Issues with clusterProfiler and WikiPathways

Question

[miccoli.andrea89]

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

Answer 1

[cfos4698]

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"