YuLab-SMU / createKEGGdb

Create KEGG.db Package
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Pay attention: [https://rest.kegg.jp/list/all] this api dose not work now! #14

Open ZWanBing opened 1 year ago

ZWanBing commented 1 year ago

Dear authors, please pay attention to this issue: image

r$> clusterProfiler:::kegg_list("all")
Reading KEGG annotation online: "https://rest.kegg.jp/list/all"...
fail to download KEGG data...
NULL
Warning message:
In download.file(url, method = method, ...) :
  cannot open URL 'https://rest.kegg.jp/list/all': HTTP status was '400 Bad Request'

r$> clusterProfiler:::kegg_list()
Error in clusterProfiler:::kegg_list() : 
  argument "db" is missing, with no default

r$> clusterProfiler:::kegg_list
function (db, species = NULL) 
{
    if (db == "pathway") {
        url <- paste("https://rest.kegg.jp/list", db, species, 
            sep = "/")
    }
    else {
        url <- paste("https://rest.kegg.jp/list", db, sep = "/")
    }
    kegg_rest(url)
}
<bytecode: 0x560062430ac8>
<environment: namespace:clusterProfiler>

I have already installed the newest createKEGGdb and clusterProfiler

SSSYDYSSS commented 11 months ago

The API was changed, new: https://www.kegg.jp/kegg/rest/keggapi.html that is right: r$> clusterProfiler:::kegg_list function (db, species = NULL) { if (db == "pathway") { url <- paste("https://rest.kegg.jp/list", db, species, sep = "/") } else { url <- paste("https://rest.kegg.jp/list", db, sep = "/") } kegg_rest(url) } eg: https://rest.kegg.jp/list/pathway/mmu