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This page was generated on 2024-05-20 11:32:17 -0400 (Mon, 20 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4381
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 1498/2233HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pgxRpi 1.1.2  (landing page)
Hangjia Zhao
Snapshot Date: 2024-05-18 09:00:01 -0400 (Sat, 18 May 2024)
git_url: https://git.bioconductor.org/packages/pgxRpi
git_branch: devel
git_last_commit: 833ff02
git_last_commit_date: 2024-05-03 12:57:02 -0400 (Fri, 03 May 2024)
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped

BUILD results for pgxRpi on kjohnson1


To the developers/maintainers of the pgxRpi package:
- 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: 1.1.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data pgxRpi
StartedAt: 2024-05-18 23:27:36 -0400 (Sat, 18 May 2024)
EndedAt: 2024-05-18 23:30:34 -0400 (Sat, 18 May 2024)
EllapsedTime: 177.2 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### 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_loadmetadata.Rmd’ using rmarkdown

Quitting from lines  at lines 66-73 [unnamed-chunk-2] (Introduction_1_loadmetadata.Rmd)
Error: processing vignette 'Introduction_1_loadmetadata.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building ‘Introduction_1_loadmetadata.Rmd’

--- re-building ‘Introduction_2_loadvariants.Rmd’ using rmarkdown

Quitting from lines  at lines 68-69 [unnamed-chunk-2] (Introduction_2_loadvariants.Rmd)
Error: processing vignette 'Introduction_2_loadvariants.Rmd' failed with diagnostics:
cannot open the connection to 'http://progenetix.org/services/samplematrix/?datasetIds=progenetix&filters=NCIT:C2948&limit=0'
--- failed re-building ‘Introduction_2_loadvariants.Rmd’

--- re-building ‘Introduction_3_loadfrequency.Rmd’ using rmarkdown

Quitting from lines  at lines 59-63 [unnamed-chunk-2] (Introduction_3_loadfrequency.Rmd)
Error: processing vignette 'Introduction_3_loadfrequency.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building ‘Introduction_3_loadfrequency.Rmd’

--- re-building ‘Introduction_4_process_pgxseg.Rmd’ using rmarkdown
2024-05-18 23:29:26.040 R[7328:61765479] XType: Using static font registry.
--- finished re-building ‘Introduction_4_process_pgxseg.Rmd’

SUMMARY: processing the following files failed:
  ‘Introduction_1_loadmetadata.Rmd’ ‘Introduction_2_loadvariants.Rmd’
  ‘Introduction_3_loadfrequency.Rmd’

Error: Vignette re-building failed.
Execution halted