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egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
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Error: Failed to extract KEGG image path from response. #122

Closed ashviyer closed 2 years ago

ashviyer commented 2 years ago

Hi,

I am trying to run the pathfindR for my dataset. When previously run (around a week ago), it was able to extract the KEGG pathways. But it has been showing this error for the same code when running the script today. Would appreciate your help. Thanks.

Here's the original error message: 'color.pathway.by.objects()' failed to extract KEGG image path from response. Cannot download PNG file: NA Here's the original error message: invalid 'url' argument

egeulgen commented 2 years ago

Hello,

I believe there was an issue with KEGGREST (the dependency of pathfindR for obtaining KEGG diagrams), which seems to be recently fixed. Updating should resolve the issue:

BiocManager::install("KEGGREST")
ashviyer commented 2 years ago

Thanks for the reply.

But even after updating, it shows the same error.

It seems like there is problem in connecting with KEGG. because when I run keggInfo("kegg") it shows me an error Error in curl::curl_fetch_memory(url, handle = handle) : Failure when receiving data from the peer.