Error on creating RCyjs object

[caligarimga]

I attempted to construct an RCyjs object in R 4.2 in order to submit my graphnel to the browser and obtain coordinates, but I received the following error (I was surprised to see the same error on the package help run example):

"Error in sprintf("port not available: %d", port): invalid format '%d'; use format %s for character objects"

It is crucial to note that the code was functioning prior to the upgrading of my system (R 4.2.3, R Studio 2023.03.0 Build 386, and packages (RCyjs 2.20.0, bioconductor 3.16, BrowserViz 2.20.0).

The code that I was running is the following:

g <- simpleDemoGraph() rcy <- RCyjs(title="rcyjs demo", graph=g)

Thank you

[paul-shannon]

Version number, please?

On Apr 13, 2023, at 12:51 PM, caligarimga @.***> wrote:

I attempted to construct an RCyjs object in R 4.2 in order to submit my graphnel to the browser and obtain coordinates, but I received the following error (I was surprised to see the same error on the package help run example): "Error in sprintf("port not available: %d", port): invalid format '%d'; use format %s for character objects" It is crucial to note that the code was functioning prior to the upgrading of my system (R, R studio, and packages). The code that I was running is the following: g <- simpleDemoGraph() rcy <- RCyjs(title="rcyjs demo", graph=g) Thank you — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.***>

[JFMSilva]

The issue is with RCyjs and BrowserViz version 2.20.0. I examined the code and compared it to version 2.16.

The function BrowserViz was altered in 2.20.0 to add the "host" parameter, which was missing in 2.16, however the call from .RCyjs was not updated to incorporate the new argument.

[paul-shannon]

Very helpful. I’ll tend to this later today, tomorrow for sure.

• Paul

On Apr 14, 2023, at 11:25 AM, JFMSilva @.***> wrote:

The issue is with RCyjs and BrowserViz version 2.20.0. I examined the code and compared it to version 2.16. The function BrowserViz was altered in 2.20.0 to add the "host" parameter, which was missing in 2.16, however the call from .RCyjs was not updated to incorporate the new argument. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>

[paul-shannon]

fixed in RCyjs 2.21.1, in Bioconductor. Thanks for the bug report, and sorry for the trouble.

[caligarimga]

Thank you, Paul