Package: epivizrChart

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:epivizrChart.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings epivizrChart_1.2.0.tar.gz

StartedAt: 2018-10-16 21:13:22 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 21:17:35 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 252.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: epivizrChart.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:epivizrChart.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings epivizrChart_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/epivizrChart.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epivizrChart/DESCRIPTION’ ... OK
* this is package ‘epivizrChart’ version ‘1.2.0’
* package encoding: UTF-8
* 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 ‘epivizrChart’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    www    2.9Mb
* 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 ... NOTE
Namespace in Imports field not imported from: 'epivizrServer'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 'epivizNav':
epivizNav
  Code: function(chr = NULL, start = NULL, end = NULL, parent = NULL,
                 interactive = FALSE, ...)
  Docs: function(chr = NULL, start = NULL, end = NULL, parent = NULL,
                 ...)
  Argument names in code not in docs:
    interactive
  Mismatches in argument names:
    Position: 5 Code: interactive Docs: ...

Codoc mismatches from documentation object 'json_parser':
json_parser
  Code: function(json_str, file, method = "C", unexpected.escape =
                 "error", simplify = TRUE)
  Docs: function(json_str, file, method = "C", unexpected.escape =
                 "error")
  Argument names in code not in docs:
    simplify

Codoc mismatches from documentation object 'json_writer':
json_writer
  Code: function(x, indent = 0, method = "C")
  Docs: function(x, method = "C")
  Argument names in code not in docs:
    indent
  Mismatches in argument names:
    Position: 2 Code: indent Docs: method

* 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 ... NOTE
  Failed with error:  'package 'DelayedArray' could not be loaded'
  Error in .requirePackage(package) : 
    unable to find required package 'SummarizedExperiment'
  Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
  Execution halted
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/epivizrChart.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL epivizrChart
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘epivizrChart’ ...
** 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 (epivizrChart)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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.

> library(testthat)
> library(epivizrChart)
> 
> test_check("epivizrChart")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 0 SKIPPED: 8 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 11.028   0.582  12.490 

name	user	system	elapsed
epivizChart	0.197	0.007	0.206
epivizEnv	0.009	0.000	0.009
epivizNav	0.007	0.000	0.007
json_parser	0.001	0.000	0.001
json_writer	0.001	0.000	0.001