| Back to Multiple platform build/check report for BioC 3.23: simplified long |
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This page was generated on 2025-12-13 11:47 -0500 (Sat, 13 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4874 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4582 |
| 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 | ||||
| Package 1725/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReactomeGSA 1.25.0 (landing page) Johannes Griss
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
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To the developers/maintainers of the ReactomeGSA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ReactomeGSA.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. |
| Package: ReactomeGSA |
| Version: 1.25.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ReactomeGSA |
| StartedAt: 2025-12-12 17:27:37 -0500 (Fri, 12 Dec 2025) |
| EndedAt: 2025-12-12 17:31:00 -0500 (Fri, 12 Dec 2025) |
| EllapsedTime: 203.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/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 (it is needed to build vignettes) * creating vignettes ... ERROR --- re-building ‘analysing-scRNAseq.Rmd’ using rmarkdown | | | 0% | |= | 2% | |=== | 4% | |==== | 6% | |===== | 8% | |======= | 10% | |======== | 12% | |========= | 13% | |=========== | 15% | |============ | 17% | |============= | 19% | |=============== | 21% | |================ | 23% | |================== | 25% | |=================== | 27% | |==================== | 29% | |====================== | 31% | |======================= | 33% | |======================== | 35% | |========================== | 37% | |=========================== | 38% | |============================ | 40% | |============================== | 42% | |=============================== | 44% | |================================ | 46% | |================================== | 48% | |=================================== | 50% | |==================================== | 52% | |====================================== | 54% | |======================================= | 56% | |======================================== | 58% | |========================================== | 60% | |=========================================== | 62% | |============================================ | 63% | |============================================== | 65% | |=============================================== | 67% | |================================================ | 69% | |================================================== | 71% | |=================================================== | 73% | |==================================================== | 75% | |====================================================== | 77% | |======================================================= | 79% | |========================================================= | 81% | |========================================================== | 83% | |=========================================================== | 85% | |============================================================= | 87% | |============================================================== | 88% | |=============================================================== | 90% | |================================================================= | 92% | |================================================================== | 94% | |=================================================================== | 96% | |===================================================================== | 98% | |======================================================================| 100% | | | 0% | |=== | 4% | |====== | 8% | |========= | 12% | |============ | 17% | |=============== | 21% | |================== | 25% | |==================== | 29% | |======================= | 33% | |========================== | 38% | |============================= | 42% | |================================ | 46% | |=================================== | 50% | |====================================== | 54% | |========================================= | 58% | |============================================ | 62% | |=============================================== | 67% | |================================================== | 71% | |==================================================== | 75% | |======================================================= | 79% | |========================================================== | 83% | |============================================================= | 88% | |================================================================ | 92% | |=================================================================== | 96% | |======================================================================| 100% 2025-12-12 17:28:35.132 R[80857:377705712] XType: Using static font registry. Quitting from analysing-scRNAseq.Rmd:180-182 [unnamed-chunk-9] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'analysing-scRNAseq.Rmd' failed with diagnostics: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct. ℹ Please use the `layer` argument instead. --- failed re-building ‘analysing-scRNAseq.Rmd’ --- re-building ‘reanalysing-public-data.Rmd’ using rmarkdown --- finished re-building ‘reanalysing-public-data.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