Multiple platform build/check report for BioC 3.20 - BUILD results for pgxRpi on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"	4665
palomino4	Windows Server 2022 Datacenter	x64	4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"	4400
merida1	macOS 12.7.4 Monterey	x86_64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4427
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*

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

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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 pgxRpi
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* checking for file ‘pgxRpi/DESCRIPTION’ ... OK
* preparing ‘pgxRpi’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Introduction_1_loadmetadata.Rmd’ using rmarkdown

Quitting from lines 66-73 [unnamed-chunk-2] (Introduction_1_loadmetadata.Rmd)
Error: processing vignette 'Introduction_1_loadmetadata.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building ‘Introduction_1_loadmetadata.Rmd’

--- re-building ‘Introduction_2_loadvariants.Rmd’ using rmarkdown

Quitting from lines 68-69 [unnamed-chunk-2] (Introduction_2_loadvariants.Rmd)
Error: processing vignette 'Introduction_2_loadvariants.Rmd' failed with diagnostics:
cannot open the connection to 'http://progenetix.org/services/samplematrix/?datasetIds=progenetix&filters=NCIT:C2948&limit=0'
--- failed re-building ‘Introduction_2_loadvariants.Rmd’

--- re-building ‘Introduction_3_loadfrequency.Rmd’ using rmarkdown

Quitting from lines 59-63 [unnamed-chunk-2] (Introduction_3_loadfrequency.Rmd)
Error: processing vignette 'Introduction_3_loadfrequency.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building ‘Introduction_3_loadfrequency.Rmd’

--- re-building ‘Introduction_4_process_pgxseg.Rmd’ using rmarkdown
--- finished re-building ‘Introduction_4_process_pgxseg.Rmd’

SUMMARY: processing the following files failed:
  ‘Introduction_1_loadmetadata.Rmd’ ‘Introduction_2_loadvariants.Rmd’
  ‘Introduction_3_loadfrequency.Rmd’

Error: Vignette re-building failed.
Execution halted

BUILD results for pgxRpi on nebbiolo2

Summary

Command output