BioinformaticsFMRP / TCGAbiolinks

TCGAbiolinks
http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html
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Error for GDCprepare - please help #474

Closed kennyyeo13 closed 2 years ago

kennyyeo13 commented 2 years ago

dataPrep <- GDCprepare(query_READ_transcript) |=============================================================================================|100% Completed after 2 s Starting to add information to samples => Add clinical information to samples Error: Input must be a vector, not a <dtplyr_step_subset/dtplyr_step> object. Run rlang::last_error() to see where the error occurred.

rlang::last_error() <error/vctrs_error_scalar_type> Input must be a vector, not a <dtplyr_step_subset/dtplyr_step> object. Backtrace:

  1. TCGAbiolinks::GDCprepare(query_READ_transcript)
  2. vctrs:::stop_scalar_type(...)
  3. vctrs:::stop_vctrs(msg, "vctrs_error_scalar_type", actual = x) Run rlang::last_trace() to see the full context. rlang::last_trace() <error/vctrs_error_scalar_type> Input must be a vector, not a <dtplyr_step_subset/dtplyr_step> object. Backtrace: █
  4. ├─TCGAbiolinks::GDCprepare(query_READ_transcript)
  5. │ └─TCGAbiolinks:::readTranscriptomeProfiling(...)
  6. │ └─TCGAbiolinks:::makeSEfromTranscriptomeProfiling(df, cases, workflow.type)
  7. │ └─TCGAbiolinks::colDataPrepare(cases)
  8. │ └─TCGAbiolinks:::splitAPICall(...)
  9. │ └─base::tryCatch(...)
  10. │ └─base:::tryCatchList(expr, classes, parentenv, handlers)
  11. │ └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
  12. │ └─value[3L]
  13. │ └─TCGAbiolinks:::FUN(items[start:end])
  14. │ └─dplyr::bind_cols(df, exposures)
  15. │ └─vctrs::vec_cbind(!!!dots, .name_repair = .name_repair)
  16. └─vctrs:::stop_scalar_type(...)
  17. └─vctrs:::stop_vctrs(msg, "vctrs_error_scalar_type", actual = x)
tiagochst commented 2 years ago

Please, could you provide the code for query_READ_transcript ?