| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-18 12:04 -0400 (Sat, 18 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4632 |
| 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 1575/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pgxRpi 1.5.5 (landing page) Hangjia Zhao
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| lconway | macOS 12.7.6 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 | ||||||||||
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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: 1.5.5 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 pgxRpi |
| StartedAt: 2025-10-17 19:14:11 -0400 (Fri, 17 Oct 2025) |
| EndedAt: 2025-10-17 19:27:37 -0400 (Fri, 17 Oct 2025) |
| EllapsedTime: 805.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 pgxRpi
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* 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
Quitting from Introduction_2_query_variants.Rmd:76-79 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `if (grepl("^https?://", domain)) ...`:
! argument is of length zero
---
Backtrace:
▆
1. └─pgxRpi::pgxLoader(type = "g_variants", biosample_id = biosample_id)
2. └─pgxRpi:::pgxVariantLoader(...)
3. └─pgxRpi:::read_variant_beacon(...)
4. └─pgxRpi:::normalize_domain(domain, use_https)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Introduction_2_query_variants.Rmd' failed with diagnostics:
argument is of length zero
--- failed 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:49-54 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `pgxFreqLoader()`:
! Request failed for filter NCIT:C3058,NCIT:C3493 (status code: 422)
---
Backtrace:
▆
1. └─pgxRpi::pgxLoader(...)
2. └─pgxRpi:::pgxFreqLoader(output = output, filters = filters, domain = domain)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Introduction_3_access_cnv_frequency.Rmd' failed with diagnostics:
Request failed for filter NCIT:C3058,NCIT:C3493 (status code: 422)
--- failed re-building ‘Introduction_3_access_cnv_frequency.Rmd’
--- re-building ‘Introduction_4_process_pgxseg.Rmd’ using rmarkdown
--- finished re-building ‘Introduction_4_process_pgxseg.Rmd’
SUMMARY: processing the following files failed:
‘Introduction_1_load_metadata.Rmd’
‘Introduction_2_query_variants.Rmd’
‘Introduction_3_access_cnv_frequency.Rmd’
Error: Vignette re-building failed.
Execution halted