[Bioc-devel] ReactomeGSA missing in Bioconductor 3.18?

[Jennifer Wokaty]

Hi Johannes,

I installed R 4.3.2 on the release builders on Thursday after the last Experiment package report. ReactomeGSA.data will be reinstalled tomorrow so this error will resolve soon; however, it's masking another error:

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ReactomeGSA
###
##############################################################################
##############################################################################


* checking for file 'ReactomeGSA/DESCRIPTION' ... OK
* preparing 'ReactomeGSA':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'analysing-scRNAseq.Rmd' using rmarkdown

Quitting from lines 58-62 [unnamed-chunk-2] (analysing-scRNAseq.Rmd)
Error: processing vignette 'analysing-scRNAseq.Rmd' failed with diagnostics:
Please run UpdateSeuratObject on your object
--- failed re-building 'analysing-scRNAseq.Rmd'

--- re-building 'using-reactomegsa.Rmd' using rmarkdown
--- finished re-building 'using-reactomegsa.Rmd'

SUMMARY: processing the following file failed:
  'analysing-scRNAseq.Rmd'

Error: Vignette re-building failed.
Execution halted

Lori was able to reproduce this on her local machine and suggested that you might need to update your data object in ReactomeGSA.data.

Jennifer Wokaty (they/them)

Waldron Lab at CUNY SPH
Bioconductor Core Team
________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Johannes Griss <johannes.griss using meduniwien.ac.at>
Sent: Friday, November 3, 2023 4:52 PM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] ReactomeGSA missing in Bioconductor 3.18?

* This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. *

Hi everyone,

For a while the build system reported an error that our ReactomeGSA
package cannot be build due to the missing dependency of the
"ReactomeGSA.data" package which is required to build the vignettes and
is listed in the "Suggests" section.

ReactomeGSA.data seems to building fine though but depends on ReactomeGSA.

Unfortunately, I cannot figure out how I could solve this issue.

Thanks for your help!

Kind regards,
Johannes

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