| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-18 11:57 -0500 (Wed, 18 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4890 |
| 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 994/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| hipathia 3.10.0 (landing page) Marta R. Hidalgo
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| See other builds for hipathia in R Universe. | ||||||||||||||
|
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: 3.10.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 hipathia |
| StartedAt: 2026-02-16 18:14:51 -0500 (Mon, 16 Feb 2026) |
| EndedAt: 2026-02-16 18:15:52 -0500 (Mon, 16 Feb 2026) |
| EllapsedTime: 61.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 hipathia
###
##############################################################################
##############################################################################
* 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
Quitting from hipathia-vignette.Rmd:239-242 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 'query': failed to connect
reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
Consider rerunning with 'localHub=TRUE'
---
Backtrace:
x
1. +-hipathia::translate_data(brca_data, "hsa")
2. | \-hipathia:::translate_matrix(mat, species)
3. | \-hipathia:::load_xref(species)
4. | \-hipathia:::hub()
5. | +-AnnotationHub::query(AnnotationHub(), "hpAnnot")
6. | \-AnnotationHub::AnnotationHub()
7. | \-AnnotationHub::.Hub(...)
8. | \-base::tryCatch(...)
9. | \-base (local) tryCatchList(expr, classes, parentenv, handlers)
10. | \-base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
11. | \-value[[3L]](cond)
12. | \-base::stop(...)
13. \-base::.handleSimpleError(...)
14. \-base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'hipathia-vignette.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'query': failed to connect
reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
Consider rerunning with 'localHub=TRUE'
--- failed re-building ‘hipathia-vignette.Rmd’
SUMMARY: processing the following file failed:
‘hipathia-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted