Hello,
I have been using the R package igraph for quite a while and have used write.graph to save my graphs as GraphML files for further use in R itself or in Cytoscape.
Now I am using the latest version of R (on RStudio Version 1.2.1335)
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
And the igraph package version
> packageVersion("igraph")
[1] ‘1.2.4.1’On Ubuntu 18.04.2 LTS.
Now I am not able to read in GraphML files that I wrote using the igraph function write.graph.
The function write.graph works with format as 'graphml'
> write.graph(graph = netgraph, file = "myNetwork.graphml", format = "graphml")
But when I read the file in with read.graph
> netgraph <- read.graph(file = "myNetwork.graphml", format = "graphml")
Error in read.graph.graphml(file, ...) :
At foreign-graphml.c:1361 : GraphML support is disabled, Unimplemented function call
The function does work on a virtual machine that has R version 3.6.0 and Ubuntu 18.04.2.
Is there something I am missing?
I can temporarily work around this by using the package RCy3 to store the graphs and download it in graphml format to save the graph. But I would prefer to put it in the script. Do you suggest any other format that perhaps works better?
Regards,
Nirupama Benis.