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cytoscape / RCy3

New version of RCy3, redesigned and collaboratively maintained by Cytoscape developer community
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sporadic error - Error in .cyFinally(res) : object 'res' not found #186

Closed risserlin closed 1 year ago

risserlin commented 2 years ago

running pipelines from docker without fail eventually I will get the error: Error in .cyFinally(res) : object 'res' not found. It doesn't matter which command I am running. One minute RCy3 is connected and working and the next I keep getting the above error.

sometimes, detach and re-attaching the RCy3 library will help fix it. sometimes, restarting cytoscape will fix it. sometimes, restarting docker will fix it.
And other I have to do all three of the above.

I don't know where this issue is coming from but is it possible that there is something that is not be cleared or an empty res variable is triggering?

AlexanderPico commented 2 years ago

Hi Ruth. You're at the cutting edge of RCy3 usage. I know of only a handful of people running docker pipelines with RCy3 like you are doing. I've ping'd those folks on Slack to get their input.

I suspect, they'll want more information. Can you tell us more about what's in your container and how you configure it? Can you share the minimal script that reproduces the error? Etc...

risserlin commented 2 years ago

HI Alex, I am using the following docker image - https://hub.docker.com/r/risserlin/survival_driver_pathways_bioc_1_14. It is just a basic bioconductor image with a bunch of installed bioconductor and R packages.

That is my biggest problem. I can't reproduce it. I can't figure out what is triggering it. Originally I thought it was an issue with the web browser loosing connection because my computer went to sleep but even when I disable the sleep settings on my computer it still does it. Then I tried to knit it from the command line instead and it seemed to run for longer but ultimately it lost connection eventually.

The error "res" not found. I am wondering if there is a way I can re-initialize the cytoscape connection. I wish there was a way to figure out if the connection loss is from cytoscape or from docker. I would be curious to know if anyone running lengthy pipelines have also encountered this (specifically without docker so it can help figure out what is the culprit).

Thanks, Ruth

AlexanderPico commented 2 years ago

As far as I've heard back so far, no one is routinely seeing this issue with RCy3 or py4cy. They also recommend running your pipeline outside of Docker as a control test.

risserlin commented 2 years ago

uh oh! That means updating R on my computer. Something I avoid like the plague. Truthfully I didn't even think of doing that because I am so programmed to use docker. I will see if that fixes it.

risserlin commented 2 years ago

Ok. I remember why I work only in docker. Although I am using Catalina my mac is on the older side (late 2013) and after updating everything still struggling to get my notebook to work unfortunately. After updating R I could only use bioc 3.15 so just updating my docker to bioc 3.15 to see if the error I am now seeing is bioc 3.15 specific or something wrong with my computer :)

risserlin commented 1 year ago

I finally solved this issue. this is not an RCy3 or a cytoscape issue. This is a docker on mac issue. I fixed it by downgrading my docker version to 4.5. There was another suggestion/recommendation but it required mac OS 11 and higher (which I don't have).
Here is the thread that helped me just in case anyone else has this issue when running pipelines in docker that use cytoscape and RCy3 - https://github.com/docker/for-mac/issues/3448