Recent build and parsing error in pathview
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Luo Weijun ★ 1.5k
@luo-weijun-1783
Last seen 3 months ago
United States

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")

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:

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.

pathview KEGGgraph gage pathway pathway analysis • 2.4k views
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Thank you for looking into this!

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Hi Dr. Luo,

Thanks for your update. However, I just got a same problem these days. The parsing error shows below:

> library(pathview)
> data(gse16873.d)
> pv.out <- pathview(gene.data = gse16873.d[, 1], pathway.id = "04110",
+                    species = "hsa", out.suffix = "gse16873")
Parsing ./hsa04110.xml file failed, please check the file!


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!

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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.

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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:

data(gse16873.d) pv.out <- pathview(gene.data = gse16873.d[, 1], pathway.id = "04110", + species = "hsa", out.suffix = "gse16873") Parsing ./hsa04110.xml file failed, please check the file!

Could you please help me to check with it? It would be very helpful! Thanks!!!

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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.

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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!!

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Hong • 0
@hong-13546
Last seen 4.3 years ago
UNC

Great! Thank you so much!!

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Luo Weijun ★ 1.5k
@luo-weijun-1783
Last seen 3 months ago
United States

you may always use pathview web server as an backup in case something like this occurred again:

https://pathview.uncc.edu/

Pathview Web server provides a intuitive GUI and API to Pathview, a full pathway analysis workflow supporting multiple omics data and integrated analysis, and much more.

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@zhang-jitao-david-5737
Last seen 19 months ago
Switzerland

Dear all,

Thanks for the report. In the latest versions (devel 1.37.2/release 1.38.1) I have exported required functions to make the example work. Please let me know if there are still problems.

Best,

Jitao David Zhang, the author of KEGGgraph

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Luo Weijun ★ 1.5k
@luo-weijun-1783
Last seen 3 months ago
United States

Thanks David, for the work. Hopefully, it would work this time. Will keep you updated.

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Luo Weijun ★ 1.5k
@luo-weijun-1783
Last seen 3 months ago
United States

pathview is running error-free now:

http://bioconductor.org/checkResults/release/bioc-LATEST/pathview/

http://bioconductor.org/packages/release/bioc/html/pathview.html

Thanks to everyone!