| Back to Multiple platform build/check report for BioC 3.23: simplified long |
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This page was generated on 2026-01-24 11:35 -0500 (Sat, 24 Jan 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" | 4811 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4545 |
| 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 1576/2345 | 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 | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | 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: 1.7.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data pgxRpi |
| StartedAt: 2026-01-23 17:22:10 -0500 (Fri, 23 Jan 2026) |
| EndedAt: 2026-01-23 17:25:49 -0500 (Fri, 23 Jan 2026) |
| EllapsedTime: 219.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/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
2026-01-23 17:23:16.285 R[79622:825141751] XType: Using static font registry.
--- 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:147-150 [unnamed-chunk-11]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `colSums()`:
! 'x' must be an array of at least two dimensions
---
Backtrace:
▆
1. └─pgxRpi::segtoFreq(segdata, cnv_column_idx = 6, cohort_name = "c1")
2. └─base::colSums(bin.dup.data1)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Introduction_3_access_cnv_frequency.Rmd' failed with diagnostics:
'x' must be an array of at least two dimensions
--- 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