bi.clique function not working

[dpuelz]

hey there,

I attempted to run a simple example of bi.clique in R, but there was a segmentation fault and the R session aborted. Code is below. Please help!

testing biclique package

library(biclique) library(Matrix) library(filematrix)

the.mat = Matrix(0,10,10) the.mat[1,2] = the.mat[2,1] = 1 the.mat = as.matrix(the.mat) fm.create.from.matrix('mat.bmat',mat=the.mat) write bi.clique('mat.bmat',filetype=1)

Thanks! David

[YupingLu]

Hi David,

I just checked your code. Your mat.bmat file has no number of vertices. You can check the example bmat format which will work with biclique here https://github.com/YupingLu/biclique/blob/master/inst/extdata/example4.bmat.

Thanks,

Yuping

[dpuelz]

Ok, great! Thanks for the help!

On Nov 16, 2018, at 1:16 PM, Yuping Lu notifications@github.com wrote:

Hi David,

I just checked your code. Your mat.bmat file has no number of vertices. You can check the example bmat format which will work with biclique here https://github.com/YupingLu/biclique/blob/master/inst/extdata/example4.bmat https://github.com/YupingLu/biclique/blob/master/inst/extdata/example4.bmat.

Thanks,

Yuping

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[dpuelz]

Hi Yuping,

One follow up issue. The function works for small dimensions but crashes R when the number of nodes gets large, see the example code below. If num1 = 200 and num2 =50, everything works .. if num1 = 3000 and num2 =2000, the function crashes. Any thoughts on what might be the issue?

@ptoulis has the same issue.

Thanks! David

testing biclique package

library(biclique) num1 = 200 num2 = 50 the.mat = matrix('',num1+2,num2+1) the.mat[3:22,2:11] = 0 the.mat[3,11] = 1 the.mat[3,10] = 1 the.mat[4,11] = 1 the.mat[4,10] = 1 the.mat[15,7] = 1 the.mat[1,1:2] = c(num1,num2) the.mat[2,1:num2] = paste('u',1:num2,sep='') the.mat[3:(num1+2),1] = paste('v',1:num1,sep='') write.table(noquote(the.mat),file='themat.bmat',row.names=F,col.names=F,quote=F) test=bi.clique('themat.bmat',filetype=1) test$biclique2