Hi,
this is a problem that occurs in the presence of two libraries (limma,
xlsx) and leads to a crash of R. The problematic code is the wrong
application of sweep or the product ("*") function on an LIMMA MAList
object. To my knowledge, limma does not define a "*" method for MAList
objects.
If only LIMMA is loaded but not package xlsx, the code does not crash
but rather produces an error ("Error: C stack usage 7970512 is too
close to the limit"). Loading only package rJava instead of xlsx does
also not produce the crash but the error message instead. Note that
xlsx functions are not explicitly used.
It could be reproduced on two different Linux machines running
R-3.2.5, R-3.3.0 and R-3.3.2.
Code to reproduce the problem:
---------------------------------
library(limma)
library(xlsx)
# a MAList
ma = new("MAList", list(A=matrix(rnorm(300), 30,10),
M=matrix(rnorm(300), 30,10)))
# This should actually be sweep(ma$M, ...) for functional code, but I
omitted the $M...
#sweep(ma, 2, c(1:10), "*")
# sweep will crash when doing the final operation of applying the
function over the input matrix, which in this case is function "*"
f = match.fun("*")
# This is not exactly the same as in sweep but it also tries to
multiply the MAList object with a matrix of same size and leads to the
crash
f(ma, ma$M)
# ma * ma$M has the same effect
---------------------------------
My output:
R version 3.3.0 (2016-05-03) -- "Supposedly Educational"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
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'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
library(limma)
library(xlsx)
Loading required package: rJava
Loading required package: xlsxjars
sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8
LC_ADDRESS=en_US.UTF-8
[10] LC_TELEPHONE=en_US.UTF-8 LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] xlsx_0.5.7 xlsxjars_0.6.1 rJava_0.9-8 limma_3.30.7
loaded via a namespace (and not attached):
[1] tools_3.3.0
ma = new("MAList", list(A=matrix(rnorm(300), 30,10),
M=matrix(rnorm(300), 30,10)))
#sweep(ma, 2, c(1:10), "*")
f = match.fun("*")
f
function (e1, e2) .Primitive("*")
f(ma, ma$M)
----> crash to command line with segfault.
Best regards,
Hilmar
