'problem too large' error

KrishnaswamyLab / MAGIC

MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.

GNU General Public License v2.0

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'problem too large' error #105

Closed lzj1769 closed 6 years ago

lzj1769 commented 6 years ago

Hi,

I run MAGIC successfully on a small dataset, but when I try to use it on a large dataset, I got the error:

Warning message: package ‘Matrix’ was built under R version 3.4.4 Warning message: package ‘Rmagic’ was built under R version 3.4.3 Error in asMethod(object) : Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 105 Calls: run_magic ... as.matrix -> as.matrix.Matrix -> as -> asMethod -> .Call Execution halted

chlee-tabin commented 6 years ago

Sometimes I had issues similar to this when the row and column was transposed (it is different from some popular scRNAseq defaults).

danieldager commented 6 years ago

Hi all,

There's a good chance that these problems were resolved with the release of MAGIC v1.0. Uninstall your current version of MAGIC and reinstall per the directions of the new README. I'm closing this for now; please feel free to open a new issue if you still have problems!