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McGranahanLab / CONIPHER-wrapper

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Some datasets need the coin package, but it seems to have been "commented out" in CONIPHER #7

Closed stefmldk closed 10 months ago

stefmldk commented 10 months ago

When running the test dataset (CASE_ID: CRUKTOY001) no errors are encountered. However, I have three datasets and all three encounter the error: Error in pvalue(coin::independence_test(as.numeric(ccfs[order(cpn.states)]) ~ : could not find function "pvalue" Calls: conipher_run ... conipher_clustering -> clustering_postprocess -> copy.driven.clusterNEW

It can thus be concluded that the Coin package is required sometimes but not always. When it gets called, the above error is thrown. A quick fix is to simply add the following line to the R script used to run CONIPHER (run_conipher.R in my case):

require(coin)

I hope this will help until a new version gets released (fingers crossed). Thanks for the software - it seems extremely useful, but at this point I have yet to get it to run to completion with any other dataset but the test dataset. I hope development will continue to make this very useful software more robust.

Thanks and best wishes, Steffen

arihueb commented 10 months ago

Hi Steffen, this issue should be fixed in the latest version of CONIPHER (v2.2.0). Please try deleting and downloading the conda environment again.