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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 TCGAWorkflow
###
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* checking for file ‘TCGAWorkflow/DESCRIPTION’ ... OK
* preparing ‘TCGAWorkflow’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘TCGAWorkflow.Rmd’ using rmarkdown
2025-08-29 13:13:03.003 R[22999:149398650] XType: com.apple.fonts is not accessible.
2025-08-29 13:13:03.003 R[22999:149398650] XType: XTFontStaticRegistry is enabled.

Quitting from TCGAWorkflow.Rmd:1691-1713 [getTagMatrix]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `keepStandardChromosomes()`:
! could not find function "keepStandardChromosomes"
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'TCGAWorkflow.Rmd' failed with diagnostics:
could not find function "keepStandardChromosomes"
--- failed re-building ‘TCGAWorkflow.Rmd’

SUMMARY: processing the following file failed:
  ‘TCGAWorkflow.Rmd’

Error: Vignette re-building failed.
Execution halted