[Bioc-devel] Cytoscape installed on bioc builders?

Robert M. Flight r|||ght79 @end|ng |rom gm@||@com
Sat Mar 6 02:23:11 CET 2021

Hi Catherine,

If I recall correctly, the builders are headless (i.e. they don't
have displays attached), and Cytoscape does require a display to run.

Anything in my vignette that required Cytoscape I cached the images and
then inserted them into the vignette, I think I had a function that would
check if Cytoscape was available, and insert the static images if it wasn't

push_graph <- try(
    # borrowed from createNetworkFromDataFrames
    nodes <- data.frame(id=c("node 0","node 1","node 2","node 3"),
    edges <- data.frame(source=c("node 0","node 0","node 0","node 2"),
           target=c("node 1","node 2","node 3","node 3"),
if (inherits(push_graph, "try-error")) {
  runCy <- FALSE
  print("No connection to Cytoscape available, subsequent visualizations
were not run")
} else {
  runCy <- TRUE

if "runCy" is FALSE from above code, the chunk will grab the previously
generated image instead.

Your only bet for testing Cytoscape functionality I believe is what you can
do locally, either on your direct machine or via a virtual machine.

Hope that helps,


Robert M Flight, PhD
Bioinformatics Research Associate
Puller of Rabbits from Hats
Research Parasite
Resource Center for Stable Isotope Resolved Metabolomics
Manager, Systems Biology and Omics Integration Journal Club
Markey Cancer Center
CC434 Roach Building
University of Kentucky
Lexington, KY

Twitter: @rmflight
Web: rmflight.github.io
ORCID: http://orcid.org/0000-0001-8141-7788
EM rflight79 using gmail.com
PH 502-509-1827 <(502)%20509-1827>

The most powerful weapon in the hands of the oppressor is the mind of the
oppressed. Biko (1978), from Birhane & Guest, Towards decolonising
computational sciences, https://arxiv.org/pdf/2009.14258.pdf

On Fri, Mar 5, 2021 at 6:36 PM Catherine Ross <
catherinem.ross using mail.utoronto.ca> wrote:

> Hi bioc-devel,
> My package contains a function that requires Cytoscape.
> For this function to run, I need to have Cytoscape installed and open on
> my computer.
> https://github.com/rosscm/fedup/blob/main/R/femap.R
> This poses an issue when attempting to test the function since I can’t
> control Cytoscape on the bioc builders, so I can’t test the function at all.
> Is it possible to have Cytoscape installed on the builders to be able to
> run such tests?
> Catherine
>         [[alternative HTML version deleted]]
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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