EHDEN / CdmInspection

R Package to support quality control inspection of an OMOP-CDM instance
Apache License 2.0
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Error: Can't rename columns that don't exist #70

Closed lhjohn closed 2 years ago

lhjohn commented 2 years ago

I see the following error when calling generateResultsDocument()

Complete CdmInspection took  109.50  minutes
The cdm inspection results have been exported to: [...]
All cdm inspection results are bundled for sharing at:  [...]/Results_Inspection_.zip
Next step: generate and complete the inspection report and share this together with the zip file.
CdmInspection run took 6570.08 secs
Error: Can't rename columns that don't exist.
✖ Column `X_CALENDAR_MONTH` doesn't exist.
Backtrace:
     █
  1. ├─CdmInspection::generateResultsDocument(...)
  2. │ └─CdmInspection:::recordsCountPlot(as.data.frame(results$dataTablesResults$totalRecords$result)) [...]/R/ResultsDocumentGeneration.R:119:4
  3. │   └─`%>%`(...) /data/home/hjohn/git/CdmInspection/R/Helper.R:127:2
  4. ├─dplyr::mutate(., Date = lubridate::parse_date_time(Date, "ym"))
  5. ├─dplyr::rename(...)
  6. └─dplyr:::rename.data.frame(...)
  7.   └─tidyselect::eval_rename(expr(c(...)), .data)
  8.     └─tidyselect:::rename_impl(...)
  9.       └─tidyselect:::eval_select_impl(...)
 10.         ├─tidyselect:::with_subscript_errors(...)
 11.         │ ├─base::tryCatch(...)
 12.         │ │ └─base:::tryCatchList(expr, classes, parentenv, handlers)
 13.         │ │   └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 14.         │ │     └─base:::doTryCatch(return(expr), name, parentenv, handler)
 15.         │ └─tidyselect:::instrument_base_errors(expr)
 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:::as_indices_sel_impl(...)
 23.                     └─tidyselect:::as_indices_impl(x, vars, strict = strict)
 24.                       └─tidyselect:::chr_as_locations(x, vars)
 25.                         └─vctrs::vec_as_location(x, n = length(vars), names = vars)
 26.                           └─(function () ...
 27.                             └─vctrs:::stop_subscript_oob(...)
 28.                               └─vctrs:::stop_subscript(...)
lhjohn commented 2 years ago

The problem was that I did not have read permission on the Achilles results schema.