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CHECK report for rWikiPathways on malbec2

This page was generated on 2020-10-17 11:55:39 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE rWikiPathways PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1563/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rWikiPathways 1.8.5
Egon Willighagen
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/rWikiPathways
Branch: RELEASE_3_11
Last Commit: 510f995
Last Changed Date: 2020-09-09 19:48:48 -0400 (Wed, 09 Sep 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: rWikiPathways
Version: 1.8.5
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:rWikiPathways.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings rWikiPathways_1.8.5.tar.gz
StartedAt: 2020-10-17 05:06:55 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:08:57 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 122.0 seconds
RetCode: 0
Status:  OK 
CheckDir: rWikiPathways.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:rWikiPathways.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings rWikiPathways_1.8.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/rWikiPathways.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.8.5’
* 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
readPathwayGMT: no visible global function definition for ‘stack’
readPathwayGMT: no visible binding for global variable ‘pathway’
Undefined global functions or variables:
  pathway stack
Consider adding
  importFrom("utils", "stack")
to your NAMESPACE file.
* 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
findPathwayIdsByLiterature 0.423  0.024   6.216
listPathwayUrls            0.028  0.000   5.357
listPathwayNames           0.014  0.004   5.347
listPathways               0.016  0.000   5.017
listPathwayIds             0.015  0.000   8.370
* 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
  ‘/home/biocbuild/bbs-3.11-bioc/meat/rWikiPathways.Rcheck/00check.log’
for details.



Installation output

rWikiPathways.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL rWikiPathways
###
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* installing to library ‘/home/biocbuild/bbs-3.11-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)

Tests output

rWikiPathways.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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 
  2.663   0.072  27.399 

Example timings

rWikiPathways.Rcheck/rWikiPathways-Ex.timings

nameusersystemelapsed
downloadPathwayArchive0.0010.0000.000
findPathwayIdsByLiterature0.4230.0246.216
findPathwayIdsByText0.0120.0000.776
findPathwayIdsByXref0.0240.0000.648
findPathwayNamesByLiterature0.2550.0044.798
findPathwayNamesByText0.0140.0000.696
findPathwayNamesByXref0.0270.0000.516
findPathwayUrlsByLiterature0.2670.0044.666
findPathwayUrlsByText0.0110.0040.704
findPathwayUrlsByXref0.0250.0040.511
findPathwaysByLiterature0.2290.0004.792
findPathwaysByText0.0140.0000.718
findPathwaysByXref0.0410.0000.546
getColoredPathway0.0000.0020.002
getCurationTagNames0.0070.0000.065
getCurationTags0.0080.0000.052
getEveryCurationTag0.0390.0400.876
getOntologyTermIds0.0080.0000.042
getOntologyTermNames0.0090.0000.044
getOntologyTerms0.0100.0000.043
getPathway0.0240.0030.065
getPathwayHistory0.0060.0040.045
getPathwayIdsByCurationTag0.0170.0040.620
getPathwayIdsByOntologyTerm0.0080.0000.063
getPathwayIdsByParentOntologyTerm0.0090.0000.058
getPathwayInfo0.0180.0010.052
getPathwaysByCurationTag0.0440.0070.655
getPathwaysByOntologyTerm0.0090.0010.056
getPathwaysByParentOntologyTerm0.0110.0000.057
getRecentChanges0.0570.0360.914
getRecentChangesIds0.0190.0000.836
getRecentChangesNames0.0290.0000.845
getXrefList0.0100.0000.189
listOrganisms0.0100.0000.043
listPathwayIds0.0150.0008.370
listPathwayNames0.0140.0045.347
listPathwayUrls0.0280.0005.357
listPathways0.0160.0005.017
readPathwayGMT0.0010.0000.000
wikipathwaysAPI0.0050.0060.011
wikipathwaysGET0.0090.0000.045