ArrayExpress dataset error
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5.9 years ago
c.chakraborty ▴ 170

I am having a small problem, and I would like to know what is the one stupid thing I am doing- I am trying to look for datasets for mouse brain in arrayexpress database through R and I am getting an error- My code-

sets = queryAE(keywords = "brain", species = "mus+musculus")

curl: (1) Protocol "https" not supported or disabled in libcurl

Error in download.file(qr, queryfilename, mode = "wb", method = "curl") :

'curl' call had nonzero exit status

Error: XML content does not seem to be XML: 'querybrainmus+musculus.xml'

I have called the library of curl and XML, and still I am unable to look for datasets; also I am connected to the internet! So, I don't understand what 's going on. The package and code looks relatively easy. I would be really glad if someone can help me.

R arrayexpress • 1.3k views
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I've added code formatting to your post, please consider doing so when posting code to increase readability. Could you double check if I formatted it right?

Entering edit mode

Apparently queryAE() uses download.file( ..., method = curl ), which uses your system curl. I am guessing the system curl is old and uses deprecated security protocols, or it was compiled without https support. What is the output of curl --version on the command-line (bash or whatever shell you use, not inside the R interpreter).


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