[Bioc-devel] ReactomeGSA missing in Bioconductor 3.18?

[Johannes Griss]

Hi Jennifer,

Thanks a lot for the quick response! Our build server was still on an 
older version of Seurat.

Data package is updated.

Kind regards,
Johannes

On 06.11.23 20:30, Jennifer Wokaty wrote:
> 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:
> 
> ##############################################################################
> ##############################################################################
> ###
> ### 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
> 
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel__%3B!!PxiZbSOawA!KW1sKP9AN51aLOcF2htPL3H8DdEYyRlR4feh3rzZMthABEc8VLPbqk8QYjwb05YfNsq-zFxH0sEJydQkAbQ4HA-Z7GbN0LJjNQWmjo6Ekv4%24&data=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7Cd0b8a0d7666d4bbfc4b808dbdcaecbe7%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638346415598213348%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=v2kHQF1w6Ks5q0vmoZAnNo3ZKXjLeqLnMn5Ou7NKF64%3D&reserved=0 <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!KW1sKP9AN51aLOcF2htPL3H8DdEYyRlR4feh3rzZMthABEc8VLPbqk8QYjwb05YfNsq-zFxH0sEJydQkAbQ4HA-Z7GbN0LJjNQWmjo6Ekv4$>