Multiple platform build/check report for BioC 3.22 - BUILD results for pgxRpi on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4821
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4599
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4553
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4539
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*

BUILD results for pgxRpi on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: pgxRpi

Version: 1.5.5

Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data pgxRpi

StartedAt: 2025-08-22 02:14:07 -0000 (Fri, 22 Aug 2025)

EndedAt: 2025-08-22 02:22:40 -0000 (Fri, 22 Aug 2025)

EllapsedTime: 512.5 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/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
--- finished re-building ‘Introduction_1_load_metadata.Rmd’

--- re-building ‘Introduction_2_query_variants.Rmd’ using rmarkdown

Quitting from Introduction_2_query_variants.Rmd:92-95 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://progenetix.org/services/pgxsegvariants/?biosampleIds=pgxbs-m84cxoly&limit=0'
---
Backtrace:
    ▆
 1. └─pgxRpi::pgxLoader(...)
 2.   └─pgxRpi:::pgxVariantLoader(...)
 3.     └─future.apply::future_lapply(...)
 4.       └─future.apply:::future_xapply(...)
 5.         └─base::tryCatch(...)
 6.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 7.             └─base (local) tryCatchOne(...)
 8.               └─value[[3L]](cond)
 9.                 └─future.apply:::onError(e, futures = fs, debug = debug)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Introduction_2_query_variants.Rmd' failed with diagnostics:
cannot open the connection to 'https://progenetix.org/services/pgxsegvariants/?biosampleIds=pgxbs-m84cxoly&limit=0'
--- failed re-building ‘Introduction_2_query_variants.Rmd’

--- re-building ‘Introduction_3_access_cnv_frequency.Rmd’ using rmarkdown
--- finished 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 file failed:
  ‘Introduction_2_query_variants.Rmd’

Error: Vignette re-building failed.
Execution halted