| Back to Build/check report for BioC 3.23: simplified long |
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This page was generated on 2026-02-24 11:32 -0500 (Tue, 24 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4872 |
| 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 1582/2354 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pgxRpi 1.7.0 (landing page) Hangjia Zhao
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| See other builds for pgxRpi in R Universe. | ||||||||||||||
|
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: 1.7.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data pgxRpi |
| StartedAt: 2026-02-23 19:21:57 -0500 (Mon, 23 Feb 2026) |
| EndedAt: 2026-02-23 19:28:08 -0500 (Mon, 23 Feb 2026) |
| EllapsedTime: 370.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data pgxRpi
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* checking for file ‘pgxRpi/DESCRIPTION’ ... OK
* preparing ‘pgxRpi’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed 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
--- 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:135-141 [unnamed-chunk-10]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://progenetix.org/services/pgxsegvariants/?biosampleIds=pgxbs-kftvhnqz&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_3_access_cnv_frequency.Rmd' failed with diagnostics:
cannot open the connection to 'https://progenetix.org/services/pgxsegvariants/?biosampleIds=pgxbs-kftvhnqz&limit=0'
--- 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 file failed:
‘Introduction_3_access_cnv_frequency.Rmd’
Error: Vignette re-building failed.
Execution halted