I have generated KEGG tables from a differential methylation table many times before with the following code

annoEPIC <- getAnnotation(IlluminaHumanMethylationEPICanno.ilm10b4.hg19)
diffMethTable0.05 <- read.csv("diffMethTable_site_cmp9_0.05.csv", header = TRUE)

tablep0.005 <- diffMethTable0.05[1:186,] 
sig.cpg0.005 <- as.character(tablep0.005[,2])

kegg <- gometh(sig.cpg = sig.cpg0.005, all.cpg = NULL, collection = "KEGG", array.type = "EPIC", 
               plot.bias = TRUE)

However, during this past week I have been getting this error message, which I had never gotten before:

Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open URL 'http://rest.kegg.jp/list/pathway/Hsa': HTTP status was '400 Bad Request'
sessionInfo( )

When I paste the URL that the error message mentions on Google, the page does not load. However, when I use the URL: https://rest.kegg.jp/list/pathway/hsa it does!

Has anyone else running gometh (with KEGG) been getting this message as well? How would I make gometh use the correct URL then?

I appreciate any help.

This has been fixed in both release and devel. It will take a day or two to propagate to the download servers, at which time you can update using BiocManager.