Multi-core in scan1snps gives error about k_loco

[kbroman]

A user reported a problem with multi-core analysis with scan1snps(), where a kinship matrix wasn't found:

I've noticed when I run scan1snps with core set to greater than 1 I get an error that my kinship file ("k_loco" is not found). It works without a problem with cores=1

2 nodes produced errors; first error: object 'k_loco' not found

This works fine (using 1 core to do whole genome snp scan):

out_snps <- scan1snps(apr, map, phenol[,81], k_loco, Xcovar = NULL,addcovar = covars, query_func=query_variants, cores =1)

But if I change the cores argument to 2:

out_snps <- scan1snps(apr, map, phenol[,81], k_loco, Xcovar = NULL,addcovar = covars, query_func=query_variants  , cores =2)
Error in checkForRemoteErrors(val) :   2 nodes produced errors; first error: object 'k_loco' not found

Interestingly if I run scan1snps on just an interval of interest there is no problem with using more than 1 core:

start=32.40
end=32.78
chr<-17
covars<-NULL
out_snps <- scan1snps(apr[,chr], map, phenol[,81], k_loco[[chr]], Xcovar = NULL,addcovar = covars, query_func=query_variants, chr=chr, start=start, end=end, keep_all_snps=TRUE, cores = 2)

[kbroman]

I'm not able to reproduce this problem.

[kbroman]

A similar problem was reported again. See this post on the R/qtl2 google group.

[kbroman]

Another instance of this on the discussions group.