Dear ArrayExpress development team,

EBI services (<https://www.ebi.ac.uk/services>), including ArrayExpress have switched to https on October 1st 2017.  The function getAE from the ArrayExpress Bioconductor package needs an update, as any retrieval fails like so:

library(ArrayExpress)

getAE("E-MTAB-5225")
Unknown IO error failed to load external entity "http://www.ebi.ac.uk/arrayexpress/xml/v2/files/E-MTAB-5225"
Error: 1: Unknown IO error2: failed to load external entity "http://www.ebi.ac.uk/arrayexpress/xml/v2/files/E-MTAB-5225"

Inspired by

<https://stackoverflow.com/questions/23584514/error-xml-content-does-not-seem-to-be-xml-r-3-1-0>

I have uploaded a gist that uses RCurl::getURL to fix this

<https://gist.github.com/b-klaus/f2a502109f852702bf7efc5ad5c0bd11>

I only change two lines of code in the function, my new getAE code:

baseURL = "https://www.ebi.ac.uk/arrayexpress/xml/v2/files"
xmlURL = getURL(paste(baseURL, accession, sep = "/"))

old getAE code

baseURL = "http://www.ebi.ac.uk/arrayexpress/xml/v2/files"
xmlURL = paste(baseURL, accession, sep = "/")

Thanks for updating!

Bernd

I was informed by the ArrayExpress package maintainer Ugis Sarkans that they plan to restore http access to ArrayExpress APIs.