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Error: cause segfault, cause 'invalid permissions'

Open xxxcha opened this issue 4 years ago • 0 comments

Hi, I am using MAGIC to impute my matrix, and I run the command below (here data is my sparse matrix)

data_magic<-magic(data,genes="all_genes",t=4,init=data)

and I encounter the error like this:

Calculating MAGIC...
  Running MAGIC on 10062 cells and 136420 genes.
  Calculating graph and diffusion operator...
    Calculating PCA...
    Calculated PCA in 69.89 seconds.
    Calculating KNN search...
    Calculated KNN search in 20.17 seconds.
    Calculating affinities...
    Calculated affinities in 19.13 seconds.
  Calculated graph and diffusion operator in 109.22 seconds.
  Running MAGIC with `solver='exact'` on 136420-dimensional data may take a long time. Consider denoising specific genes with `genes=<list-like>` or using `solver='approximate'`.
  Calculating imputation...

 *** caught segfault ***
address 0x7fbcf5e62000, cause 'invalid permissions'

Traceback:
 1: py_call_impl(callable, dots$args, dots$keywords)
 2: operator$fit_transform(data, genes = genes, t_max = t.max)
 3: magic.default(data, genes = "all_genes", t = 4, init = data)
 4: magic(data, genes = "all_genes", t = 4, init = data)

So what is the problem and how can I solve it? Thank you a lot in advance!

xxxcha avatar Aug 17 '21 16:08 xxxcha