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Accio / KEGGgraph

The KEGGgraph package to parse KEGG pathways in R into graph objects
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Failure to download KEGG pathways when using pathfindR #6

Closed apelin20 closed 2 years ago

apelin20 commented 2 years ago

Hello,

I am trying to use pathfindR which relies on KEGGgraph for KEGG pathway download and mapping, but I am getting these odd errors:

`Downloading pathway diagrams of 286 KEGG pathways

| | 0%Cannot retrieve PNG url: hsa03010 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: 'url' must be a length-one character vector Cannot retrieve PNG url: hsa05171 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: 'url' must be a length-one character vector | | 1%Cannot retrieve PNG url: hsa03040 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: 'url' must be a length-one character vector |= | 1%Cannot retrieve PNG url: hsa04141 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: 'url' must be a length-one character vector Cannot retrieve PNG url: hsa05012 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: 'url' must be a length-one character vector |= | 2%Cannot retrieve PNG url: hsa05020 Here's the original error message: 'color.pathway.by.objects()' failed to extract KEGG image path from response. Cannot download PNG file: NA `

I was wondering if this is because of a recent change in KEGG urls?

Thanks

Accio commented 2 years ago

thanks for reporting, @apelin20! This is new to me. Do you mind attaching a minimal reproducible example so that I can check it as well? Thanks and best regards, David

apelin20 commented 2 years ago

Thanks for getting back to me Accio. This got resolved with KEGGREST - https://github.com/Bioconductor/KEGGREST/issues/12

The trick was to use install_github("Bioconductor/KEGGREST")

Accio commented 2 years ago

Thanks for the update!