Error: C stack usage is too close to the limit

[vkartha]

Hi there, thanks for developing this package.

I'm running into the following error when running the object initialization step:

sceptre_object <- import_data(
  response_matrix = rnaMat,
  grna_matrix = gRNAMat,
  grna_target_data_frame = grna_target_data_frame,
  moi = "low",
  extra_covariates = extra_covariates,
  response_names = rownames(rnaMat))

Error: C stack usage 9612268 is too close to the limit

I get this error regardless of using the ondisc option or not

Some searching suggests this has to do with function recursion, but I was wondering if there's a fix? All my input variables are in the right format as far as I checked (both matrices are sparse matrices and the rest are data frames with relevant metadata)

Thanks in advance

[timothy-barry]

Hi,

How big is your rnaMat? In particular, how many rows, columns, and nonzero entries does it have? Also, what is its class? You can determine this via class(rnaMat).

Tim

[vkartha]

Hey! rnaMat is a sparse Matrix format object that has ~27k genes, and ~92k cells. ~10% of the entries are non zero

Output below:

> class(rnaMat)
[1] "dgCMatrix"
attr(,"package")
[1] "Matrix"

> dim(rnaMat)
[1] 27743 92104

> sum(rnaMat!=0)
[1] 278826597

[timothy-barry]

Hi Vinay,

Thanks for the info. That matrix should be well within the limits of what the standard R console interface to sceptre can handle. My hunch is that something might be a bit off with the input argument formatting. Would you be able to send me your data so that I can take a look? (Of course, we will keep the data confidential and delete the data after we resolve the bug.) You could send me a list (in .rds format) containing response_matrix, grna_matrix, grna_target_data_frame, moi, extra_covariates, and response_names. My email is tbarry@hsph.harvard.edu.

[timothy-barry]

Closing due to inactivity. Please let me know if you need further assistance.