| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-15 12:06 -0500 (Mon, 15 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" | 4882 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 1583/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pgxRpi 1.6.0 (landing page) Hangjia Zhao
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the pgxRpi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pgxRpi.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: pgxRpi |
| Version: 1.6.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data pgxRpi |
| StartedAt: 2025-12-11 22:05:05 -0500 (Thu, 11 Dec 2025) |
| EndedAt: 2025-12-11 22:18:13 -0500 (Thu, 11 Dec 2025) |
| EllapsedTime: 788.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data pgxRpi
###
##############################################################################
##############################################################################
* checking for file ‘pgxRpi/DESCRIPTION’ ... OK
* preparing ‘pgxRpi’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Introduction_1_load_metadata.Rmd’ using rmarkdown
Quitting from Introduction_1_load_metadata.Rmd:183-188 [unnamed-chunk-13]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `if (nrow(meta.sel.df) == 0) ...`:
! argument is of length zero
---
Backtrace:
▆
1. └─pgxRpi::pgxMetaplot(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Introduction_1_load_metadata.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘Introduction_1_load_metadata.Rmd’
--- re-building ‘Introduction_2_query_variants.Rmd’ using rmarkdown
--- finished re-building ‘Introduction_2_query_variants.Rmd’
--- re-building ‘Introduction_3_access_cnv_frequency.Rmd’ using rmarkdown
Quitting from Introduction_3_access_cnv_frequency.Rmd:86-89 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Stream error in the HTTP/2 framing layer [progenetix.org]:
HTTP/2 stream 45 was not closed cleanly: INTERNAL_ERROR (err 2)
---
Backtrace:
▆
1. ├─pgxRpi::pgxLoader(...)
2. │ └─pgxRpi:::pgxFreqLoader(output = output, filters = filters, domain = domain)
3. │ └─httr::GET(encoded_url)
4. │ └─httr:::request_perform(req, hu$handle$handle)
5. │ ├─httr:::request_fetch(req$output, req$url, handle)
6. │ └─httr:::request_fetch.write_memory(req$output, req$url, handle)
7. │ └─curl::curl_fetch_memory(url, handle = handle)
8. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Introduction_3_access_cnv_frequency.Rmd' failed with diagnostics:
Stream error in the HTTP/2 framing layer [progenetix.org]:
HTTP/2 stream 45 was not closed cleanly: INTERNAL_ERROR (err 2)
--- failed re-building ‘Introduction_3_access_cnv_frequency.Rmd’
--- re-building ‘Introduction_4_process_pgxseg.Rmd’ using rmarkdown
2025-12-11 22:14:01.802 R[75044:114025713] XType: com.apple.fonts is not accessible.
2025-12-11 22:14:01.803 R[75044:114025713] XType: XTFontStaticRegistry is enabled.
--- finished re-building ‘Introduction_4_process_pgxseg.Rmd’
SUMMARY: processing the following files failed:
‘Introduction_1_load_metadata.Rmd’
‘Introduction_3_access_cnv_frequency.Rmd’
Error: Vignette re-building failed.
Execution halted