Package: ENCODExplorer

Version: 2.8.0

Command: /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_2.8.0.tar.gz

StartedAt: 2019-04-15 23:44:34 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:46:43 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 129.4 seconds

RetCode: 0

Status:  OK

CheckDir: ENCODExplorer.Rcheck

Warnings: 0

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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_2.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/ENCODExplorer.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘2.8.0’
* 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 ... NOTE
  installed size is 72.1Mb
  sub-directories of 1Mb or more:
    data     23.9Mb
    extdata  48.0Mb
* 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
clean_column: no visible binding for global variable ‘col_name’
clean_column: no visible binding for global variable ‘value’
createDesign: no visible global function definition for ‘data’
createDesign: no visible binding for global variable ‘encode_df’
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 ‘data’
downloadEncode: no visible binding for global variable ‘encode_df’
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’
download_single_file: no visible global function definition for
  ‘download.file’
export_ENCODEdb_matrix: no visible binding for global variable
  ‘accession’
fuzzySearch: no visible global function definition for ‘data’
queryEncode: no visible global function definition for ‘data’
queryEncode: no visible binding for global variable ‘encode_df’
searchToquery: no visible global function definition for ‘data’
shinyEncode: no visible binding for global variable ‘ui’
shinyEncode: no visible binding for global variable ‘server’
step11: no visible binding for global variable ‘submitted_by’
step3: no visible binding for global variable ‘project’
step3: no visible binding for global variable ‘platform’
step3: no visible binding for global variable ‘lab’
step4: no visible binding for global variable
  ‘biological_replicate_number’
step4: no visible binding for global variable ‘replicate_library’
step4: no visible binding for global variable ‘replicate_antibody’
step4: no visible binding for global variable ‘antibody_target’
step4: no visible binding for global variable
  ‘antibody_characterization’
step4: no visible binding for global variable ‘antibody_caption’
step4: no visible binding for global variable
  ‘technical_replicate_number’
step4: no visible binding for global variable ‘treatment’
step4: no visible binding for global variable ‘nucleic_acid_term’
step6_assay: no visible binding for global variable ‘assay’
step6_biosample_name: no visible binding for global variable
  ‘biosample_name’
step6_biosample_type: no visible binding for global variable
  ‘biosample_type’
step6_control: no visible binding for global variable ‘controls’
step6_date_released: no visible binding for global variable
  ‘date_released’
step6_status: no visible binding for global variable ‘status’
step6_target: no visible binding for global variable ‘target’
step7: no visible binding for global variable ‘organism’
step8: no visible binding for global variable ‘investigated_as’
step8: no visible binding for global variable ‘target’
step9: no visible binding for global variable ‘organism’
Undefined global functions or variables:
  . Experiment Value accession antibody_caption
  antibody_characterization antibody_target assay
  biological_replicate_number biosample_name biosample_type col_name
  controls data date_released download.file encode_df file_accession
  file_format href investigated_as lab nucleic_acid_term organism
  platform project replicate_antibody replicate_library server status
  submitted_by target technical_replicate_number treatment ui value
Consider adding
  importFrom("utils", "data", "download.file")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... NOTE
  Note: found 771 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... 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
createDesign  4.658  1.133   4.922
searchToquery 4.028  0.432   5.766
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/ENCODExplorer.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 ENCODExplorer
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘ENCODExplorer’ ...
** 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 (ENCODExplorer)

R version 3.5.3 (2019-03-11) -- "Great Truth"
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

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
Results : 30 files, 10 datasets
results : 4


RUNIT TEST PROTOCOL -- Mon Apr 15 23:46:38 2019 
*********************************************** 
Number of test functions: 31 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ENCODExplorer RUnit Tests - 31 test functions, 0 errors, 0 failures
Number of test functions: 31 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 28.514  13.374  28.270 

name	user	system	elapsed
createDesign	4.658	1.133	4.922
downloadEncode	0.365	0.537	0.116
export_ENCODEdb_matrix	0.005	0.007	0.001
fuzzySearch	0.228	0.335	0.072
prepare_ENCODEdb	0.498	0.868	1.491
queryEncode	0.000	0.001	0.000
searchEncode	0.887	0.023	2.395
searchToquery	4.028	0.432	5.766
shinyEncode	0.001	0.000	0.000