Error using cBioportalData on Genie data

[ZWael]

Hello CbioPortalData Team,

I was using the R package cBioPortalData as recommended here by genie.cbioportal.org https://docs.cbioportal.org/web-api-and-clients/#r-client but having some errors here is my code

cbio=cBioPortal(
    hostname = "genie.cbioportal.org",
    token = "xxxxx" # extracted from the https://genie.cbioportal.org/webAPI#using-data-access-tokens (download button)
)

Error in cBioPortal(hostname = "genie.cbioportal.org", token = "xx") : 
unused argument (token = "xx")

1) Does the cBioPortal function support a token argument ?

I commented the token argument but I had an other error when extracting studies

getStudies(cbio)
Error in x[["pmid"]] : object of type 'externalptr' is not subsettable

2) Does cBioPortalData works on genie.cbioportal.org

[LiNk-NY]

Hi @ZWael Thank you for submitting the issue. I've added a helper function to parse tokens from the genie service. You can try and see the updated version 2.13.6 It should work with the data at genie.cbioportal.org. If not open a new issue specific to the data

[ZWael]

@LiNk-NY Nice work, could you have a friendly update with R 4.1.1 ?

[LiNk-NY]

@ZWael Bioconductor versions are tied to R versions so unfortunately, I don't have one. If possible, update your R version. Otherwise, you could try to install from GitHub but it is not guaranteed to work.

[ZWael]

@LiNk-NY, I will try a a work around or updating my R version. Thank you for this nice package.