There is a build error showed up with both release and devel version of pathview package since several days ago. And multiple users also complaint on a emerging parsing error (the same issue as the build error) as below:
> pv.out <- pathview(gene.data = gse16873.d[, 1], pathway.id = "04110",
+ species = "hsa", out.suffix = "gse16873")
Info: Downloading xml files for hsa04110, 1/1 pathways..
Info: Downloading png files for hsa04110, 1/1 pathways..
Warning: Parsing ./hsa04110.xml file failed, please check the file!
It is quite confusing as the package has not been changed in the past few weeks. It turns out that pathview imports some parsing functions from another package KEGGgraph, which was not exported anymore in the KEGGgraph namespace (latest release 1.38.0) For details see: http://bioconductor.org/packages/release/bioc/news/KEGGgraph/NEWS.
So the current solution is to manually download/install a recent version like on Unix-like systems:
R CMD INSTALL KEGGgraph_1.32.0.tar.gz
Windows user can download the .zip version and installed from R console manually. And the error would be gone with this fix.
We also modify the pathview package to explicitly import from the specific version KEGGgraph 1.32.0. the update should show up in the next few days in both release and devel version of pathview:
Make sure to resist the tempatation to update to the latest KEGGgraph version at this time! We are also contacting the maintainer of KEGGgraph about exporting the old function.
Thank you for your patience and support to pathview.