Bug in newest R versions

[saezlab]

Bug in newest R versions

[cgeyskens]

Hi,

I was also working with some data and got the same error, see below:

all_interactions_mouse <- import_all_interactions(organism = 10090)
Error in mutate():
ℹ In argument: n_references = ifelse(...).
Caused by error in map():
ℹ In index: 1.
Caused by error in .f():
! Arguments in ... must be passed by position, not name.
✖ Problematic argument:
• outsep = outsep
Run rlang::last_error() to see where the error occurred.

[deeenes]

This is an interesting regression that appeared probably in December, with the combination of the latest purrr and tidyselect or rlang. I think raising this error for purrr::map is inappropriate, I don't understand the motivation, though almost sure it is intentional design decision. Thanks for reporting, and I am sorry that it failed in your course!

[WeiqiangChen]

I have installed OmnipathR 3.7.2. But still get following Purrr error. I have purrr 1.0.1. R 4.2.2

go_data <- go_annot_download(organism = "human", aspects = c("C", "F", "P"), slim = TRUE)
[2023-03-16 08:47:51] [SUCCESS] [OmnipathR] Building GO slim (organism: human; aspects: C, F, P; slim: generic). This will take 20-40 min at the first time, and will be saved in the cache for later use.
[2023-03-16 08:47:52] [SUCCESS] [OmnipathR] Gene Ontology (current.geneontology.org): loaded 630196 records from cache
Error in mutate():
ℹ In argument: ancestors = map(...).
Caused by error in map():
ℹ In index: 1.
Caused by error in simple_vs_index():
! Unknown vertex selected
Run rlang::last_trace() to see where the error occurred.

[deeenes]

Hi @WeiqiangChen, This is a completely different error, in a very specific part of the package, which builds a Gene Ontology graph structure. It's great that you've found it, and I will take a look soon.