R help - Jun 2017 - getting error while trying to make dendogram based on gene expression

I am trying to make dendogram based on gene expression matrix , but getting
some error:

I
countMatrix =
read.table("count.row.txt",header=T,sep='\t',check.names=F)

colnames(countMatrix)

count_matrix <- countMatrix[,-1]                   #  remove first column
(gene names)
rownames(count_matrix) <- countMatrix[,1]     #added first column gene
names as rownames)
> nonzero_row <- count_matrix[rowSums(count_matrix) > 0, # removed row
sum
0 across all sample
> x1= as.matrix(nonzero_row)                    # converted data into matrix
> x=log2(x1+1)                                          # converted into
log value
> d <- dist(x, method="euclidean")
> h <- hclust(d, method="complete")

*Error:*

 *** caught segfault ***
address 0x7fa39060af28, cause 'memory not mapped'

Traceback:
 1: hclust(d, method = "complete")

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:

Thanks
Yogesh

	[[alternative HTML version deleted]]

>>>>> Yogesh Gupta <yogesh2cute at gmail.com>
>>>>>     on Wed, 21 Jun 2017 13:42:15 +0900 writes:
    > I am trying to make dendogram based on gene expression matrix , but
getting
    > some error:

    > I
    > countMatrix =
read.table("count.row.txt",header=T,sep='\t',check.names=F)

    > colnames(countMatrix)

    > count_matrix <- countMatrix[,-1]                   #  remove first
column
    > (gene names)
    > rownames(count_matrix) <- countMatrix[,1]     #added first column
gene
    > names as rownames)

    >> nonzero_row <- count_matrix[rowSums(count_matrix) > 0, #
removed row sum
    > 0 across all sample

    >> x1= as.matrix(nonzero_row)                    # converted data into
matrix

    >> x=log2(x1+1)                                          # converted
into
    > log value
    >> d <- dist(x, method="euclidean")

    >> h <- hclust(d, method="complete")


    > *Error:*

    > *** caught segfault ***
    > address 0x7fa39060af28, cause 'memory not mapped'

    > Traceback:
    > 1: hclust(d, method = "complete")

    > Possible actions:
    > 1: abort (with core dump, if enabled)
    > 2: normal R exit
    > 3: exit R without saving workspace
    > 4: exit R saving workspace
    > Selection:

This looks like a problem that should not happen.
Though it could be that it's just too large a problem (for your
hardware, or "in general").
However, we cannot reproduce what you show above.

To help us help you please provide (to this mailing list!)

   - a (minimal) reproducible example
   - sessionInfo()

It is best to take time to carefully read
   https://www.r-proejct.org/help.html

and/or then just search "reproducible example R" :
       http://lmgtfy.com/?q=reproducible+example+R

Martin


    > Thanks
    > Yogesh