I'm trying to use KEGGREST to grab some data. But I'm finding that some basic examples don't seem to work.
library("KEGGREST")
listDatabases() # as expected
keggList("pathway") # no go
keggList("hsa") # no go
keggList("organism") # gives an answer
The error is always:
Error in .getUrl(url, .listParser, nameColumn = 1, valueColumn = 2) : invalid request, server returned Success: (200) OK (http://rest.kegg.jp/list/hsa)
Thanks for any insight.
Session Info:
R Under development (unstable) (2016-03-02 r70268)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.3 (El Capitan)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets
[6] methods base
other attached packages:
[1] KEGGREST_1.8.1
loaded via a namespace (and not attached):
[1] zlibbioc_1.14.0 httr_1.1.0
[3] R6_2.1.2 IRanges_2.2.9
[5] tools_3.3.0 XVector_0.8.0
[7] parallel_3.3.0 curl_0.9.6
[9] Biostrings_2.36.4 S4Vectors_0.6.6
[11] BiocGenerics_0.14.0 stats4_3.3.0
[13] png_0.1-7
These examples work for me. Can you try again? Maybe the KEGG website was having issues when you were trying earlier. Or perhaps there is a problem with the place you are trying to connect from.
I actually observed the problem yesterday, and thinking along the same lines as you, I waited and tested this morning. So if they work for you, it's not KEGG. I wonder what on my end could be the problem. I'm on Mac, latest everything basically. I'll try to find a Windows computer around here and try that.
Are you behind a firewall or proxy? Can you try connecting to a different network that is not?
PS., it is possible that it was an intermittent failure at KEGG when you last tried it. But if it consistently fails for you when it works for others than it is likely an issue with your network.
Also, is your KEGGREST package up to date? Please post
sessionInfo().Yes, up to date (installed yesterday, whatever the system gave me). `sessionInfo()` in original post. I'm at a university, never run into this before. Will try from home tonight and report. Thanks for your suggestions.
Ah, now wait. I see my version has an older version nomenclature and may not be up to date. I installed yesterday with
source("https://bioconductor.org/biocLite.R") biocLite("KEGGREST")But maybe I got a stale version in the process. I will go direct to the tarball.
You are not up to date. (Sorry, forgot you had posted sessionInfo() before).
You are using R-devel but the packages you have installed are not bioc-devel packages Please run biocLite() without arguments to update everything.
Alright, I can't quite get everything updated correctly yet, but it does seem one or more packages are stale or not devel-ready. I'll keep trying. Thanks for your help Dan.
You might try starting R like this:
R --vanillaAnd then doing:
remove.packages("BiocInstaller")source("https://bioconductor.org/biocLite.R")
It SHOULD say "Bioconductor version 3.3". If it does, then update all packages with:
biocLite()Success! Thanks. Your most recent suggestion got all the stale stuff out and now it works on 3.3 RC (r70268). I appreciate your help Dan.