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nolanlab / spade

SPADE: Spanning Tree Progression of Density Normalized Events
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SPADE.installPlugin("/Applications/Cytoscape_v3.0.0") fails with Error (R version 2.15.3) #62

Closed davidwolski closed 11 years ago

davidwolski commented 11 years ago

Hi guys,

I tried installing the SPADE Plugin for Cytoscape v3.0.0 in R version 2.15.3 (using RStudio) on a Mac after install spade through Bioconductor 2.11and get the following result:

library(spade) Loading required package: igraph0 Scalable Robust Estimators with High Breakdown Point (version 1.3-02)

SPADE.installPlugin("/Applications/Cytoscape_v3.0.0/") Error in if (!file.exists(target_path) && !file.info(target_path)$isdir) { : missing value where TRUE/FALSE needed

I also tried with Cytoscape v2.8.3, the R.app and R64.app, to no avail.

Do you have any ideas what the problem might be here? Your help would be much appreciated.

Best, David

davidwolski commented 11 years ago

Nevermind. To whoever might have the same problem down the line:

Create the "plugins" folder in the Cytoscape directory manually and the install will work.

zbjornson commented 11 years ago

Glad you found a work-around. Please note that we haven't tested Cytoscape 3.0. I don't know if any features are broken in that version.

davidwolski commented 11 years ago

Thanks, for the quick reply. I actually went back to version 2.8.3, since it seems that Cytoscape has moved away from a Plugin based interface towards something they call Apps (with accompanying App Store). Unfortunately, simply copying the cytospade.jar file into the corresponding folder won't do the trick. So unless I am missing something really obvious here, SPADE can't be properly installed for version 3.0.0.