createKEGGdb
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Pay attention: [https://rest.kegg.jp/list/all] this api dose not work now!
Dear authors,
please pay attention to this issue:
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$> clusterProfiler:::kegg_list
function (db, species = NULL)
{
if (db == "pathway") {
url <- paste("https://rest.kegg.jp/list", db, species,
sep = "/")
}
else {
url <- paste("https://rest.kegg.jp/list", db, sep = "/")
}
kegg_rest(url)
}
<bytecode: 0x560062430ac8>
<environment: namespace:clusterProfiler>
I have already installed the newest createKEGGdb and clusterProfiler
The API was changed, new: https://www.kegg.jp/kegg/rest/keggapi.html that is right: r$> 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