Segmentation Fault with Perf

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Issue #108 closed
Brannon Imamura created an issue

When running Perf, the program errors and closes out. The following is the code.

library(mixOmics)

print("reading")
x <- read.csv("GeneX.csv")
y <- read.csv("GeneY.csv")
print("Loaded")

# everything past this point will not work unless it is performed on a computer with more RAM

# PLS run with 6 components
tox6.pls <- pls(x,
y,
ncomp = 6,
mode = c("regression"),
scale = TRUE,
)

print("Running XValidation")
# Shows how much explanation each component adds
tune.pls <- perf(tox6.pls, validation = "Mfold", folds = 3, progressBar = FALSE, criterion = "all")

I will attach a Valgrind Dump

Comments (4)

  1. Florian Rohart

    Dear Brannon, Thanks for your message.

    What is your environment? Windows, Linux, Mac? Are you using Rstudio, Rgui? Are you running that on your machine, on a cluster? What is the size of your data?

    PS: it seems your segfault.txt was run on tox10.pls whereas your R code is tox6.pls, is there just a different number of components?

  2. Brannon Imamura reporter

    Sorry for the inconsistencies in my Valgrind vs the code I put in.

    I changed the name to tox6.pls from tox10.pls to better reflect that I was using 6 components instead of 10, but the rest of the code is identical.

    This was run on a Linux server, not a cluster. Data has 63 rows and 49,927 columns for a total size of 26,589KB.

    R platform:

    R version 3.4.1 (2017-06-30) -- "Single Candle" Copyright (C) 2017 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit)

  3. Brannon Imamura reporter

    This appears to work fine on a windows machine.

    We are going to run a memory check on the Linux machine to see if a bad stick of ram is the issue.

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