Package: biomaRt

Version: 2.42.1

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:biomaRt.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings biomaRt_2.42.1.tar.gz

StartedAt: 2020-04-15 00:14:19 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 00:16:54 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 155.2 seconds

RetCode: 0

Status:  OK

CheckDir: biomaRt.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:biomaRt.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings biomaRt_2.42.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/biomaRt.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biomaRt/DESCRIPTION’ ... OK
* this is package ‘biomaRt’ version ‘2.42.1’
* 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 or elapsed time > 5s
       user system elapsed
getBM 0.636  0.012  17.764
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/biomaRt.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL biomaRt
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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.

> library(testthat)
> library(biomaRt)
> 
> test_check("biomaRt", encoding = "UTF-8")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 79 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 11.292   0.280  47.769 

name	user	system	elapsed
NP2009code	0	0	0
attributePages	0	0	0
exportFASTA	0	0	0
filterOptions	0	0	0
filterType	0	0	0
getBM	0.636	0.012	17.764
getBMlist	0	0	0
getGene	0.004	0.000	0.001
getLDS	0	0	0
getSequence	0.004	0.000	0.002
getXML	0	0	0
listAttributes	0.000	0.000	0.001
listDatasets	0.000	0.000	0.001
listEnsembl	0.000	0.000	0.001
listEnsemblArchives	0.012	0.000	0.285
listFilterValues	0.000	0.000	0.001
listFilters	0.000	0.000	0.001
listMarts	0	0	0
select	0.744	0.036	2.796
useDataset	0	0	0
useEnsembl	0	0	0
useMart	0.004	0.000	0.000