[Bioc-devel] Replacement for CytoscapeWindowClass from devel RCy3

Robert M. Flight rflight79 at gmail.com
Fri Mar 30 18:13:24 CEST 2018

My package, categoryCompare, is failing in Bioc devel.

The reason appears to be exports in previous versions of RCy3 no longer
being exported, namely the "CytoscapeWindowClass".

I had some methods where behavior was defined based on being passed an
object of "CytoscapeWindowClass" (see
an example).

It appears this class no longer exists in the devel version of RCy3, and
what is noted as a replacement for the deprecated function that created it
(example being createNetworkFromGraph), has no specific class outside of
returning a "function".

I could use some advice on how I should modify my method signature to
handle this for the next version of RCy3, or if the object returned will
indeed have a "class" attached to them that can be checked via method



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 at gmail.com
PH 502-509-1827 <(502)%20509-1827>

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. - Ronald Fisher

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