Multiple platform build/check report for BioC 3.20 - BUILD results for pathview on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4505
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4506
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4538
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4486
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4493
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 pathview on kjohnson3

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

Version: 1.46.0

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

StartedAt: 2024-11-08 18:31:32 -0500 (Fri, 08 Nov 2024)

EndedAt: 2024-11-08 18:34:12 -0500 (Fri, 08 Nov 2024)

EllapsedTime: 159.8 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 pathview
###
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* checking for file ‘pathview/DESCRIPTION’ ... OK
* preparing ‘pathview’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘pathview.Rnw’ using Sweave

##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
Info: Downloading xml files for hsa04110, 1/1 pathways..
Warning in download.file(xml.url, xml.target, quiet = T) :
  URL 'https://rest.kegg.jp/get/hsa04110/kgml': status was 'SSL connect error'
Warning: Download of hsa04110 xml file failed!
This pathway may not exist!
Info: Downloading png files for hsa04110, 1/1 pathways..
Warning: Download of hsa04110 png file failed!
This pathway may not exist!
Warning: Failed to download KEGG xml/png files, hsa04110 skipped!

Error: processing vignette 'pathview.Rnw' failed with diagnostics:
 chunk 15 (label = kegg.native) 
Error in pv.out$plot.data.gene : $ operator is invalid for atomic vectors

--- failed re-building ‘pathview.Rnw’

SUMMARY: processing the following file failed:
  ‘pathview.Rnw’

Error: Vignette re-building failed.
Execution halted