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Question: EBImage -- local machine VS cluster -- could not find function "slot"
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gravatar for Mathieu Gendarme
5 days 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,

Cheers,

Mathieu

Here is the code I used:

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

ADD COMMENTlink written 5 days 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 days ago by Andrzej OleĊ›710

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

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

ADD REPLYlink written 5 days ago by Mathieu Gendarme10
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