[Bioc-devel] KEGG REST issue

Dan Tenenbaum dtenenba at fredhutch.org
Wed Sep 23 18:46:31 CEST 2015

Hi Weijun,

----- Original Message -----
> From: "Luo Weijun" <luo_weijun at yahoo.com>
> To: maintainer at bioconductor.org, dtenenba at fredhutch.org
> Cc: "Martin Morgan" <mtmorgan at fredhutch.org>, Bioc-devel at r-project.org
> Sent: Wednesday, September 23, 2015 9:44:13 AM
> Subject: KEGG REST issue
> Dear BioC team,
> I noticed some problem with keggLink() function of KEGGREST package,
> and it can be traced back to KEGG REST API Linked entries. Some of
> this API function is broken. For example, the following line used to
> get all gene-pathway mapping for human, but retrieves nothing now.
> path.hsa= KEGGREST::keggLink("pathway", "hsa")
> In fact, these two bulk queries with the rest api don’t work anymore.
> http://rest.kegg.jp/link/pathway/hsa
> http://rest.kegg.jp/link/hsa/pathway
> but smaller queries on Linked entries seem to be fine. not sure
> whether other REST API functions are affected or not. As a
> consequence, KEGGREST and many dependent packages had build error.
> http://bioconductor.org/checkResults/release/bioc-LATEST/KEGGREST/morelia-buildsrc.html
> anway, just want you know about this, see if you can do anything on
> this.

Yes, I am aware of this. It's an issue on the KEGG side and I have contacted the KEGG team. I have not heard back yet.


> Weijun

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