pathview - cannot open URL : HTTP status was '403 Forbidden'

Question

[Itamar]

Hi, I'm trying to use "pathview" on my data. after a long struggle with the package, eventually the following example code produce the error below:

> data(gse16873.d)
> pv.out <- pathview(gene.data = gse16873.d[, 1], pathway.id = "04110",
                         species = "hsa", out.suffix = "gse16873")

[1] "Downloading xml files for hsa04110, 1/1 pathways.."
[1] "Downloading png files for hsa04110, 1/1 pathways.."
Parsing ./hsa04110.xml file failed, please check the file!
Warning message:
In download.file(xml.url, xml.target, quiet = T) :
  cannot open URL 'https://www.genome.jp/kegg-bin/download?entry=hsa04110&format=kgml': HTTP status was '403 Forbidden'

checking the given URL (by the error prompt) in the browser does result in page which only says "forbidden".

My question is, is the problem on my end (see session info below) or is there currently something wrong with Kegg's web databases, API etc.

Thanks in advance.

Edit:

The problem was solved by removing the "pathview" package, then reinstalling it by:

devtools::install_github("javadnoorb/pathview")

A second problem which popped later was solved by:

rm(korg)

[Itamar]

see Edit

Answer 1

[lianchee11]

It has solved my problem perfectly, thanks for the sharing!