Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:05:54 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for rWikiPathways on nebbiolo2


To the developers/maintainers of the rWikiPathways package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rWikiPathways.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1684/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rWikiPathways 1.14.0  (landing page)
Egon Willighagen
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/rWikiPathways
git_branch: RELEASE_3_14
git_last_commit: b83547a
git_last_commit_date: 2021-10-26 12:43:34 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: rWikiPathways
Version: 1.14.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:rWikiPathways.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings rWikiPathways_1.14.0.tar.gz
StartedAt: 2022-04-12 09:11:05 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 09:13:04 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 119.5 seconds
RetCode: 0
Status:   OK  
CheckDir: rWikiPathways.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:rWikiPathways.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings rWikiPathways_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/rWikiPathways.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.14.0’
* 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 ... NOTE
Found the following non-portable file path:
  rWikiPathways/docs/articles/rWikiPathways-and-BridgeDbR_files/accessible-code-block-0.0.1/empty-anchor.js

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* 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 binding for global variable ‘pathway’
Undefined global functions or variables:
  pathway
* 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
findPathwaysByLiterature     0.272  0.080   6.384
findPathwayIdsByLiterature   0.210  0.008   7.260
findPathwayNamesByLiterature 0.191  0.000   6.508
findPathwayUrlsByLiterature  0.168  0.004   6.578
listPathways                 0.016  0.000   5.285
listPathwayIds               0.013  0.000   5.194
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/rWikiPathways.Rcheck/00check.log’
for details.



Installation output

rWikiPathways.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL rWikiPathways
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 27 ]
> 
> proc.time()
   user  system elapsed 
  2.032   0.187  27.566 

Example timings

rWikiPathways.Rcheck/rWikiPathways-Ex.timings

nameusersystemelapsed
downloadPathwayArchive000
findPathwayIdsByLiterature0.2100.0087.260
findPathwayIdsByText0.0130.0001.150
findPathwayIdsByXref0.0390.0000.819
findPathwayNamesByLiterature0.1910.0006.508
findPathwayNamesByText0.0180.0041.247
findPathwayNamesByXref0.0220.0030.858
findPathwayUrlsByLiterature0.1680.0046.578
findPathwayUrlsByText0.0140.0001.116
findPathwayUrlsByXref0.0300.0000.826
findPathwaysByLiterature0.2720.0806.384
findPathwaysByText0.0150.0001.089
findPathwaysByXref0.0250.0040.773
getCurationTagNames0.0090.0000.056
getCurationTags0.0100.0010.059
getEveryCurationTag0.0360.0160.869
getOntologyTermIds0.0070.0000.043
getOntologyTermNames0.0100.0000.045
getOntologyTerms0.0090.0000.043
getPathway0.0230.0000.060
getPathwayHistory0.0040.0040.045
getPathwayIdsByCurationTag0.0150.0040.790
getPathwayIdsByOntologyTerm0.0030.0040.064
getPathwayIdsByParentOntologyTerm0.0100.0000.063
getPathwayInfo0.0130.0000.048
getPathwaysByCurationTag0.0290.0080.795
getPathwaysByOntologyTerm0.0050.0040.076
getPathwaysByParentOntologyTerm0.0040.0040.089
getRecentChanges0.0110.0080.230
getRecentChangesIds0.0100.0000.194
getRecentChangesNames0.0160.0000.206
getXrefList0.0070.0000.323
listOrganisms0.0060.0000.059
listPathwayIds0.0130.0005.194
listPathwayNames0.0140.0004.647
listPathwayUrls0.0160.0004.659
listPathways0.0160.0005.285
readGMT000
readGMTnames000
readPathwayGMT000
wikipathwaysAPI000
wikipathwaysGET0.0070.0000.041
writeGMT0.0010.0000.000