Multiple platform build/check report for BioC 3.21 - BUILD results for gemma.R on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4824
palomino7	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4566
merida1	macOS 12.7.5 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4604
kjohnson1	macOS 13.6.6 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4545
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4579
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 gemma.R on palomino7

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

Version: 3.4.5

Command: chmod a+r gemma.R -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data gemma.R

StartedAt: 2025-08-11 19:39:42 -0400 (Mon, 11 Aug 2025)

EndedAt: 2025-08-11 19:46:27 -0400 (Mon, 11 Aug 2025)

EllapsedTime: 404.6 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   chmod a+r gemma.R -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data gemma.R
###
##############################################################################
##############################################################################


* checking for file 'gemma.R/DESCRIPTION' ... OK
* preparing 'gemma.R':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'gemma.R.Rmd' using rmarkdown
Warning: ggrepel: 2 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building 'gemma.R.Rmd'

--- re-building 'metadata.Rmd' using rmarkdown

Quitting from metadata.Rmd:131-142 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `sum()`:
! invalid 'type' (list) of argument
---
Backtrace:
    ▆
 1. └─... %>% sum
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'metadata.Rmd' failed with diagnostics:
invalid 'type' (list) of argument
--- failed re-building 'metadata.Rmd'

--- re-building 'metanalysis.Rmd' using rmarkdown

Quitting from metanalysis.Rmd:468-484 [unnamed-chunk-20]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `saveRDS()`:
! error writing to connection
---
Backtrace:
    ▆
 1. ├─gemma.R::get_dataset_object(...)
 2. │ └─unique_sets %>% ...
 3. └─base::lapply(...)
 4.   └─gemma.R (local) FUN(X[[i]], ...)
 5.     └─gemma.R::get_dataset_samples(dataset, memoised = memoised)
 6.       └─gemma.R:::memget_dataset_samples(...)
 7.         └─gemma.R (local) mem_call(...)
 8.           └─encl$`_cache`$set(key, res)
 9.             └─base::saveRDS(value, file = file.path(path, key), compress = compress)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'metanalysis.Rmd' failed with diagnostics:
error writing to connection
--- failed re-building 'metanalysis.Rmd'

SUMMARY: processing the following files failed:
  'metadata.Rmd' 'metanalysis.Rmd'

Error: Vignette re-building failed.
Execution halted