Pathview .xml parsing issue

[Deanho]

Hi Guangchuang,

I know you don't actually look after Pathview but it seems to be broken. Do you know of a fix? It doesn't even work if you follow the vignette, using their sample data. No matter how I try it, I get this error (for e.g., for yeast Carbohydrate metabolism sce01200):

Info: Getting gene ID data from KEGG... Info: Done with data retrieval! Info: Downloading xml files for sce01200, 1/1 pathways.. Info: Downloading png files for sce01200, 1/1 pathways.. Warning: Parsing ./sce01200.xml file failed, please check the file!

Any ideas?

Beat Regards,

Dean

[GuangchuangYu]

> require(clusterProfiler)
> require(pathview)
> data(geneList)
> hsa04110 <- pathview(gene.data = geneList, 
                         pathway.id = "hsa04110",  species    = "hsa", 
                         limit = list(gene=max(abs(geneList)), cpd=1))
Info: Downloading xml files for hsa04110, 1/1 pathways..
Info: Downloading png files for hsa04110, 1/1 pathways..
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /home/ygc
Info: Writing image file hsa04110.pathview.png
> 

I can't reproduce your issue.

[Deanho]

Mmmm?

It fails for me:

[cid:image002.jpg@01D2FFE4.5C19D970]

Dean

From: Guangchuang Yu [mailto:notifications@github.com] Sent: 18 July 2017 16:36 To: GuangchuangYu/clusterProfiler clusterProfiler@noreply.github.com Cc: Hammond, Dean becks11@liverpool.ac.uk; Author author@noreply.github.com Subject: Re: [GuangchuangYu/clusterProfiler] Pathview .xml parsing issue (#94)

require(clusterProfiler)

require(pathview)

data(geneList)

hsa04110 <- pathview(gene.data = geneList, pathway.id = "hsa04110", species = "hsa", limit = list(gene=max(abs(geneList)), cpd=1))

Info: Downloading xml files for hsa04110, 1/1 pathways..

Info: Downloading png files for hsa04110, 1/1 pathways..

'select()' returned 1:1 mapping between keys and columns

Info: Working in directory /home/ygc

Info: Writing image file hsa04110.pathview.png

I can't reproduce your issue.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/GuangchuangYu/clusterProfiler/issues/94#issuecomment-316103656, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AJXbGExNBkrcrwiBX_mEBA9XPqmxVVWRks5sPNDxgaJpZM4ObhR6.

[yasirs]

@Deanho What does the downloaded xml file look like? I am getting an empty file. It might be something to do with the URL path for the xml file.