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This page was generated on 2025-01-28 11:44 -0500 (Tue, 28 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4659
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4454
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4465
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4419
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4409
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

Package 1823/2286HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rWikiPathways 1.27.0  (landing page)
Egon Willighagen
Snapshot Date: 2025-01-27 13:40 -0500 (Mon, 27 Jan 2025)
git_url: https://git.bioconductor.org/packages/rWikiPathways
git_branch: devel
git_last_commit: 75875b0
git_last_commit_date: 2024-10-29 10:27:20 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for rWikiPathways on lconway

To the developers/maintainers of the rWikiPathways package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: rWikiPathways
Version: 1.27.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rWikiPathways.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rWikiPathways_1.27.0.tar.gz
StartedAt: 2025-01-27 22:39:22 -0500 (Mon, 27 Jan 2025)
EndedAt: 2025-01-27 22:41:41 -0500 (Mon, 27 Jan 2025)
EllapsedTime: 139.1 seconds
RetCode: 0
Status:   OK  
CheckDir: rWikiPathways.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rWikiPathways.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rWikiPathways_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/rWikiPathways.Rcheck’
* using R Under development (unstable) (2025-01-22 r87618)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rWikiPathways/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rWikiPathways’ version ‘1.27.0’
* 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 ... 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 ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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
findPathwaysByLiterature: no visible binding for global variable ‘refs’
findPathwaysByLiterature: no visible binding for global variable
  ‘citations’
findPathwaysByOrcid: no visible binding for global variable ‘orcids’
findPathwaysByText: no visible binding for global variable ‘citedIn’
getOntologyTerms: no visible binding for global variable ‘terms’
getPathwaysByCommunity: no visible binding for global variable
  ‘pathways’
getPathwaysByCommunity: no visible binding for global variable
  ‘community-tag’
getPathwaysByOntologyTerm: no visible binding for global variable
  ‘pathways’
getPathwaysByParentOntologyTerm: no visible binding for global variable
  ‘terms’
getPathwaysByParentOntologyTerm: no visible binding for global variable
  ‘terms_parent’
getRecentChanges: no visible binding for global variable ‘revision’
getRecentChanges: no visible binding for global variable ‘revision_ymd’
getRecentChanges: no visible binding for global variable ‘authors’
getRecentChanges: no visible binding for global variable ‘description’
getRecentChanges: no visible binding for global variable ‘citedIn’
listCommunities: no visible binding for global variable ‘pathways’
listPathways: no visible binding for global variable ‘species’
readPathwayGMT: no visible binding for global variable ‘pathway’
Undefined global functions or variables:
  authors citations citedIn community-tag description orcids pathway
  pathways refs revision revision_ymd species terms terms_parent
Consider adding
  importFrom("stats", "terms")
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
findPathwaysByLiterature     8.612  0.159   9.799
findPathwayNamesByLiterature 6.434  0.118   7.328
findPathwayIdsByLiterature   6.385  0.116   7.494
findPathwayUrlsByLiterature  6.094  0.103   7.088
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/rWikiPathways.Rcheck/00check.log’
for details.


Installation output

rWikiPathways.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rWikiPathways
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘rWikiPathways’ ...
** this is package ‘rWikiPathways’ version ‘1.27.0’
** 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 Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 1 | SKIP 0 | PASS 26 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 26 ]
> 
> proc.time()
   user  system elapsed 
 21.347   0.691  26.410 

Example timings

rWikiPathways.Rcheck/rWikiPathways-Ex.timings

nameusersystemelapsed
downloadPathwayArchive000
findPathwayIDsByOrcid0.3270.0210.941
findPathwayIdsByLiterature6.3850.1167.494
findPathwayIdsByText2.1970.0262.499
findPathwayIdsByXref1.1830.0581.871
findPathwayNamesByLiterature6.4340.1187.328
findPathwayNamesByOrcid0.3000.0120.491
findPathwayNamesByText1.8260.0222.026
findPathwayNamesByXref1.1260.0491.628
findPathwayUrlsByLiterature6.0940.1037.088
findPathwayUrlsByOrcid0.3390.0120.552
findPathwayUrlsByText2.2900.0262.518
findPathwayUrlsByXref0.9530.0401.429
findPathwaysByLiterature8.6120.1599.799
findPathwaysByOrcid0.3970.0130.577
findPathwaysByText2.5440.0452.994
findPathwaysByXref1.0820.0411.793
getCounts0.0140.0010.081
getCurationStatus0.0150.0020.076
getOntologyTermIds1.1470.0201.392
getOntologyTermNames1.1470.0151.343
getOntologyTerms1.1400.0191.321
getPathway0.0560.0080.154
getPathwayHistory000
getPathwayIdsByCommunity0.1100.0050.251
getPathwayIdsByOntologyTerm0.1290.0050.307
getPathwayIdsByParentOntologyTerm1.0420.0141.227
getPathwayInfo0.2500.0100.441
getPathwayNamesByCommunity0.1570.0050.274
getPathwayUrlsByCommunity0.1380.0050.274
getPathwaysByCommunity0.2510.0070.366
getPathwaysByOntologyTerm0.1270.0050.240
getPathwaysByParentOntologyTerm0.9980.0491.210
getRecentChanges0.5870.0940.848
getRecentChangesIds0.3130.0210.484
getRecentChangesNames0.2950.0390.497
getXrefList0.3570.0410.470
listCommunities0.1400.0050.296
listOrganisms0.0160.0020.090
listPathwayIds0.2370.0100.395
listPathwayNames0.2200.0120.372
listPathwayUrls0.2020.0110.344
listPathways0.2120.0140.431
readGMT0.0000.0010.001
readGMTnames000
readPathwayGMT0.0010.0000.000
writeGMT000