| Back to Build/check report for BioC 3.23: simplified long |
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This page was generated on 2025-10-31 08:34 -0400 (Fri, 31 Oct 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" | 4428 |
| 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 980/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| hipathia 3.11.0 (landing page) Marta R. Hidalgo
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
|
To the developers/maintainers of the hipathia package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hipathia.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: hipathia |
| Version: 3.11.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data hipathia |
| StartedAt: 2025-10-30 17:29:33 -0400 (Thu, 30 Oct 2025) |
| EndedAt: 2025-10-30 17:31:12 -0400 (Thu, 30 Oct 2025) |
| EllapsedTime: 99.1 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 hipathia
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* checking for file ‘hipathia/DESCRIPTION’ ... OK
* preparing ‘hipathia’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘hipathia-vignette.Rmd’ using rmarkdown
Quitting from hipathia-vignette.Rmd:326-328 [unnamed-chunk-14]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! failed to load resource
name: AH69111
title: meta_graph_info_hsa_v2.rda
reason: At vendor/cigraph/src/graph/iterators.c:831 : Cannot create iterator, invalid vertex ID. Invalid vertex ID
---
Backtrace:
x
1. \-hipathia::load_pathways(species = "hsa")
2. \-hipathia:::load_mgi(species)
3. +-base::suppressMessages(hp[[names(hp)[hp$title == file]]])
4. | \-base::withCallingHandlers(...)
5. +-hp[[names(hp)[hp$title == file]]]
6. \-hp[[names(hp)[hp$title == file]]]
7. \-AnnotationHub (local) .local(x, i, j = j, ...)
8. \-AnnotationHub:::.Hub_get1(...)
9. \-base::tryCatch(...)
10. \-base (local) tryCatchList(expr, classes, parentenv, handlers)
11. \-base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
12. \-value[[3L]](cond)
13. \-base::tryCatch(...)
14. \-base (local) tryCatchList(expr, classes, parentenv, handlers)
15. \-base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
16. \-value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'hipathia-vignette.Rmd' failed with diagnostics:
failed to load resource
name: AH69111
title: meta_graph_info_hsa_v2.rda
reason: At vendor/cigraph/src/graph/iterators.c:831 : Cannot create iterator, invalid vertex ID. Invalid vertex ID
--- failed re-building ‘hipathia-vignette.Rmd’
SUMMARY: processing the following file failed:
‘hipathia-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted