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Describe the bug Calling the function getDrugIngredientCodes with the argument "name" specified returns the following error
Error in `dplyr::filter()`: ℹ In argument: `tidyWords(.data$concept_name) %in% tidyWords(.env$name)`. Caused by error in `sub()`: ! input string 32262 is invalid UTF-8 The error comes from lines ingredientConcepts <- cdm$concept %>% dplyr::filter(.data$standard_concept == "S") %>% dplyr::filter(.data$concept_class_id == "Ingredient") %>% dplyr::select("concept_id", "concept_name", "concept_code") %>% dplyr::collect() if (!is.null(name)) { ingredientConcepts <- ingredientConcepts %>% dplyr::filter(tidyWords(.data$concept_name) %in% tidyWords(.env$name)) }
The error is caused by the standard RxNorm Extension drug ingredient concept 1253507 "[ ¹⁸ F]AlF-NOTA-FAPI-04" present in our concept-table.
To Reproduce getDrugIngredientCodes(cdm = cdm, name = "Adalimumab")
getDrugIngredientCodes(cdm = cdm, name = "Adalimumab")
The text was updated successfully, but these errors were encountered:
To be more exact, this seems to be an issue with the helper function tidyWords:
> tidyWords("[ ¹⁸ F]AlF-NOTA-FAPI-04") Error in sub(re, "", x, perl = TRUE) : input string 1 is invalid UTF-8 In addition: Warning message: In sub(re, "", x, perl = TRUE) : unable to translate '[ ¹â<81>¸ F]AlF-NOTA-FAPI-04' to UTF-8
More specifically the following lines:
Encoding(words) <- "latin1" # some generic formatting workingWords <- trimws(words)
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Describe the bug
Calling the function getDrugIngredientCodes with the argument "name" specified returns the following error
The error is caused by the standard RxNorm Extension drug ingredient concept 1253507 "[ ¹⁸ F]AlF-NOTA-FAPI-04" present in our concept-table.
To Reproduce
getDrugIngredientCodes(cdm = cdm, name = "Adalimumab")
The text was updated successfully, but these errors were encountered: