curl::curl_fetch_memory(url, handle = handle) : Unrecognized content encoding type. libcurl understands deflate, gzip content encodings

General
1

Hi,

I am trying to create a Cytoscape network using RCY3 package. When I run the following code, I get the error message below-

createNetworkFromDataFrames(edges = edge_df, nodes = NULL, title = "gene coexpression network")

Error in curl::curl_fetch_memory(url, handle = handle) : Unrecognized content encoding type. libcurl understands deflate, gzip content encodings.

Traceback: Error in curl::curl_fetch_memory(url, handle = handle) : Unrecognized content encoding type. libcurl understands deflate, gzip content encodings. 7. curl::curl_fetch_memory(url, handle = handle) 6.request_fetch.write_memory(req$output, req$url, handle) 5.request_fetch(req$output, req$url, handle) 4.request_perform(req, hu$handle$handle) 3.POST(url = URLencode(q.url), body = q.body, encode = "json", content_type_json()) 2.cyrestPOST("networks", parameters = list(title = title, collection = collection), body = json_network, base.url = base.url) 1.createNetworkFromDataFrames(edges = edge_df, nodes = NULL, title = "gene coexpression network")

curl package is installed and loaded in the workflow. I have seen people having similar problem. Unfortunately none of the issues are related to cytoscape/rcy3 or R and I could not solve it from existing answers.

The data frame edge_df looks like below-
image

2

This is a known bug for the RCy3 project and has been fixed for the next Bioconductor release at the end of this month. You can install the dev version in the meantime. https://github.com/cytoscape/RCy3

3

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