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Question: pathview: Warning: Download of hsa04110 xml and png files failed!
0
gravatar for masamiwata
7 months ago by
masamiwata0
masamiwata0 wrote:

I have been trouble with using pathview command. I followed the path view help and wrote the sample codes as following.

library(pathview)

data(gse16873.d)
data(demo.paths)
i <- 1
pv.out <- pathview(gene.data = gse16873.d[, 1], pathway.id = demo.paths$sel.paths[i], species = "hsa", out.suffix = "gse16873", kegg.native = TRUE)

However, pathview command did not work and the following messages appeared.

Info: Downloading xml files for hsa04110, 1/1 pathways..
Info: Downloading png files for hsa04110, 1/1 pathways..
Warning: Download of hsa04110 xml and png files failed!
Warning: Failed to download KEGG xml/png files, hsa04110 skipped!

Please let me know how to fix this problem.

Thank you. 

pathview • 268 views
ADD COMMENTlink written 7 months ago by masamiwata0

Could you please provide the version of the package you use and the R version number

ADD REPLYlink written 7 months ago by Lluís Revilla Sancho460

My R version is following.

R version 3.1.3 (2015-03-09) -- "Smooth Sidewalk"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin10.8.0 (64-bit)

Thank you.

 

ADD REPLYlink written 7 months ago by masamiwata0

This is not the latest version of R nor of Biocondutor, for these reason I would recommend you to upgrade your R and Bioconductor versions and check in the new version if the error persist.

ADD REPLYlink written 7 months ago by Lluís Revilla Sancho460

Dear  Lluís

Thank you. I can fix this problem. I have learned to check the R version regularly.

 

 

ADD REPLYlink written 7 months ago by masamiwata0
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