EBImage -- local machine VS cluster -- could not find function "slot"
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@mathieu-gendarme-15885
Last seen 3.3 years ago
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?

Cheers,

Mathieu

Here is the code I used:

https://www.dropbox.com/s/bd4fo0p6q4yzatk/IfTestCluster_Bioconductor.R?dl=0

ebimage • 801 views
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How exactly do you run your script on the cluster, do you call it in a different way than locally?

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

https://www.dropbox.com/s/x1477r7xvrgm0r3/IfTestCluster_Bioconductor.sh?dl=0

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Andrzej Oleś ▴ 750
@andrzej-oles-5540
Last seen 18 months ago
Heidelberg, Germany

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.

#### UPDATE

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.

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Fantastic Andrzej!

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