Hello,
are there any known issues with WikiPathways-related functions in clusterProfiler v. 4.0.5? I'm not able to retrieve even the list of supported organism using the get_wp_organisms() because I'm returned with: "Error in file(con, "r") : cannot open the connection".
I had experienced similar issues with the gseKEGG function, which I solved by setting R.utils::setOption("clusterProfiler.download.method","auto"). This doesn't seem to work for WikiPathways.
Thanks for your support.
AM
•
written
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miccoli.andrea89 •
1 answer
As far as I can tell, the 'connection' part isn't referring to an internet connection for downloading data, so the download method strategy wouldn't fix it. Instead, "Error in file(con, "r") : cannot open the connection" is likely referring to the fact that the function/R is trying to access a directory that doesn't exist or it doesn't have permission to access.
Make sure R has the correct permission. Also perhaps try upgrading your version of clusterProfiler. For example, I have the following:
packageVersion('clusterProfiler')
[1] ‘4.2.2’
clusterProfiler::get_wp_organisms()
[1] "Sus scrofa" "Solanum lycopersicum" "Saccharomyces cerevisiae"
[4] "Rattus norvegicus" "Populus trichocarpa" "Pan troglodytes"
[7] "Mus musculus" "Homo sapiens" "Gallus gallus"
[10] "Equus caballus" "Drosophila melanogaster" "Danio rerio"
[13] "Canis familiaris" "Caenorhabditis elegans" "Bos taurus"
[16] "Arabidopsis thaliana"
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