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CHECK report for BridgeDbR on tokay1

This page was generated on 2021-05-06 12:30:05 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the BridgeDbR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 210/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BridgeDbR 2.0.2  (landing page)
Egon Willighagen
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/BridgeDbR
Branch: RELEASE_3_12
Last Commit: a66f65e
Last Changed Date: 2021-04-26 04:07:23 -0400 (Mon, 26 Apr 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: BridgeDbR
Version: 2.0.2
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:BridgeDbR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BridgeDbR_2.0.2.tar.gz
StartedAt: 2021-05-06 01:02:30 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 01:04:01 -0400 (Thu, 06 May 2021)
EllapsedTime: 91.6 seconds
RetCode: 0
Status:   OK   
CheckDir: BridgeDbR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:BridgeDbR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BridgeDbR_2.0.2.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BridgeDbR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BridgeDbR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BridgeDbR' version '2.0.2'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'BridgeDbR' 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 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/BridgeDbR.Rcheck/00check.log'
for details.



Installation output

BridgeDbR.Rcheck/00install.out

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch BridgeDbR
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
* installing *source* package 'BridgeDbR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BridgeDbR'
    finding HTML links ... done
    BridgeDbR                               html  
    fullNameExists                          html  
    getAttributes                           html  
    getBridgeNames                          html  
    getDataSource                           html  
    getDatabase                             html  
    getFullName                             html  
    getMatchingSources                      html  
    getOrganismCode                         html  
    getProperties                           html  
    getSystemCode                           html  
    loadDatabase                            html  
    map                                     html  
    maps                                    html  
    registerDataSource                      html  
    systemCodeExists                        html  
** 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 (BridgeDbR)
Making 'packages.html' ... done

Tests output

BridgeDbR.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(BridgeDbR)
Loading required package: rJava
> 
> test_check("BridgeDbR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 20 ]
> 
> 
> proc.time()
   user  system elapsed 
   1.56    0.17    1.59 

Example timings

BridgeDbR.Rcheck/BridgeDbR-Ex.timings

nameusersystemelapsed
fullNameExists000
getAttributes000
getBridgeNames0.050.000.16
getDataSource000
getDatabase000
getFullName000
getMatchingSources0.000.010.01
getOrganismCode000
getProperties000
getSystemCode000
loadDatabase000
map000
maps000
registerDataSource0.030.000.02
systemCodeExists000