Multiple platform build/check report for BioC 3.9 - CHECK report for ENCODExplorer on celaya2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ENCODExplorer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ENCODExplorer_2.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ENCODExplorer.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ENCODExplorer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ENCODExplorer’ version ‘2.10.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ENCODExplorer’ 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 ... NOTE
Package in Depends field not imported from: ‘DT’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
clean_column: no visible binding for global variable ‘col_name’
clean_column: no visible binding for global variable ‘value’
clean_column: no visible global function definition for ‘is’
createDesign: no visible binding for global variable ‘file_format’
createDesign: no visible binding for global variable ‘status’
createDesign: no visible binding for global variable ‘accession’
createDesign: no visible binding for global variable ‘controls’
createDesign : get_ctrl_design: no visible binding for global variable
  ‘accession’
createDesign : get_ctrl_design: no visible binding for global variable
  ‘href’
createDesign: no visible global function definition for ‘.’
createDesign: no visible binding for global variable ‘href’
createDesign: no visible binding for global variable ‘Experiment’
createDesign: no visible binding for global variable ‘Value’
downloadEncode: no visible global function definition for ‘is’
downloadEncode: no visible binding for global variable ‘file_accession’
downloadEncode: no visible binding for global variable ‘file_format’
downloadEncode: no visible binding for global variable ‘accession’
shinyEncode: no visible binding for global variable ‘ui’
shinyEncode: no visible binding for global variable ‘server’
Undefined global functions or variables:
  . Experiment Value accession col_name controls file_accession
  file_format href is server status ui value
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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
get_encode_df_full 81.369  2.839  84.813
get_encode_df      34.158  1.525  36.303
queryEncodeGeneric  7.687  0.617   7.318
* 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-3.9-bioc/meat/ENCODExplorer.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ENCODExplorer
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ENCODExplorer’ ...
** 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 (ENCODExplorer)

Tests output


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.

> #Run all tests in the ENCODExplorer package
> BiocGenerics:::testPackage("ENCODExplorer")

Attaching package: 'DT'

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

    dataTableOutput, renderDataTable

snapshotDate(): 2019-05-02
downloading 0 resources
loading from cache 
    'AH69290 : 76036'
Results : 2 files, 1 datasets
[1] "Success downloading file : ./ENCFF002COC.bed.gz"
[1] "Success downloading file : ./ENCFF001VDM.bed.gz"
[1] "Files can be found at /Users/biocbuild/bbs-3.9-bioc/meat/ENCODExplorer.Rcheck/tests"
[1] "Success downloading file : ./ENCFF002COC.bed.gz"
[1] "Success downloading file : ./ENCFF001VDM.bed.gz"
[1] "Files can be found at /Users/biocbuild/bbs-3.9-bioc/meat/ENCODExplorer.Rcheck/tests"
[1] "Success downloading file : Test_dir/ENCFF002COC.bed.gz"
[1] "Success downloading file : Test_dir/ENCFF001VDM.bed.gz"
[1] "Files can be found at /Users/biocbuild/bbs-3.9-bioc/meat/ENCODExplorer.Rcheck/tests"
Results: 9 files, 1 datasets
Results: 9 files, 1 datasets
Results: 16 files, 5 datasets
Results: 16 files, 5 datasets
Results: 16 files, 5 datasets
Results: 9 files, 1 datasets
No result found in encode_df. You can try the  function or set the fuzzy option to TRUE.
Results : 318 files, 11 datasets
Results : 81 files, 23 datasets
Results : 3 files, 1 datasets
Results : 318 files, 11 datasets
Results : 338 files, 53 datasets
Results : 228 files, 8 datasets
results : 4


RUNIT TEST PROTOCOL -- Tue Oct 15 02:21:30 2019 
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Number of test functions: 36 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ENCODExplorer RUnit Tests - 36 test functions, 0 errors, 0 failures
Number of test functions: 36 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 59.394   8.620  78.847

name	user	system	elapsed
createDesign	0.491	0.262	0.317
downloadEncode	0.109	0.057	0.055
fuzzySearch	0.067	0.027	0.071
get_encode_df	34.158	1.525	36.303
get_encode_df_demo	0.052	0.008	0.060
get_encode_df_full	81.369	2.839	84.813
queryEncode	0.150	0.075	0.110
queryEncodeGeneric	7.687	0.617	7.318
searchEncode	0.362	0.028	2.484
searchToquery	0.078	0.017	1.560
shinyEncode	0.001	0.000	0.001

CHECK report for ENCODExplorer on celaya2

Summary

Command output

Installation output

Tests output

Example timings