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Old 07-16-2017, 09:09 PM   #1
Hongm
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Location: UNC

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Default Parsing issue in pathview package

I got a parsing error when using pathview package to visualize pathways in my RNAseq data. This error still showed up even I tried to run the example (quick start with demo data) in the vignette. I found that XML was loaded successfully as shown in sessionInfo. Could someone help me to see what's wrong? Thank you very much!

> library(pathview)
Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘packagearallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport,
clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply,
parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,
colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

Vignettes contain introductory material; view with 'browseVignettes()'.
To cite Bioconductor, see 'citation("Biobase")', and for packages
'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

expand.grid


##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
> 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!
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 15063)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods
[9] base

other attached packages:
[1] pathview_1.16.1 org.Hs.eg.db_3.4.1 AnnotationDbi_1.38.1
[4] IRanges_2.10.2 S4Vectors_0.14.3 Biobase_2.36.2
[7] BiocGenerics_0.22.0

loaded via a namespace (and not attached):
[1] graph_1.54.0 Rcpp_0.12.12 KEGGgraph_1.38.0 XVector_0.16.0
[5] zlibbioc_1.22.0 bit_1.1-12 R6_2.2.2 rlang_0.1.1
[9] blob_1.1.0 httr_1.2.1 tools_3.4.1 grid_3.4.1
[13] png_0.1-7 DBI_0.7 bit64_0.9-7 digest_0.6.12
[17] tibble_1.3.3 Rgraphviz_2.20.0 KEGGREST_1.16.0 memoise_1.1.0
[21] RSQLite_2.0 compiler_3.4.1 Biostrings_2.44.1 XML_3.98-1.9
[25] pkgconfig_2.0.1
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Old 07-17-2017, 02:09 PM   #2
Hongm
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I happen to keep another version of R (3.3.1) on my PC. I tried the same code using R_3.3.1 and it worked. I'm not sure whether it is a version issue. But at least it works. Just let anyone who's interested in known.

> 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..
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory C:/Users/mahon/Desktop
Info: Writing image file hsa04110.gse16873.png
> list.files(pattern = "hsa04110*")
[1] "hsa04110.gse16873.png" "hsa04110.png" "hsa04110.xml"
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Old 07-19-2017, 04:14 PM   #3
Sam Hinshaw
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Default

Thank you so much for reporting your results! I was having the same issue and it was driving me nuts.

I used Shiny's debugging breakpoints to drill into the pathview function, and traced the error to what seems to be a namespace problem between `pathview` and `KEGGgraph`. If you print the error message passed to tryCatch, you get:

```
Error in parsePathwayInfo(r): could not find function "parsePathwayInfo"
```

If you simply redefine `parsePathwayInfo()` in the global namespace, you get the same error with `xmlAttrs()`.

Fortunately pathview functions normally in R 3.3.x, but hopefully the package developer can fix this for R 3.4!
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Old 07-20-2017, 10:22 AM   #4
Hongm
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Weijun is very nice to help to figure out the issue and give a solution posted in Bioconductor website (see below). Thank you, Weijun!

https://support.bioconductor.org/p/98334/
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Old 07-20-2017, 10:26 AM   #5
bigmw
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Dear all,
Thank you for reporting this issue. Indeed, I was able to replicate the same problem with the latest R/BioC versions.
I just posted the cause and solution for this problem on bioc support forum:
https://support.bioconductor.org/p/98334/

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.

please do not hesitate to contact us for any future issues. Thank you for your patience and support to pathview.
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Old 07-26-2017, 01:08 PM   #6
bigmw
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pathview package is running error-free now with the latest R/BioC and KEGGgraph:
http://bioconductor.org/checkResults...TEST/pathview/
http://bioconductor.org/packages/rel.../pathview.html

Thanks to everyone!
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Old 07-27-2017, 04:52 PM   #7
Hongm
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Thank you so much!
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