Error in summary.connection(connection) : invalid connection

[peuclide]

Hi Alex,

I think I am having an issue with the doParallel portion of the assign.kfold() and assign.MC() functions. When I was running the scripts I made a issue so killed the run to start over and when I tried again I got the following error "Error in summary.connection(connection) : invalid connection"

my script was:

assign.kfold( genin80_3pops_rd, k.fold=c(3, 4, 5), train.loci=c( 1),

•          loci.sample="random", model="svm", dir="./Baseline_analysis/assignPOP/Result_kf_3pop_svm_grand_comb/", multiprocess = T)
  

the output I got was: 7 cores/threads of CPU will be used for analysis... Error in summary.connection(connection) : invalid connection

through some searching I found that I think it has something to do with stopCluster(), but was have not been able to fix it and get anything to run in parallel (the multiprocesses=FALSE method works just fine).

Thanks for your help!

Peter

[alexkychen]

Hi Peter,

Thank you for reporting this issue. It looks like there is a for-loop issue in my codes, and therefore it doesn't allow you to run multiple sets of K-fold (e.g., k.fold=c(3,4,5) ) with parallel computing. At this point, you can only set one k-fold at a time (e.g., k.fold=c(3) ) in order to run in parallel.

I will see if I can fix this bug in the next few days, and let you know.

Thanks.

[alexkychen]

Hi Peter,

I updated the function assign.kfold, and now it should run multiple sets of K-fold in parallel. Please update or reinstall your library to v.1.1.6 and see if it works.

Thanks.

[peuclide]

Thanks Alex!

On Jun 10, 2019, at 8:09 AM, Alex Chen [email protected] wrote:

Hi Peter,

I updated the function assign.kfold, and now it should run multiple sets of K-fold in parallel. Please update or reinstall your library to v.1.1.6 and see if it works.

Thanks.

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