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This page was generated on 2025-10-23 12:05 -0400 (Thu, 23 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4894
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4684
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4629
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4642
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 1577/2355HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pgxRpi 1.5.5  (landing page)
Hangjia Zhao
Snapshot Date: 2025-10-22 13:45 -0400 (Wed, 22 Oct 2025)
git_url: https://git.bioconductor.org/packages/pgxRpi
git_branch: devel
git_last_commit: 1f5717c
git_last_commit_date: 2025-08-17 00:38:58 -0400 (Sun, 17 Aug 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
lconwaymacOS 12.7.6 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

BUILD results for pgxRpi on lconway

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.

raw results


Summary

Package: pgxRpi
Version: 1.5.5
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data pgxRpi
StartedAt: 2025-10-22 18:09:03 -0400 (Wed, 22 Oct 2025)
EndedAt: 2025-10-22 18:18:16 -0400 (Wed, 22 Oct 2025)
EllapsedTime: 552.7 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### 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

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: 522)
---
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: 522)
--- failed re-building ‘Introduction_3_access_cnv_frequency.Rmd’

--- re-building ‘Introduction_4_process_pgxseg.Rmd’ using rmarkdown
2025-10-22 18:16:38.721 R[90593:613377934] XType: com.apple.fonts is not accessible.
2025-10-22 18:16:38.721 R[90593:613377934] XType: XTFontStaticRegistry is enabled.
--- 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