get_collectri() and OmnipathR download not working

[nvokes]

get_collectri() and OmnipathR download not working

[nvokes]

Updated the packages and that worked. Thanks so much for the help!

[deeenes]

Thanks for reporting this! I forgot to add R/cookie.R to git tracking, I've just fixed it in 73dca2e

If you do again remotes::install_github('saezlab/OmnipathR'), it should work

[nvokes]

Thank you! I was able to download the latest version (3.9.7) so that took care of that!

It looks like I'm still getting the same error in calling the function though:

[2023-09-12 15:40:04] [SUCCESS] [OmnipathR] Downloaded 64958 interactions.
Error in mutate():
ℹ In argument: across(columns, ~filter_evs_lst(.x, datasets, resources, columns)).
Caused by error in across():
! Can't compute column undirected.
Caused by error in map():
ℹ In index: 1.
Caused by error in keep():
ℹ In index: 1.
Caused by error in ev$dataset:
! $ operator is invalid for atomic vectors
Run rlang::last_trace() to see where the error occurred.

[deeenes]

I can not reproduce this second issue. The reason might be an old package, best to make sure all packages, especially dplyr, purrr and the other tidyverse ones, are up to date. If the issue still persists, you can try with an empty cache:

library(OmnipathR)
omnipath_set_cachedir('tmpcache')
ci <- collectri()

unlink('tmpcache', recursive = TRUE)

If it still fails, please show me here a log trace:

library(OmnipathR)
omnipath_set_cachedir('tmpcache')
omnipath_set_console_loglevel('trace')
ci <- collectri()