##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SingscoreAMLMutations
###
##############################################################################
##############################################################################


* 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
5d650ac1-5544-45ec-a1b6-00f98081d2b8/24125fc9-e366-49a0-a35f-004bfabd559b.rna_seq.augmented_star_gene_counts.tsv: truncated gzip input
tar: Error exit delayed from previous errors.

Quitting from workflow_transcriptional_mut_sig.Rmd:193-195 [gdc_prepare]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `GDCprepare()`:
! I couldn't find all the files from the query. Please check if the directory parameter is right or `GDCdownload` downloaded the samples.
---
Backtrace:
    ▆
 1. └─TCGAbiolinks::GDCprepare(query_rna, directory = datapath)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'workflow_transcriptional_mut_sig.Rmd' failed with diagnostics:
I couldn't find all the files from the query. Please check if the directory parameter is right or `GDCdownload` downloaded the samples.
--- failed re-building ‘workflow_transcriptional_mut_sig.Rmd’

--- re-building ‘workflow_transcriptional_mut_sig_chinese.Rmd’ using rmarkdown
6e52e950-7e51-4e12-b194-68d935cb96f0/adc73ced-098f-49a4-b86a-5715804d094f.rna_seq.augmented_star_gene_counts.tsv: truncated gzip input
tar: Error exit delayed from previous errors.

Quitting from workflow_transcriptional_mut_sig_chinese.Rmd:190-192 [gdc_prepare]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `GDCprepare()`:
! I couldn't find all the files from the query. Please check if the directory parameter is right or `GDCdownload` downloaded the samples.
---
Backtrace:
    ▆
 1. └─TCGAbiolinks::GDCprepare(query_rna, directory = datapath)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'workflow_transcriptional_mut_sig_chinese.Rmd' failed with diagnostics:
I couldn't find all the files from the query. Please check if the directory parameter is right or `GDCdownload` downloaded the samples.
--- 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