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Question: EBImage -- local machine VS cluster -- could not find function "slot"
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gravatar for Mathieu Gendarme
4 months 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 modified 3 months ago by Andrzej Oleś720 • written 4 months 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 4 months ago by Andrzej Oleś720

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 4 months ago by Mathieu Gendarme10
0
gravatar for Andrzej Oleś
3 months ago by
Andrzej Oleś720
Heidelberg, Germany
Andrzej Oleś720 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.

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.

ADD COMMENTlink modified 3 months ago • written 3 months ago by Andrzej Oleś720

Fantastic Andrzej!

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

ADD REPLYlink written 3 months ago by Mathieu Gendarme10
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