When using the CalculateOraScore function within the pathwayAnalysis feature of MetaboAnalystR, the following error occurred:
Error in curl::curl_fetch_memory(url, handle = handle) :
Timeout was reached: [www.xialab.ca] Failed to connect to www.xialab.ca port 443 after 10014 ms: Timeout was reached
Tracing back to the source code, the issue arises from the following snippet:
request ← httr::POST( url = call, body = list(rds = upload_file(file.send, “application/octet-stream”)), encode = “multipart” )
Here, the call variable points to the URL: “https://www.xialab.ca/api/pathwayora”
However, using smpdb does not cause any issues. Moreover, when running KEGG on the official website, results are produced without error. This phenomenon raises the question of whether the file location corresponding to call on the server side has changed.
Below is the exact code used to run KEGG:
mSet ← InitDataObjects(“conc”, “pathora”, FALSE)
cmpd.vec ← c(“HMDB0000564”, “HMDB0007983”, “HMDB0008048”, “HMDB0005360”, “HMDB0005379”, “HMDB0011707”, “HMDB0005382”, “HMDB0005384”, “HMDB0005453”, “HMDB0005455”, “HMDB0005461”, “HMDB0005474”, “HMDB0010382”, “HMDB0010383”, “HMDB0010384”, “HMDB0002815”, “HMDB0010386”, “HMDB0010395”, “HMDB0010404”, “HMDB0007969”, “HMDB0007972”, “HMDB0007973”)
mSet ← Setup.MapData(mSet, cmpd.vec)
mSet ← CrossReferencing(mSet, “hmdb”)
mSet ← CreateMappingResultTable(mSet)
mSet ← SetKEGG.PathLib(mSet, “mmu”, “current”)
mSet ← SetMetabolomeFilter(mSet, F)
mSet ← CalculateOraScore(mSet, “rbc”, “hyperg”)
I would like to extend my deepest gratitude to the team and everyone who provided assistance. Thank you so much for all your help!