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###
### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/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:193-195 [gdc_prepare]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/vctrs_error_subscript_oob>
Error in `dplyr::select()`:
! Can't select columns that don't exist.
✖ Column `disease_response` doesn't exist.
---
Backtrace:
     ▆
  1. ├─TCGAbiolinks::GDCprepare(query_rna, directory = datapath)
  2. │ └─TCGAbiolinks:::readTranscriptomeProfiling(...)
  3. │   └─TCGAbiolinks:::makeSEfromTranscriptomeProfilingSTAR(...)
  4. │     └─TCGAbiolinks::colDataPrepare(cases)
  5. │       └─TCGAbiolinks:::splitAPICall(...)
  6. │         └─base::tryCatch(...)
  7. │           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  8. │             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9. │               └─value[[3L]](cond)
 10. │                 └─TCGAbiolinks (local) FUN(items[start:end])
 11. │                   └─... %>% ...
 12. ├─dplyr::rename(., days_to_last_follow_up = days_to_follow_up)
 13. ├─dplyr::rename_at(...)
 14. │ └─dplyr:::tbl_at_vars(.tbl, .vars, .include_group_vars = TRUE)
 15. │   └─dplyr::tbl_vars(tbl)
 16. │     ├─dplyr:::new_sel_vars(tbl_vars_dispatch(x), group_vars(x))
 17. │     │ └─base::structure(...)
 18. │     └─dplyr:::tbl_vars_dispatch(x)
 19. ├─dplyr::ungroup(.)
 20. ├─dplyr::filter(., dplyr::row_number() == which.max(days_to_follow_up))
 21. ├─dplyr::group_by(., submitter_id)
 22. ├─dplyr::filter(., !is.na(submitter_id), !is.na(days_to_follow_up))
 23. ├─dplyr::select(., c(submitter_id, days_to_follow_up, disease_response))
 24. └─dplyr:::select.data.frame(., c(submitter_id, days_to_follow_up, disease_response))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'workflow_transcriptional_mut_sig.Rmd' failed with diagnostics:
Can't select columns that don't exist.
✖ Column `disease_response` doesn't exist.
--- 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:190-192 [gdc_prepare]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/vctrs_error_subscript_oob>
Error in `dplyr::select()`:
! Can't select columns that don't exist.
✖ Column `disease_response` doesn't exist.
---
Backtrace:
     ▆
  1. ├─TCGAbiolinks::GDCprepare(query_rna, directory = datapath)
  2. │ └─TCGAbiolinks:::readTranscriptomeProfiling(...)
  3. │   └─TCGAbiolinks:::makeSEfromTranscriptomeProfilingSTAR(...)
  4. │     └─TCGAbiolinks::colDataPrepare(cases)
  5. │       └─TCGAbiolinks:::splitAPICall(...)
  6. │         └─base::tryCatch(...)
  7. │           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  8. │             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9. │               └─value[[3L]](cond)
 10. │                 └─TCGAbiolinks (local) FUN(items[start:end])
 11. │                   └─... %>% ...
 12. ├─dplyr::rename(., days_to_last_follow_up = days_to_follow_up)
 13. ├─dplyr::rename_at(...)
 14. │ └─dplyr:::tbl_at_vars(.tbl, .vars, .include_group_vars = TRUE)
 15. │   └─dplyr::tbl_vars(tbl)
 16. │     ├─dplyr:::new_sel_vars(tbl_vars_dispatch(x), group_vars(x))
 17. │     │ └─base::structure(...)
 18. │     └─dplyr:::tbl_vars_dispatch(x)
 19. ├─dplyr::ungroup(.)
 20. ├─dplyr::filter(., dplyr::row_number() == which.max(days_to_follow_up))
 21. ├─dplyr::group_by(., submitter_id)
 22. ├─dplyr::filter(., !is.na(submitter_id), !is.na(days_to_follow_up))
 23. ├─dplyr::select(., c(submitter_id, days_to_follow_up, disease_response))
 24. └─dplyr:::select.data.frame(., c(submitter_id, days_to_follow_up, disease_response))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'workflow_transcriptional_mut_sig_chinese.Rmd' failed with diagnostics:
Can't select columns that don't exist.
✖ Column `disease_response` doesn't exist.
--- 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