error when running parGOSim()

[Denise Duma]

Hi,

I'm trying to use the function parGOSim(). However, when running the example in the vignette on my Linux machine

genelist = list(c("150", "151", "152", "1814", "1815", "1816"))
gsimmat2 = parGOSim(genelist, type = "gene")
print(gsimmat2)

I get the following error:

Error in GOSemSim::mgeneSim(unlist(golist), ont = ont, organism = organism, :
unused arguments (ont = ont, organism = organism)

It seems that somehow the call to a function in the GOSemSim package goes wrong.

Could you please fix this problem in protr so I can use parGOSim()?

Thank you,
Denise

[Nan Xiao]

Hi @deniseduma -thanks for the feedback! It looks like the twoGOSim and parGOSim function and code examples are both not working due to some upstream API changes. I've just updated them all and submitted a new version to CRAN (v1.6-0). Before the new version is available on CRAN, you can try the GitHub version with devtools::install_github("road2stat/protr"). Hope this helps! -Nan

[Denise Duma]

Thank you!!