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I am trying to use GOSemSim, code which run previously does not run anymore. It does not seem to fin the function godata, but why? Minimal reproducible example:
> library("GOSemSim")
> library("org.Sc.sgd.db")
> library("GO.db")
> yeastGO <- godata('org.Sc.sgd.db', keytype = "ENSEMBL", ont="BP", computeIC = TRUE)
Error: could not find function "godata"
I am using R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree".
It looks like you are using an outdated version of R and therefore also outdated Bioconductor packages. I might suggest updating the version of R to 3.5.0 and Bioconductor to 3.7, as I can run your minimal example with no errors. In the future it will also help to include your
sessionInfo()so we know your system os and versions of packages.Thank you, yes, I could now make it work with R 3.4!
(Could not install R 3.5 because this led to some package confusion loop).
R version 3.2.3 is what comes with Ubuntu 16.04 LTS so I think a great number of people are using it. I am not contradicting you, just saying that although 3.2.3 might be outdated, it is still very widespread I think.