Question: EBImage -- local machine VS cluster -- could not find function "slot"
gravatar for Mathieu Gendarme
5 weeks ago by
Mathieu Gendarme10 wrote:
Dear all,

I am currently trying to run a script for image segmentation using EBImage. The script I used was tested on two different platform, either a local workstation running Ubuntu or on a cluster running CentOS version 7.

Everything runs fine on the workstation but on the cluster I keep getting this error:

Error in slot(nucMask, ".Data") : could not find function "slot"
Calls: ImageProcessing -> [ -> [ -> eval.parent -> eval -> eval
Execution halted

As far as I can assess all the dependencies for this script are installed and I can load both libraries required for the job.

Does anyone know how to fix this problem?

Many thanks in advance,



Here is the code I used:

ADD COMMENTlink modified 14 days ago by Andrzej Oleś710 • written 5 weeks ago by Mathieu Gendarme10

How exactly do you run your script on the cluster, do you call it in a different way than locally?

ADD REPLYlink written 5 weeks ago by Andrzej Oleś710

The script is called from a .sh script that can be found here:

ADD REPLYlink written 5 weeks ago by Mathieu Gendarme10
gravatar for Andrzej Oleś
14 days ago by
Andrzej Oleś710
Heidelberg, Germany
Andrzej Oleś710 wrote:

Thanks Mathieu for reporting this problem. I could reproduce the described behavior when trying to subset an image in a script executed through Rscript, see Issue #31. The issue is related to methods package not being loaded by Rscript. Until this is fixed please add a call to library(methods) at the beginning of your script.


The issue has been resolved in both release and devel such that it shouldn't be necessary anymore to load methods package when EBImage is used through Rscript.

ADD COMMENTlink modified 12 days ago • written 14 days ago by Andrzej Oleś710

Fantastic Andrzej!

It runs without any problem with your bug fix. Thanks you very much!

ADD REPLYlink written 13 days ago by Mathieu Gendarme10
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