I am trying to use the Bioconductor package SPIA to analyze KEGG pathways in Vitis vinifera. The first step is to import the KEGG xml file into the SPIA format using makeSPIAdata and this should generate an .Rdata object for downstream analysis.
I tried downloading a random pathway in Vitis by pressing "Download KGML" on this link and saving in the test directory, but when running the command
makeSPIAdata(kgml.path="test/",organism="vvi",out.path="SPIA_pathways/")
The function returned the value
[[1]] FALSE
And no file was saved.
Trying the same using a random human pathway, as this one gave no problem.
The function returned
[[1]] TRUE
And the file was created.
Can someone help with this issue?
EDIT: December 6, 2016 Further trials showed that not all the pathways give error (but several of them do!) and I was unlucky in selecting several pathways that all gave error. I can provide updates on my trials if someone is interested, otherwise I will not provide further updates.
