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CHECK report for biomaRt on merida1

This page was generated on 2021-05-06 12:34:26 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the biomaRt package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 177/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biomaRt 2.46.3  (landing page)
Mike Smith
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/biomaRt
Branch: RELEASE_3_12
Last Commit: 607b632
Last Changed Date: 2021-02-08 05:38:06 -0400 (Mon, 08 Feb 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: biomaRt
Version: 2.46.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:biomaRt.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings biomaRt_2.46.3.tar.gz
StartedAt: 2021-05-05 23:42:08 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 23:45:22 -0400 (Wed, 05 May 2021)
EllapsedTime: 194.2 seconds
RetCode: 0
Status:   OK  
CheckDir: biomaRt.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:biomaRt.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings biomaRt_2.46.3.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/biomaRt.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biomaRt/DESCRIPTION’ ... OK
* this is package ‘biomaRt’ version ‘2.46.3’
* package encoding: UTF-8
* 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 ‘biomaRt’ 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
Unexported object imported by a ':::' call: ‘AnnotationDbi:::smartKeys’
  See the note in ?`:::` about the use of this operator.
* 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
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
select 5.616  0.108  17.232
getBM  5.364  0.075  20.867
* 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/biomaRt.Rcheck/00check.log’
for details.



Installation output

biomaRt.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL biomaRt
###
##############################################################################
##############################################################################


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

Tests output

biomaRt.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-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(mockery)
> library(biomaRt)
> 
> #biomartCacheClear()
> 
> #test_check("biomaRt", encoding = "UTF-8")
> 
> proc.time()
   user  system elapsed 
  5.898   0.343   8.801 

Example timings

biomaRt.Rcheck/biomaRt-Ex.timings

nameusersystemelapsed
NP2009code0.0000.0010.001
attributePages0.0000.0010.001
exportFASTA0.0010.0000.001
filterOptions0.0000.0010.001
filterType0.0000.0000.001
getBM 5.364 0.07520.867
getBMlist0.0000.0000.001
getGene0.0010.0000.002
getLDS0.0000.0000.002
getSequence0.0020.0010.003
listAttributes0.0020.0010.003
listDatasets0.0020.0010.002
listEnsembl0.0000.0000.001
listEnsemblArchives0.0470.0040.488
listFilterValues0.0010.0010.002
listFilters0.0010.0010.002
listMarts0.0010.0000.001
select 5.616 0.10817.232
useDataset000
useEnsembl0.0010.0000.004
useMart0.0000.0000.001