| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-12 11:32 -0500 (Wed, 12 Nov 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" | 4823 |
| 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 1719/2325 | 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 | |||||||||
|
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: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ReactomeGSA |
| StartedAt: 2025-11-11 19:37:36 -0500 (Tue, 11 Nov 2025) |
| EndedAt: 2025-11-11 19:44:22 -0500 (Tue, 11 Nov 2025) |
| EllapsedTime: 406.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ReactomeGSA
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* 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
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Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "Analysing single-cell RNAseq data", and the latter is "Analysing single-cell RNA-sequencing Data". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘analysing-scRNAseq.Rmd’
--- re-building ‘reanalysing-public-data.Rmd’ using rmarkdown
Quitting from reanalysing-public-data.Rmd:153-164 [unnamed-chunk-10]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to find an inherited method for function 'pathways' for signature 'x = "NULL"'
---
Backtrace:
▆
1. └─ReactomeGSA::pathways(res)
2. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'reanalysing-public-data.Rmd' failed with diagnostics:
unable to find an inherited method for function 'pathways' for signature 'x = "NULL"'
--- failed 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:
‘reanalysing-public-data.Rmd’
Error: Vignette re-building failed.
Execution halted