[Bioc-devel] Cytoscape installed on bioc builders?

Catherine Ross c@ther|nem@ro@@ @end|ng |rom m@||@utoronto@c@
Wed Mar 10 00:03:53 CET 2021

Hi Robert, Kozo,

Thank you both for your responses!

I’ve now set up a testable tryCatch for my Cytoscape-using function that returns NULL on connection fail error, rather than stopping the function completely.


> On Mar 6, 2021, at 1:12 PM, Kozo Nishida <knishida using riken.jp> wrote:
> Hi Catherine,
> As far as I know, it is impossible.
> See the comments from Martin Morgan and Paul Shannon below
> https://github.com/Bioconductor/Contributions/issues/1513#issuecomment-644113558
> 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
> --
> 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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