Multiple platform build/check report for BioC 3.20 - BUILD results for paxtoolsr on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4764
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4495
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4522
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4449
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4426
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*

BUILD results for paxtoolsr on merida1

To the developers/maintainers of the paxtoolsr package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/paxtoolsr.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: paxtoolsr

Version: 1.40.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data paxtoolsr

StartedAt: 2025-03-31 20:54:41 -0400 (Mon, 31 Mar 2025)

EndedAt: 2025-03-31 20:55:20 -0400 (Mon, 31 Mar 2025)

EllapsedTime: 38.5 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data paxtoolsr
###
##############################################################################
##############################################################################


* checking for file ‘paxtoolsr/DESCRIPTION’ ... OK
* preparing ‘paxtoolsr’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘using_paxtoolsr.Rmd’ using rmarkdown
2025-03-31 20:55:06,580 1725 [main] INFO  org.biopax.paxtools.PaxtoolsMain  - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
2025-03-31 20:55:07,476 2621 [main] INFO  org.biopax.paxtools.PaxtoolsMain  - toSifnx: not blacklisting ubiquitous molecules (no blacklist.txt found)

Quitting from using_paxtoolsr.Rmd:168-171 [searchResultsExampleVerbose]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `getPcRequest()`:
! ERROR: Code: 404 Message: Unknown Error (PC Webservice Error)
---
Backtrace:
    ▆
 1. └─paxtoolsr::searchPc(q = "glycolysis", type = "pathway", verbose = TRUE)
 2.   └─paxtoolsr:::getPcRequest(url, verbose)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'using_paxtoolsr.Rmd' failed with diagnostics:
ERROR: Code: 404 Message: Unknown Error (PC Webservice Error)
--- failed re-building ‘using_paxtoolsr.Rmd’

SUMMARY: processing the following file failed:
  ‘using_paxtoolsr.Rmd’

Error: Vignette re-building failed.
Execution halted