| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-09-25 11:41 -0400 (Thu, 25 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4827 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4581 |
| 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 1726/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Chi-Lam Poon
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the ReactomeContentService4R package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ReactomeContentService4R.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: ReactomeContentService4R |
| Version: 1.16.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ReactomeContentService4R |
| StartedAt: 2025-09-23 07:23:38 -0400 (Tue, 23 Sep 2025) |
| EndedAt: 2025-09-23 07:24:02 -0400 (Tue, 23 Sep 2025) |
| EllapsedTime: 23.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ReactomeContentService4R
###
##############################################################################
##############################################################################
* checking for file ‘ReactomeContentService4R/DESCRIPTION’ ... OK
* preparing ‘ReactomeContentService4R’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘ReactomeContentService4R.Rmd’ using rmarkdown
starting worker pid=95385 on localhost:11770 at 07:23:45.982
starting worker pid=95386 on localhost:11770 at 07:23:45.988
Loading required package: ReactomeContentService4R
Loading required package: ReactomeContentService4R
loaded ReactomeContentService4R and set parent environment
loaded ReactomeContentService4R and set parent environment
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|======================================================================| 100%Warning message:
In fun(libname, pkgname) :
Package 'ReactomeContentService4R' is deprecated and will be removed
from Bioconductor version 3.22
Warning message:
In fun(libname, pkgname) :
Package 'ReactomeContentService4R' is deprecated and will be removed
from Bioconductor version 3.22
Quitting from ReactomeContentService4R.Rmd:158-162 [ref-all]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Could not connect to server [reactome.org]:
Failed to connect to reactome.org port 443 after 78 ms: Could not connect to server
---
Backtrace:
▆
1. └─ReactomeContentService4R::map2RefEntities("TP53")
2. └─ReactomeContentService4R:::.retrieveData(url, as = "text")
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'ReactomeContentService4R.Rmd' failed with diagnostics:
Could not connect to server [reactome.org]:
Failed to connect to reactome.org port 443 after 78 ms: Could not connect to server
--- failed re-building ‘ReactomeContentService4R.Rmd’
SUMMARY: processing the following file failed:
‘ReactomeContentService4R.Rmd’
Error: Vignette re-building failed.
Execution halted