[Bioc-devel] Cytoscape installed on bioc builders?

Kozo Nishida kn|@h|d@ @end|ng |rom r|ken@jp
Sat Mar 6 19:12:21 CET 2021

Hi Catherine,

As far as I know, it is impossible.
See the comments from Martin Morgan and Paul Shannon below

I am maintaining a package for Cytoscape workflow (called transomics2cytoscape).
I test it only on the local Desktop environment, not on the bioc builders.

RCy3 is also tested only on the local Desktop environment, not on the
bioc builders.

I think that your fedup package can only be tested locally .
(about the functions using Cytoscape.)


Kozo Nishida
knishida using riken.jp

Laboratory for Biologically Inspired Computing
6-2-3, Furuedai, Suita, Osaka 565-0874, JAPAN
RIKEN Center for Biosystems Dynamics Research

On Sat, Mar 6, 2021 at 8:36 AM 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]]
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