| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-15 12:06 -0400 (Fri, 15 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4554 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
| 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 975/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| hipathia 3.9.0 (landing page) Marta R. Hidalgo
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 3.9.0 |
| Command: chmod a+r hipathia -R && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data hipathia |
| StartedAt: 2025-08-14 20:48:22 -0400 (Thu, 14 Aug 2025) |
| EndedAt: 2025-08-14 20:53:54 -0400 (Thu, 14 Aug 2025) |
| EllapsedTime: 332.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### chmod a+r hipathia -R && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe 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 to build vignettes
* creating vignettes ... ERROR
--- re-building 'hipathia-vignette.Rmd' using rmarkdown
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
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:828 : 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:828 : 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