Skip to content

using apply with sparse matrix from package Matrix

1 message · Jennifer Lyon

Jennifer Lyon
# 
Hi:

I was trying to use apply on a sparse matrix from package Matrix,
and I get the error:

Error in asMethod(object) :
  Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 106

Is there a way to apply a function to all the rows without bumping
into this problem?

Here is a simplified example:
[1] 72913 43052
[1] "dgCMatrix"
attr(,"package")
[1] "Matrix"
Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  ..@ i       : int [1:6590004] 789 801 802 1231 1236 11739 17817
17943 18148 18676 ...
  ..@ p       : int [1:43053] 0 147 303 450 596 751 908 1053 1188 1347 ...
  ..@ Dim     : int [1:2] 72913 43052
  ..@ Dimnames:List of 2
  .. ..$ : NULL
  .. ..$ : NULL
  ..@ x       : num [1:6590004] 0.601 0.527 0.562 0.641 0.684 ...
  ..@ factors : list()
Error in asMethod(object) :
  Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 106
R version 2.15.1 (2012-06-22)
Platform: x86_64-unknown-linux-gnu (64-bit)

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=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] Matrix_1.0-6   lattice_0.20-6 stringr_0.6.1

loaded via a namespace (and not attached):
[1] grid_2.15.1 plyr_1.7.1

Thanks.

Jen