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CHECK report for BridgeDbR on merida1

This page was generated on 2020-09-28 11:29:45 -0400 (Mon, 28 Sep 2020).

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 202/1923HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BridgeDbR 1.23.1
Egon Willighagen
Snapshot Date: 2020-09-27 14:41:58 -0400 (Sun, 27 Sep 2020)
URL: https://git.bioconductor.org/packages/BridgeDbR
Branch: master
Last Commit: a8769f4
Last Changed Date: 2020-09-01 14:42:27 -0400 (Tue, 01 Sep 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BridgeDbR
Version: 1.23.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BridgeDbR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BridgeDbR_1.23.1.tar.gz
StartedAt: 2020-09-28 01:54:36 -0400 (Mon, 28 Sep 2020)
EndedAt: 2020-09-28 01:55:34 -0400 (Mon, 28 Sep 2020)
EllapsedTime: 58.1 seconds
RetCode: 0
Status:  OK 
CheckDir: BridgeDbR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BridgeDbR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BridgeDbR_1.23.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/BridgeDbR.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BridgeDbR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BridgeDbR’ version ‘1.23.1’
* 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 for sufficient/correct file permissions ... 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
  ‘/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:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BridgeDbR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘BridgeDbR’ ...
** 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 (BridgeDbR)

Tests output

BridgeDbR.Rcheck/tests/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(BridgeDbR)
Loading required package: rJava
> 
> test_check("BridgeDbR")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 20 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> 
> proc.time()
   user  system elapsed 
  2.865   0.223   2.853 

Example timings

BridgeDbR.Rcheck/BridgeDbR-Ex.timings

nameusersystemelapsed
fullNameExists0.0000.0000.001
getAttributes0.0000.0010.000
getBridgeNames0.0420.0050.075
getDataSource0.0010.0000.002
getDatabase0.1140.0612.649
getFullName0.0040.0010.004
getMatchingSources0.0180.0030.011
getOrganismCode0.0030.0000.002
getProperties0.0010.0000.000
getSystemCode0.0030.0000.002
loadDatabase2.9910.3004.064
map0.5750.0922.747
maps0.2710.0742.577
registerDataSource0.0090.0010.004
systemCodeExists0.0010.0010.001