GDCquery_clinic not working for some TCGA projects #640
Description
The previous issue was fixed in the dev github branch, so when I do:
remotes::install_github("https://github.com/BioinformaticsFMRP/TCGAbiolinks",ref = "devel")
library(TCGAbiolinks)
clin.gbm <- GDCquery_clinic("TCGA-GBM", "clinical")
it works fine. But if I change the project I then get a different error:
clin.gbm <- GDCquery_clinic("TCGA-SARC", "clinical")
> clin.gbm <- GDCquery_clinic("TCGA-SARC", "clinical")
Warning: Unknown or uninitialised column: `submitter_id`.
Error in `dplyr::select()`:
! Can't select columns that don't exist.
✖ Column `updated_datetime` doesn't exist.
Backtrace:
1. TCGAbiolinks::GDCquery_clinic("TCGA-SARC", "clinical")
4. dplyr:::select.data.frame(., !c("updated_datetime", "state", "created_datetime"))
> rlang::last_trace(drop = FALSE)
<error/vctrs_error_subscript_oob>
Error in `dplyr::select()`:
! Can't select columns that don't exist.
✖ Column `updated_datetime` doesn't exist.
---
Backtrace:
▆
1. ├─TCGAbiolinks::GDCquery_clinic("TCGA-SARC", "clinical")
2. │ └─treatments %>% ...
3. ├─dplyr::select(., !c("updated_datetime", "state", "created_datetime"))
4. ���─dplyr:::select.data.frame(., !c("updated_datetime", "state", "created_datetime"))
5. │ └─tidyselect::eval_select(expr(c(...)), data = .data, error_call = error_call)
6. │ └─tidyselect:::eval_select_impl(...)
7. │ ├─tidyselect:::with_subscript_errors(...)
8. │ │ └─base::withCallingHandlers(...)
9. │ └─tidyselect:::vars_select_eval(...)
10. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
11. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
12. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
13. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
14. │ └─tidyselect:::eval_bang(expr, data_mask, context_mask)
15. │ └─tidyselect:::walk_data_tree(expr[[2]], data_mask, context_mask)
16. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
17. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
18. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
19. │ └─tidyselect:::as_indices_sel_impl(...)
20. │ └─tidyselect:::as_indices_impl(...)
21. │ └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
22. │ └─vctrs::vec_as_location(...)
Maybe i can fix it locally but it will come up for other people.