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-boun...@r-project.org> on behalf of
Johannes Griss <johannes.gr...@meduniwien.ac.at>
*Sent:* Friday, November 3, 2023 4:52 PM
*To:* bioc-devel@r-project.org <bioc-devel@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@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$>
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
