Package: rWikiPathways

Version: 1.0.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rWikiPathways.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rWikiPathways_1.0.5.tar.gz

StartedAt: 2018-10-16 23:53:21 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 23:55:19 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 117.4 seconds

RetCode: 0

Status:  OK

CheckDir: rWikiPathways.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rWikiPathways.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rWikiPathways_1.0.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/rWikiPathways.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.0.5’
* 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 ... NOTE
downloadPathwayArchive: no visible global function definition for
  ‘readHTMLTable’
Undefined global functions or variables:
  readHTMLTable
* 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
getColoredPathway 0.218  0.044  10.590
listPathways      0.048  0.017   5.221
listPathwayUrls   0.022  0.003   5.080
listPathwayNames  0.017  0.002   5.161
listPathwayIds    0.012  0.001   5.120
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/rWikiPathways.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rWikiPathways
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘rWikiPathways’ ...
** 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
* DONE (rWikiPathways)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(rWikiPathways)
> 
> test_check("rWikiPathways")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 30 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  1.433   0.190  31.213 

name	user	system	elapsed
downloadPathwayArchive	0.000	0.000	0.001
findPathwayIdsByLiterature	0.138	0.022	4.026
findPathwayIdsByText	0.010	0.001	0.275
findPathwayIdsByXref	0.020	0.002	0.307
findPathwayNamesByLiterature	0.072	0.007	4.601
findPathwayNamesByText	0.014	0.002	0.419
findPathwayNamesByXref	0.024	0.002	0.356
findPathwayUrlsByLiterature	0.085	0.008	3.844
findPathwayUrlsByText	0.013	0.002	0.319
findPathwayUrlsByXref	0.024	0.002	0.309
findPathwaysByLiterature	0.341	0.108	4.011
findPathwaysByText	0.032	0.011	0.331
findPathwaysByXref	0.120	0.051	0.502
getColoredPathway	0.218	0.044	10.590
getCurationTagNames	0.009	0.001	0.084
getCurationTags	0.009	0.001	0.089
getEveryCurationTag	0.090	0.036	1.038
getOntologyTermIds	0.008	0.001	0.075
getOntologyTermNames	0.009	0.000	0.070
getOntologyTerms	0.007	0.000	0.067
getPathway	0.043	0.001	0.118
getPathwayHistory	0.008	0.001	0.087
getPathwayIdsByCurationTag	0.017	0.001	0.567
getPathwayIdsByOntologyTerm	0.010	0.001	0.103
getPathwayIdsByParentOntologyTerm	0.007	0.000	0.095
getPathwayInfo	0.008	0.000	0.074
getPathwaysByCurationTag	0.041	0.012	0.718
getPathwaysByOntologyTerm	0.009	0.001	0.093
getPathwaysByParentOntologyTerm	0.010	0.002	0.090
getRecentChanges	0.029	0.009	0.311
getRecentChangesIds	0.011	0.001	0.218
getRecentChangesNames	0.012	0.001	0.218
getXrefList	0.007	0.000	0.088
listOrganisms	0.009	0.001	0.070
listPathwayIds	0.012	0.001	5.120
listPathwayNames	0.017	0.002	5.161
listPathwayUrls	0.022	0.003	5.080
listPathways	0.048	0.017	5.221
wikipathwaysAPI	0.006	0.003	0.008
wikipathwaysGET	0.008	0.000	0.069