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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SingscoreAMLMutations
###
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* checking for file ‘SingscoreAMLMutations/DESCRIPTION’ ... OK
* preparing ‘SingscoreAMLMutations’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘workflow_transcriptional_mut_sig.Rmd’ using rmarkdown

Quitting from workflow_transcriptional_mut_sig.Rmd:183-186 [gdc_download]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `GDCdownload.aux()`:
! There was an error in the download process (we might had a connection problem with GDC server).
Please run this function it again.
Try using method = `client` or setting files.per.chunk to a small number.
---
Backtrace:
    ▆
 1. └─TCGAbiolinks::GDCdownload(query_rna, directory = datapath)
 2.   └─base::tryCatch(...)
 3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5.         └─value[[3L]](cond)
 6.           └─TCGAbiolinks:::GDCdownload.by.chunk(...)
 7.             └─TCGAbiolinks:::GDCdownload.aux(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'workflow_transcriptional_mut_sig.Rmd' failed with diagnostics:
There was an error in the download process (we might had a connection problem with GDC server).
Please run this function it again.
Try using method = `client` or setting files.per.chunk to a small number.
--- failed re-building ‘workflow_transcriptional_mut_sig.Rmd’

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

Quitting from workflow_transcriptional_mut_sig_chinese.Rmd:180-183 [gdc_download]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `GDCdownload.aux()`:
! There was an error in the download process (we might had a connection problem with GDC server).
Please run this function it again.
Try using method = `client` or setting files.per.chunk to a small number.
---
Backtrace:
    ▆
 1. └─TCGAbiolinks::GDCdownload(query_rna, directory = datapath)
 2.   └─base::tryCatch(...)
 3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5.         └─value[[3L]](cond)
 6.           └─TCGAbiolinks:::GDCdownload.by.chunk(...)
 7.             └─TCGAbiolinks:::GDCdownload.aux(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'workflow_transcriptional_mut_sig_chinese.Rmd' failed with diagnostics:
There was an error in the download process (we might had a connection problem with GDC server).
Please run this function it again.
Try using method = `client` or setting files.per.chunk to a small number.
--- failed re-building ‘workflow_transcriptional_mut_sig_chinese.Rmd’

SUMMARY: processing the following files failed:
  ‘workflow_transcriptional_mut_sig.Rmd’
  ‘workflow_transcriptional_mut_sig_chinese.Rmd’

Error: Vignette re-building failed.
Execution halted