Kegg Graph not proper xml

Question

[saamar.rajput]

I am new to KEGG graph. I am trying to parse the KGML to get a graph but I get an error saying the KEGG xml is not xml format. Here is my code and error :

library(KEGGgraph)
tcell<- system.file( "extdata/hsa04350.xml", package="KEGGgraph")
map.t<-parseKGML2Graph(tcell)
plot(map.t)

And the error i get on step 3 is:

Error: XML content does not seem to be XML: ''

How can I handle this ?

Answer 1

[Pierre Lindenbaum]

what's the output of

file extdata/hsa04350.xml

if it's not something like:

extdata/hsa04350.xml: XML  document text

then...

[saamar.rajput]

I am sorry I did not understand your question. Did you mean output of tcell ?

[Pierre Lindenbaum]

no, use the linux cmd file https://linux.die.net/man/1/file to test the nature of extdata/hsa04350.xml

[saamar.rajput]

Thank you so much Pierre, I think I figured out what went wrong :)