OmnipathR::collectri(organism=9606L, genesymbols=TRUE, loops=TRUE) ERROR

[LorNic97]

Hi Saezlab, Thanks for your precious work and for developing this tool! Unfortunately when I follow this command:

OmnipathR::collectri(organism=9606L, genesymbols=TRUE, loops=TRUE)

I get this error: Error in map_int(): ℹ In index: 1. Caused by error in map_int(): ℹ In index: 1. Caused by error in full_join(): ! Can't join x$ncbi_tax_id with y$ncbi_tax_id due to incompatible types. ℹ x$ncbi_tax_id is a . ℹ y$ncbi_tax_id is a .

Could you help me solve this issue? Thanks in advance!

[deeenes]

Hi @LorNic97, I have the suspicion this error is related to this one. I'd recommend you to try a similar solution: reinstall OmnipathR, and try the download with an empty cache:

library(remotes)
remotes::install_github('saezlab/OmnipathR')

In a new R session:

library(OmnipathR)

tmpcache <- tempdir()
omnipath_set_cachedir(tmpcache)
omnipath_set_console_loglevel('trace')

ci <- collectri(organism=9606L, genesymbols=TRUE, loops=TRUE)

If it works, in a new R session wipe the OmniPath cache of your user:

library(OmnipathR)

omnipath_cache_wipe()

If the error appears also with the updated package and empty cache, please share the traceback and the log:

library(OmnipathR)

ci <- collectri(organism=9606L, genesymbols=TRUE, loops=TRUE)
# error happens

traceback()

omnipath_log()
# or call omnipath_logfile() for the path

[LorNic97]

Thank you very much, it worked!