lines’
plotDesign450k: no visible global function definition for ‘par’
plotDesign450k: no visible global function definition for ‘plot’
plotDiscrepancyGenders: no visible global function definition for
  ‘legend’
plotInternalControls: no visible global function definition for ‘plot’
plotInternalControls: no visible global function definition for ‘grid’
plotInternalControls: no visible global function definition for
  ‘abline’
plotLegendDesign450k: no visible global function definition for ‘plot’
plotLegendDesign450k: no visible global function definition for
  ‘legend’
plotPCA: no visible global function definition for ‘plot’
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 ‘plot’
plotPredictedGender: no visible global function definition for ‘abline’
plotQC: no visible global function definition for ‘plot’
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 ‘plot’
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 plot points prcomp rect write.csv
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "grid", "legend", "lines", "par",
             "plot", "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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
shinySummarize-methods 43.851  3.775  48.506
* 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-3.6-bioc/meat/shinyMethyl.Rcheck/00check.log’
for details.



Installation output

shinyMethyl.Rcheck/00install.out

* installing *source* package ‘shinyMethyl’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (shinyMethyl)

Tests output

shinyMethyl.Rcheck/tests/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    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: Biobase
Welcome to Bioconductor

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

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    apply

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    type

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 1.5-9.1 	 2013-03-22
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 Apr 12 09:39:07 2018 
*********************************************** 
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 
 50.148   3.972  54.958 

Example timings

shinyMethyl.Rcheck/shinyMethyl-Ex.timings

nameusersystemelapsed
runShinyMethyl0.0010.0010.001
shinyMethylSet-class0.0020.0000.002
shinySummarize-methods43.851 3.77548.506