Hello,
I have been recently getting a warning message with KEGGgraph. See the following example:
library(KEGGgraph)
library(RCurl)
path = "rno00010"
file = paste("http://rest.kegg.jp/get/", path, "/kgml", sep = "")
pathway = try(getURL(file), silent = TRUE)
reactions = try(getReactions(parseKGML(pathway)), silent = TRUE)
Then I get loads of warnings like:
warnings()
48: In structure(x$children, class = "XMLNodeList") :
Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
49: In structure(x$children, class = "XMLNodeList") :
Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
50: In structure(x$children, class = "XMLNodeList") :
Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Any help?
Thanks very much,
Andrea
Thanks very much for your reply. See below:
> library(KEGGgraph)
Attaching package: ‘KEGGgraph’
The following object is masked from ‘package:graphics’:
plot
> library(RCurl)
Loading required package: bitops
> path = "rno00010"
> path = "rno00010"
> file = paste("http://rest.kegg.jp/get/", path, "/kgml", sep = "")
> pathway = try(getURL(file), silent = TRUE)
> reactions = try(getReactions(parseKGML(pathway)), silent = TRUE)
There were 50 or more warnings (use warnings() to see the first 50)
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RCurl_1.95-4.8 bitops_1.0-6 KEGGgraph_1.35.0
loaded via a namespace (and not attached):
[1] compiler_3.4.0 parallel_3.4.0 tools_3.4.0 BiocGenerics_0.23.0 stats4_3.4.0
[6] XML_3.98-1.7 graph_1.55.0
Best wishes,
Andrea