Package: rWikiPathways

Version: 1.6.1

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:rWikiPathways.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings rWikiPathways_1.6.1.tar.gz

StartedAt: 2020-04-15 05:38:46 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:40:29 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 102.9 seconds

RetCode: 0

Status:  OK

CheckDir: rWikiPathways.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:rWikiPathways.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings rWikiPathways_1.6.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/rWikiPathways.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 ‘rWikiPathways/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rWikiPathways’ version ‘1.6.1’
* 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:
  .travis.yml
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 ‘rWikiPathways’ 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
Examples with CPU or elapsed time > 5s
                              user system elapsed
findPathwayIdsByLiterature   0.168  0.016   6.903
findPathwaysByLiterature     0.132  0.040   6.477
findPathwayNamesByLiterature 0.052  0.000   6.299
findPathwayUrlsByLiterature  0.052  0.000   6.475
* 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/rWikiPathways.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 rWikiPathways
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘rWikiPathways’ ...
** 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 (rWikiPathways)

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(rWikiPathways)
> 
> test_check("rWikiPathways")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 27 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  1.760   0.064  24.347 

name	user	system	elapsed
downloadPathwayArchive	0	0	0
findPathwayIdsByLiterature	0.168	0.016	6.903
findPathwayIdsByText	0.004	0.004	0.993
findPathwayIdsByXref	0.060	0.000	0.586
findPathwayNamesByLiterature	0.052	0.000	6.299
findPathwayNamesByText	0.020	0.000	0.962
findPathwayNamesByXref	0.016	0.000	0.594
findPathwayUrlsByLiterature	0.052	0.000	6.475
findPathwayUrlsByText	0.012	0.000	1.065
findPathwayUrlsByXref	0.020	0.004	0.554
findPathwaysByLiterature	0.132	0.040	6.477
findPathwaysByText	0.016	0.008	1.022
findPathwaysByXref	0.072	0.036	0.639
getColoredPathway	0.000	0.000	0.001
getCurationTagNames	0.008	0.000	0.058
getCurationTags	0.004	0.004	0.057
getEveryCurationTag	0.056	0.044	0.930
getOntologyTermIds	0.008	0.000	0.043
getOntologyTermNames	0.004	0.000	0.041
getOntologyTerms	0.008	0.000	0.042
getPathway	0.024	0.000	0.065
getPathwayHistory	0.004	0.004	0.045
getPathwayIdsByCurationTag	0.016	0.000	0.649
getPathwayIdsByOntologyTerm	0.008	0.000	0.061
getPathwayIdsByParentOntologyTerm	0.008	0.000	0.059
getPathwayInfo	0.012	0.000	0.047
getPathwaysByCurationTag	0.036	0.012	0.683
getPathwaysByOntologyTerm	0.008	0.000	0.056
getPathwaysByParentOntologyTerm	0.008	0.000	0.058
getRecentChanges	0.012	0.020	0.322
getRecentChangesIds	0.016	0.000	0.243
getRecentChangesNames	0.012	0.004	0.245
getXrefList	0.008	0.000	0.187
listOrganisms	0.008	0.000	0.041
listPathwayIds	0.012	0.000	4.601
listPathwayNames	0.020	0.000	4.467
listPathwayUrls	0.012	0.004	4.636
listPathways	0.032	0.008	4.617
wikipathwaysAPI	0.000	0.004	0.007
wikipathwaysGET	0.008	0.004	0.042