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This page was generated on 2026-03-09 11:34 -0400 (Mon, 09 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" 4508
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2026-02-28 r89501) -- "Unsuffered Consequences" 3381
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 1585/2360HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pgxRpi 1.7.0  (landing page)
Hangjia Zhao
Snapshot Date: 2026-03-08 13:40 -0400 (Sun, 08 Mar 2026)
git_url: https://git.bioconductor.org/packages/pgxRpi
git_branch: devel
git_last_commit: 8de3d7a
git_last_commit_date: 2025-10-29 11:26:40 -0400 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped
See other builds for pgxRpi in R Universe.

BUILD results for pgxRpi on kjohnson3

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: 1.7.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data pgxRpi
StartedAt: 2026-03-08 16:05:39 -0400 (Sun, 08 Mar 2026)
EndedAt: 2026-03-08 16:08:54 -0400 (Sun, 08 Mar 2026)
EllapsedTime: 194.3 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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


* 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
2026-03-08 16:06:35.366 R[80883:117844172] XType: Using static font registry.
The magick package is required to crop "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpasjVaO/Rbuild13b2c55c20b02/pgxRpi/vignettes/Introduction_1_load_metadata_files/figure-html/unnamed-chunk-13-1.png" but not available.
--- 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
The magick package is required to crop "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpasjVaO/Rbuild13b2c55c20b02/pgxRpi/vignettes/Introduction_4_process_pgxseg_files/figure-html/unnamed-chunk-6-1.png" but not available.
The magick package is required to crop "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpasjVaO/Rbuild13b2c55c20b02/pgxRpi/vignettes/Introduction_4_process_pgxseg_files/figure-html/unnamed-chunk-7-1.png" but not available.
The magick package is required to crop "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpasjVaO/Rbuild13b2c55c20b02/pgxRpi/vignettes/Introduction_4_process_pgxseg_files/figure-html/unnamed-chunk-8-1.png" but not available.
The magick package is required to crop "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpasjVaO/Rbuild13b2c55c20b02/pgxRpi/vignettes/Introduction_4_process_pgxseg_files/figure-html/unnamed-chunk-13-1.png" but not available.
The magick package is required to crop "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpasjVaO/Rbuild13b2c55c20b02/pgxRpi/vignettes/Introduction_4_process_pgxseg_files/figure-html/unnamed-chunk-14-1.png" but not available.
The magick package is required to crop "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpasjVaO/Rbuild13b2c55c20b02/pgxRpi/vignettes/Introduction_4_process_pgxseg_files/figure-html/unnamed-chunk-15-1.png" but not available.
The magick package is required to crop "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpasjVaO/Rbuild13b2c55c20b02/pgxRpi/vignettes/Introduction_4_process_pgxseg_files/figure-html/unnamed-chunk-16-1.png" but not available.
--- 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