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

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"	4451
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4417
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4456
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4489
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4436
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4435
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 pgxRpi on lconway

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.

raw results

Summary

Package: pgxRpi

Version: 1.1.7

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

StartedAt: 2024-09-26 18:04:46 -0400 (Thu, 26 Sep 2024)

EndedAt: 2024-09-26 18:09:48 -0400 (Thu, 26 Sep 2024)

EllapsedTime: 301.9 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data 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
2024-09-26 18:05:40.780 R[22998:349583620] XType: com.apple.fonts is not accessible.
2024-09-26 18:05:40.780 R[22998:349583620] XType: XTFontStaticRegistry is enabled.
--- finished re-building ‘Introduction_1_loadmetadata.Rmd’

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

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

Quitting from lines 87-89 [unnamed-chunk-6] (Introduction_3_loadfrequency.Rmd)
Error: processing vignette 'Introduction_3_loadfrequency.Rmd' failed with diagnostics:
invalid rownames length
--- 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 file failed:
  ‘Introduction_3_loadfrequency.Rmd’

Error: Vignette re-building failed.
Execution halted