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Accio / KEGGgraph

The KEGGgraph package to parse KEGG pathways in R into graph objects
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Warning message when I expanded embedded pathways #1

Open HelloYiHan opened 5 years ago

HelloYiHan commented 5 years ago

Hi, Zhang, When I expanded embedded pathways with parseKGMLexpandMaps, there was a warning message. The code I used and the warning were as below.

The code I used was: mapkKGML <- system.file("extdata/hsa04010.xml",package="KEGGgraph") mapkGembed <- parseKGMLexpandMaps(mapkKGML,downloadmethod = 'internal')

trying URL 'http://rest.kegg.jp/get/hsa04010/kgml' Content type 'text/xml' length unknown downloaded 62 KB

trying URL 'http://rest.kegg.jp/get/hsa04070/kgml' Content type 'text/xml' length unknown downloaded 50 KB

trying URL 'http://rest.kegg.jp/get/hsa04110/kgml' Content type 'text/xml' length unknown downloaded 45 KB

trying URL 'http://rest.kegg.jp/get/hsa04210/kgml' Content type 'text/xml' length unknown downloaded 53 KB

trying URL 'http://rest.kegg.jp/get/hsa04310/kgml' Content type 'text/xml' length unknown downloaded 40 KB

trying URL 'http://rest.kegg.jp/get/hsa04115/kgml' Content type 'text/xml' length unknown downloaded 28 KB

Warning message: In [<-(tmp, length(mapgrs) + 1, value = gR) : implicit list embedding of S4 objects is deprecated

I was wondering if I need to worry about the warning message. Thank you for your help.

Accio commented 5 years ago

Thanks for reporting.

(1) Please check the versions of the packages. In the test environment that I have (R-3.5.1, KEGGgraph 1.45.0), the code works normally. The failure to download KGML files correctly was a known issue after the REST API was introduced and was then fixed. (2) Thanks for pointing out the warning message. It is now fixed in the 1.45.1 version.