is.na > 1 error

[bmgarcia]

Hello,

I am trying to use cir_query on a list of compound "common names" to convert these to "smiles". When I run this (and most of the other webchem functions) on this list I get the following error:

cir_query(mets,"smiles","all")

Error in if (is.na(identifier)) { : the condition has length > 1

Can you provide some guidance on why I am getting this error and how to resolve it?

Thank you, Brianna Garcia

[Aariq]

Thanks for reporting this issue. Can you provide a reproducible example? (e.g., I'm not sure what mets is in this example)

[bmgarcia]

Aariq,

Hello - apologies for not attaching the example. It looks like I've resolved the issue - the initial upload of the compound name list was in the form of a tibble rather than a character vector, after changing the format the code seems to run as expected.

[Aariq]

Ah ok, thanks! We might want to add some checks that inputs are of the expected type.

[stitam]

Thanks @bmgarcia for raising this issue! @Aariq I know we use match.arg() for some argument types but that wouldn't work for queries. Wondering if something like stopifnot(is.character(query)) could solve this? What do you think?

[Aariq]

Yup, stopifnot(is.character(query)) would be sufficient. Another option is the assertthat package which produces friendlier error messages by default. It has zero dependencies so it would only introduce itself as a dependency if we wanted to use it. Might open a separate issue for it so we can keep track of which functions have this and which still need it. Not a huge priority I think, but probably good to do eventually.