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CHECK report for ENCODExplorerData on malbec1

This page was generated on 2020-08-05 15:30:06 -0400 (Wed, 05 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ENCODExplorerData PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1/11HostnameOS / ArchINSTALLBUILDCHECK
ENCODExplorerData 0.99.5
Eric Fournier
Snapshot Date: 2020-08-05 08:00:01 -0400 (Wed, 05 Aug 2020)
URL: https://git.bioconductor.org/packages/ENCODExplorerData
Branch: master
Last Commit: c69d7b9
Last Changed Date: 2019-12-04 22:43:28 -0400 (Wed, 04 Dec 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: ENCODExplorerData
Version: 0.99.5
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ENCODExplorerData.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ENCODExplorerData_0.99.5.tar.gz
StartedAt: 2020-08-05 09:02:59 -0400 (Wed, 05 Aug 2020)
EndedAt: 2020-08-05 09:05:10 -0400 (Wed, 05 Aug 2020)
EllapsedTime: 131.3 seconds
RetCode: 0
Status:  OK 
CheckDir: ENCODExplorerData.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ENCODExplorerData.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ENCODExplorerData_0.99.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-data-annotation/meat/ENCODExplorerData.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ENCODExplorerData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ENCODExplorerData’ version ‘0.99.5’
* 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 ‘ENCODExplorerData’ 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 ... 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 ... 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 (user + system) or elapsed time > 5s
                 user system elapsed
encode_df_full 52.692  0.844  55.095
encode_df_lite 19.896  0.264  20.517
get_schemas    16.260  0.368  32.736
* 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: OK


Installation output

ENCODExplorerData.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL ENCODExplorerData
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘ENCODExplorerData’ ...
** 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 (ENCODExplorerData)

Tests output

ENCODExplorerData.Rcheck/tests/runTests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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.

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


RUNIT TEST PROTOCOL -- Wed Aug  5 09:05:08 2020 
*********************************************** 
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ENCODExplorerData RUnit Tests - 9 test functions, 0 errors, 0 failures
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  0.584   0.040   0.620 

Example timings

ENCODExplorerData.Rcheck/ENCODExplorerData-Ex.timings

nameusersystemelapsed
build_file_db_from_raw_tables000
clean_table0.3640.0161.870
encode_df_full52.692 0.84455.095
encode_df_lite19.896 0.26420.517
fetch_and_clean_raw_ENCODE_tables0.2200.0081.891
generate_encode_df_full000
generate_encode_df_lite0.0000.0000.001
get_encode_types0.0640.0120.298
get_schema_urls0.0760.0040.166
get_schemas16.260 0.36832.736