BinneR crashes when only one scan is selected

[elliotfontaine]

When only one scan is selected by detectInfusionScans (which can happen if thres value is too high), BinneR will crash during binneRlyse.

[elliotfontaine]

Different approaches:

• Automatically rerun the mzml_to_features task with a lower threshold value, until at least n scans are selected.
• Do it inside the binner_cli script.
• Change the interface of binner_cli so that instead of a %max(TIC) thres (the one exposed by BinneR), the workflow user can give a target fraction of the total number of scans.

The last one make sense if you know for exemple that the sample is injected in the spectrometer in 30s, and the spectrometer run last for 5 minutes -> 10% of nb of scans.

[elliotfontaine]

binneR v2.6.4 Thu Apr 25 14:11:51 2024
________________________________________________________________________________
Scans: 18:18 
________________________________________________________________________________

Reading raw data
Gathering bins
Removing single scan events
Averaging intensities across scans
Calculating bin metrics
Error in `all_of()`:
! Can't subset columns that don't exist.
✖ Columns `idx`, `fileName`, `class`, `polarity`, and `bin` don't exist.
Backtrace:
     ▆
  1. ├─binneR::binneRlyse(file, info, parameters)
  2. │ └─x %>% spectralBinning(verbose = verbose)
  3. ├─binneR:::spectralBinning(., verbose = verbose)
  4. ├─binneR:::spectralBinning(., verbose = verbose)
  5. │ └─binneR:::calcBinMeasures(pks, cls)
  6. │   └─... %>% ...
  7. ├─dplyr::summarise(...)
  8. ├─dplyr::group_by_at(...)
  9. │ └─dplyr:::manip_at(...)
 10. │   └─dplyr:::tbl_at_syms(...)
 11. │     └─dplyr:::tbl_at_vars(tbl, vars, .include_group_vars = .include_group_vars, error_call = error_call)
 12. │       └─tidyselect::vars_select(tibble_vars, !!!vars)
 13. │         └─tidyselect:::eval_select_impl(...)
 14. │           ├─tidyselect:::with_subscript_errors(...)
 15. │           │ └─rlang::try_fetch(...)
 16. │           │   └─base::withCallingHandlers(...)
 17. │           └─tidyselect:::vars_select_eval(...)
 18. │             └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
 19. │               └─tidyselect:::eval_c(expr, data_mask, context_mask)
 20. │                 └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
 21. │                   └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
 22. │                     └─tidyselect:::eval_context(expr, context_mask, call = error_call)
 23. │                       ├─tidyselect:::with_chained_errors(...)
 24. │                       │ └─rlang::try_fetch(...)
 25. │                       │   ├─base::tryCatch(...)
 26. │                       │   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 27. │                       │   │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 28. │                       │   │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 29. │                       │   └─base::withCallingHandlers(...)
 30. │                       └─rlang::eval_tidy(as_quosure(expr, env), context_mask)
 31. ├─tidyselect::all_of(c("idx", "fileName", cls, "polarity", "bin"))
 32. │ └─tidyselect:::as_indices_impl(x, vars = vars, strict = TRUE)
 33. │   └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
 34. │     └─vctrs::vec_as_location(...)
 35. └─vctrs (local) `<fn>`()
 36.   └─vctrs:::stop_subscript_oob(...)
 37.     └─vctrs:::stop_subscript(...)
 38.       └─rlang::abort(...)
Message d'avis :
Dans fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (1.0.11)
than is installed on your system (1.0.12). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at 
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
Exécution arrêtée
2024-04-25T14:11:53+02:00 CRITICAL - failed/ERR