Parallel execution of GENIE3

[alnf]

When using nCores parameter I've encountered problem: could not find function "%dopar%"

The code is following:

library(netbenchmark) # needed for dataset
library(GENIE3)
GENIE3(t(gnw2000.data[, 1:20]), nCores=4)

Session info:

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /home/aln/miniconda3/envs/bnf/lib/R/lib/libRblas.so
LAPACK: /home/aln/miniconda3/envs/bnf/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] GENIE3_1.0.0        netbenchmark_1.10.0 grndata_1.10.0     

loaded via a namespace (and not attached):
 [1] igraph_1.1.2        Rcpp_0.12.14        magrittr_1.5       
 [4] PCIT_1.5-3          fdrtool_1.2.15      doParallel_1.0.11  
 [7] xtable_1.8-2        lattice_0.20-35     doRNG_1.6.6        
[10] foreach_1.4.4       stringr_1.2.0       pkgmaker_0.22      
[13] rngtools_1.2.4      tools_3.4.1         c3net_1.1.1        
[16] grid_3.4.1          registry_0.5        corpcor_1.6.9      
[19] iterators_1.0.9     digest_0.6.14       GeneNet_1.2.13     
[22] randomForest_4.6-12 Matrix_1.2-12       codetools_0.2-15   
[25] longitudinal_1.1.12 stringi_1.1.6       pracma_2.1.1       
[28] compiler_3.4.1      minet_3.36.0        pkgconfig_2.0.1    

Any ideas how to fix that? Thanks.

[davetang]

You need to install these two libraries doParallel and doRNG.

[alnf]

@davetang would you be so kind to look closely on my sessionInfo() output?

[davetang]

They are not attached. This works for me:

library(netbenchmark)
library(GENIE3)
library(doParallel)
library(doRNG)
GENIE3(t(gnw2000.data[, 1:20]), nCores=4)

[alnf]

@davetang It seems to help me as well, thx. I thought GENIE would load the packages internally. Closing the issue.

[mschubert]

Forgive me digging up this old issue, but why should those packages be attached?

Is there any advantage of requiring the user to pollute their global namespace in order to run GENIE3 in parallel?