Chengcheng Ma
| Snapshot Date: 2025-12-04 13:45 -0500 (Thu, 04 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/RGSEA |
| git_branch: RELEASE_3_22 |
| git_last_commit: b670bf4 |
| git_last_commit_date: 2025-10-29 10:20:00 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-08 12:02 -0500 (Mon, 08 Dec 2025).
| 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" | 4879 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4668 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| 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 1786/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RGSEA 1.44.0 (landing page) Chengcheng Ma
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the RGSEA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RGSEA.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: RGSEA |
| Version: 1.44.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data RGSEA |
| StartedAt: 2025-12-05 04:55:53 -0000 (Fri, 05 Dec 2025) |
| EndedAt: 2025-12-05 05:08:10 -0000 (Fri, 05 Dec 2025) |
| EllapsedTime: 737.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data RGSEA
###
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* checking for file ‘RGSEA/DESCRIPTION’ ... OK
* preparing ‘RGSEA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘RGSEA.Rnw’ using knitr
Quitting from RGSEA.Rnw:83-87 [RGSEA-DOWNLOAD]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 'colnames': error in evaluating the argument 'object' in selecting a method for function 'Table': Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [ftp.ncbi.nlm.nih.gov]:
Operation too slow. Less than 1 bytes/sec transferred the last 600 seconds
---
Backtrace:
x
1. +-GEOquery::GDS2eSet(getGEO("GDS4102"))
2. | +-base::grep("GSM", colnames(Table(GDS)))
3. | | \-base::is.factor(x)
4. | +-BiocGenerics::colnames(Table(GDS))
5. | \-GEOquery::Table(GDS)
6. +-GEOquery::getGEO("GDS4102")
7. | \-GEOquery::getGEOfile(GEO, destdir = destdir, AnnotGPL = AnnotGPL)
8. | \-GEOquery:::downloadFile(myurl, destfile, mode)
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::message(e)
14. | +-base::withRestarts(...)
15. | | \-base (local) withOneRestart(expr, restarts[[1L]])
16. | | \-base (local) doWithOneRestart(return(expr), restart)
17. | \-base::signalCondition(cond)
18. +-base (local) `<fn>`(`<httr2_fl>`)
19. \-base::.handleSimpleError(...)
20. \-base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'RGSEA.Rnw' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'colnames': error in evaluating the argument 'object' in selecting a method for function 'Table': Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [ftp.ncbi.nlm.nih.gov]:
Operation too slow. Less than 1 bytes/sec transferred the last 600 seconds
--- failed re-building ‘RGSEA.Rnw’
SUMMARY: processing the following file failed:
‘RGSEA.Rnw’
Error: Vignette re-building failed.
Execution halted