protect(): protection stack overflow

Published by onesixx on

Windows-specific ( not work for UNIX-like systems )

memory.limit(size=8000000)

Unix-like system

http://r.789695.n4.nabble.com/R-3-5-0-vector-memory-exhausted-error-on-readBin-td4750237.html

set the $R_MAX_VSIZE environmental variable prior to running RStudio 

https://stat.ethz.ch/R-manual/R-devel/library/base/html/Memory.html

Additionally, ‘–max-ppsize’ controls the maximum size of the protection stack

https://stackoverflow.com/questions/32826906/how-to-solve-protection-stack-overflow-issue-in-r-studio

via your .Rprofileor at runtime by using the options(expressions = 5e5) command.

options(expressions = 5e5)

For UNIX or Linux systems, we will want to set the $R_MAX_VSIZE environmental variable prior to running RStudio or R from the cli. See the following thread for more info on solving this problem:

https://www.researchgate.net/post/error_protect_protection_stack_overflow_in_R

> dd %>% dim
[1]    12 39319

to change the data from data.frame to matrix form.

==========================================================

You probably have to set –max-ppsize See http://stat.ethz.ch/R-manual/R-devel/library/base/html/Memory.html You’ll also find some discussions about this on StackOverflow. See http://stackoverflow.com/questions/28728774/how-to-set-max-ppsize-in-r for instance   ================================ ‘memory.limit’ function recommended by Maurizio may work for some users, but it is Windows-specific, and thus will not work for UNIX-like systems. For UNIX or Linux systems, we will want to set the $R_MAX_VSIZE environmental variable prior to running RStudio or R from the cli. See the following thread for more info on solving this problem:   http://r.789695.n4.nabble.com/R-3-5-0-vector-memory-exhausted-error-on-readBin-td4750237.html   Another option to for UNIX/Linux users to try when they get the protect error is the ‘options’ expressions setting, e.g.:   options(expressions = 5e5)   as recommended at the following URL:   https://stackoverflow.com/questions/32826906/how-to-solve-protection-stack-overflow-issue-in-r-studio   Additionally, ‘–max-ppsize’ controls the maximum size of the protection stack, as per the Memory entry in the manual, at the following URL:   https://stat.ethz.ch/R-manual/R-devel/library/base/html/Memory.html   ==================================================================================  

ranger(formula = NULL, data = NULL, num.trees = 500, mtry = NULL,
  importance = "none", write.forest = TRUE, probability = FALSE,
  min.node.size = NULL, replace = TRUE, sample.fraction = ifelse(replace,
  1, 0.632), case.weights = NULL, class.weights = NULL, splitrule = NULL,
  num.random.splits = 1, alpha = 0.5, minprop = 0.1,
  split.select.weights = NULL, always.split.variables = NULL,
  respect.unordered.factors = NULL, scale.permutation.importance = FALSE,
  keep.inbag = FALSE, holdout = FALSE, quantreg = FALSE,
  num.threads = NULL, save.memory = FALSE, verbose = TRUE, seed = NULL,
  dependent.variable.name = NULL, status.variable.name = NULL,
  classification = NULL)

Arguments

formula

Object of class formula or characterdescribing the model to fit. Interaction terms supported only for numerical variables.

data

Training data of class data.frame, matrix, dgCMatrix (Matrix) or gwaa.data(GenABEL).

Coercion of matrix to sparse matrix (dgCMatrix) and maintaining dimnames.

http://gallery.rcpp.org/articles/sparse-matrix-coercion/

https://github.com/imbs-hl/ranger/issues/135

library(ranger)
library(Matrix)
iris_sparse <- Matrix(data.matrix(iris), sparse = TRUE)
ranger(data = iris_sparse, dependent.variable.name = "Species", classification = TRUE)

Categories: R Basic

onesixx

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