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:
> library(pathview)
> data(gse16873.d)
> 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:
curl -O http://bioconductor.org/packages/3.4/bioc/src/contrib/KEGGgraph_1.32.0.tar.gz
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:
http://bioconductor.org/packages/release/bioc/html/pathview.html
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.
Thank you for looking into this!
Hi Dr. Luo,
Thanks for your update. However, I just got a same problem these days. The parsing error shows below:
I've checked the versions: KEGGgraph 1.42.0, Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02). In order to deal with this, I tried in the work/my own computer, and edited the KEGG version to 1.32.0. But the problem still happened. I'm so confused about this happened. Any help or suggestions would be greatly appreciated in solving thisproblem. Thank-you so much!
The KEGGgraph version should be at least 1.38.0. I tried the code above with the latest KEGGgraph (1.42.0) and pathview (1.22.1) and encountered no error.
Hi David, thanks for your reply! I double check the version I got for these 2 packages, it appears: KEGGgraph (1.42.0) and pathview (1.3.5). Other versions: org.Hs.eg.db (3.7.0), png (0.1-7), Rgraphviz (2.26.0), XML (3.98-1.16).
Here're the code I have from installation part. (Same code from the author's document) source("http://bioconductor.org/biocLite.R") biocLite("pathview") install.packages("pathview",repos="http://R-Forge.R-project.org") library(pathview)
And then run the pathview:
Could you please help me to check with it? It would be very helpful! Thanks!!!
you just need these two lines to install pathview:
source("http://bioconductor.org/biocLite.R")
biocLite("pathview")
This following line installs an old version from R-Forge, likely caused the problem.
install.packages("pathview",repos="http://R-Forge.R-project.org")
you seemed to copy and paste the two redundant options from tutorial installation section.
Hi Weijun, I tried to install pathview via biocLite as you mentioned, but R said "'biocLite' is deprecated. Use 'BiocManager::install' instead." So I tried "BiocManager::install("pathview")".
Unfortunately, I still received this error message: "Parsing ./hsa04110.xml file failed, please check the file!"
Do you have any good idea to address this problem? Thanks!!