Package: wiggleplotr

Version: 1.6.1

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:wiggleplotr.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings wiggleplotr_1.6.1.tar.gz

StartedAt: 2019-04-16 03:41:36 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 03:42:41 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 65.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: wiggleplotr.Rcheck

Warnings: 2

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:wiggleplotr.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings wiggleplotr_1.6.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/wiggleplotr.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wiggleplotr/DESCRIPTION’ ... OK
* this is package ‘wiggleplotr’ version ‘1.6.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘wiggleplotr’ 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
plotCoverage: no visible global function definition for ‘is’
plotTranscripts: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'getGenotypePalette':
getGenotypePalette
  Code: function(old = FALSE)
  Docs: function()
  Argument names in code not in docs:
    old

* 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 ... WARNING
Found the following significant warnings:

  Warning: 'AnnotationFilter::GenenameFilter' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                           user system elapsed
plotCoverageFromEnsembldb 8.884  0.384  10.017
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/wiggleplotr.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL wiggleplotr
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘wiggleplotr’ ...
** R
** data
*** moving datasets to lazyload DB
** 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
* DONE (wiggleplotr)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

> library(testthat)
> library(wiggleplotr)
> 
> test_check("wiggleplotr")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 6 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  4.440   0.152   4.599 

name	user	system	elapsed
getGenotypePalette	0	0	0
makeManhattanPlot	0.324	0.020	0.343
plotCoverage	2.560	0.060	2.621
plotCoverageFromEnsembldb	8.884	0.384	10.017
plotCoverageFromUCSC	0.564	0.004	0.569
plotTranscripts	0.640	0.004	0.642
plotTranscriptsFromEnsembldb	1.752	0.024	1.795
plotTranscriptsFromUCSC	3.044	0.172	3.218