I am using the magic for loop but i don't think its the code as it is working for my work laptop fine - it just keeps stalling on my personal laptop. The loop is pretty long....

library(data.table)
library(magicfor)
library(pROC)
setwd("C:/Users/*******")
base<-fread("******", header=T, data.table=F)
target<-fread("*******", header=F, data.table=F)

base$Pvalue<-as.numeric(base$Pvalue) 
magic_for(print, silent=T)
for(i in seq(0.00000005, 0.5, 0.000005)){
Threshold<-i
print(Threshold)
snps<-base[base$Pvalue<=Threshold, ]
Total.SNPs<-nrow(snps)
print(Total.SNPs)
a<-which(snps$MarkerName %in% target$V2)
Common.SNPS<-length(a)
print(Common.SNPS)
training<-base[a, ]
test<-nrow(training)
print(test)
write.table(training[,c(3,4,6)], "training.score", col.names=F, row.names=F, quote=F, sep="\t")
command<-sprintf("/Users/*********/plink --bfile NeuroChipAPOE --score training.score --out prs")
system(command)
prs<-fread("prs.profile", header=T, data.table=F)
prs$SCORE<-as.numeric(prs$SCORE)
prs$PHENO<-as.numeric(prs$PHENO)
score<-prs$SCORE
case<-prs$PHENO-1
glm<-glm(case~score, family=binomial)
P.value<-coef(summary(glm))[2,4]
print(P.value)
}

summary<- magic_result_as_dataframe()
write.table(summary, "Summary.txt", col.names=T, row.names=F, quote=F, sep="\t")