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nanxstats / protr

🧬 Toolkit for generating various numerical features of protein sequences
https://nanx.me/protr/
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error when running parGOSim() #24

Closed deniseduma closed 5 years ago

deniseduma commented 5 years ago

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

nanxstats commented 5 years ago

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

deniseduma commented 5 years ago

Thank you!!