Re: [Bioc-devel] ReactomeGSA missing in Bioconductor 3.18?
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 on behalf of Johannes Griss *Sent:* Friday, November 3, 2023 4:52 PM *To:* 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=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7Cd0b8a0d7666d4bbfc4b808dbdcaecbe7%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638346415598213348%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=v2kHQF1w6Ks5q0vmoZAnNo3ZKXjLeqLnMn5Ou7NKF64%3D=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
Re: [Bioc-devel] ReactomeGSA missing in Bioconductor 3.18?
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 on behalf of Johannes Griss Sent: Friday, November 3, 2023 4:52 PM To: 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=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7Cd0b8a0d7666d4bbfc4b808dbdcaecbe7%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638346415598213348%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=v2kHQF1w6Ks5q0vmoZAnNo3ZKXjLeqLnMn5Ou7NKF64%3D=0<https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!KW1sKP9AN51aLOcF2htPL3H8DdEYyRlR4feh3rzZMthABEc8VLPbqk8QYjwb05YfNsq-zFxH0sEJydQkAbQ4HA-Z7GbN0LJjNQWmjo6Ekv4$> [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] ReactomeGSA missing in Bioconductor 3.18?
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://stat.ethz.ch/mailman/listinfo/bioc-devel
