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Re: [igraph] Issues with read.graph in graphml format

From: Nirupama Benis
Subject: Re: [igraph] Issues with read.graph in graphml format
Date: Tue, 13 Aug 2019 10:15:24 +0200

Thank you, thank you! It works now!

On Mon, Aug 12, 2019 at 6:01 PM Tamas Nepusz <address@hidden> wrote:

The "GraphML support is disabled" error message is shown when the development versions of the libraries required to _parse_ a GraphML file (libxml2 and libiconv) were not installed on the machine where the igraph extension for R was compiled. Writing still works in this case because we don't use these libraries for producing the output, only for reading it.

The bottom line is that you need to remove the igraph extension and then install it again _after_ installing libxml2-dev and libiconv-dev (these are the development packages in Ubuntu for these libraries).


On Mon, 12 Aug 2019 at 17:05, Nirupama Benis <address@hidden> wrote:

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] ‘’
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?

Nirupama Benis.
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