From berger at mpiib-berlin.mpg.de  Wed Apr 19 10:01:37 2017
From: berger at mpiib-berlin.mpg.de (Hilmar Berger)
Date: Wed, 19 Apr 2017 10:01:37 +0200
Subject: [Rd] Crash after (wrongly) applying product operator on object
 from LIMMA package
In-Reply-To: <e3a03266-b7f3-d5df-6940-906f9bd41104@mpiib-berlin.mpg.de>
References: <e3a03266-b7f3-d5df-6940-906f9bd41104@mpiib-berlin.mpg.de>
Message-ID: <9c987df5-1852-56b6-3de5-89358aaffb0a@mpiib-berlin.mpg.de>

Hi,

following up on my own question, I found smaller example that does not 
require LIMMA:

setClass("FOOCLASS",
          representation("list")
)
ma = new("FOOCLASS", list(M=matrix(rnorm(300), 30,10)))

 > ma * ma$M
Error: C stack usage  7970512 is too close to the limit

 > library(xlsx)
Loading required package: rJava
Loading required package: xlsxjars
 > ma * ma$M
---> Crash

xlsx seems to act like a catalyst here, with the product operator 
running in a deep nested iteration, exhausting the stack. Valgrind shows 
thousands of invalid stack accesses when loading xslx, which might 
contribute to the problem. Package xlsx has not been updated since 2014, 
so it might fail with more current versions of R or Java (I'm using 
Oracle Java 8).

Still, even if xlsx was the package to be blamed for the crash, I fail 
to understand what exactly the product operator is trying to do in the 
multiplication of the matrix with the object.

Best regards,
Hilmar

On 18/04/17 18:57, Hilmar Berger wrote:
> 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$M has the same effect
> ---------------------------------
>
> My output:
>
> R version 3.3.0 (2016-05-03) -- "Supposedly Educational"
> Copyright (C) 2016 The R Foundation for Statistical Computing
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
>   Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
> > library(limma)
> > library(xlsx)
> Loading required package: rJava
> Loading required package: xlsxjars
> >
> > sessionInfo()
> R version 3.3.0 (2016-05-03)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 14.04.5 LTS
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8          LC_NUMERIC=C LC_TIME=en_US.UTF-8
>  [4] LC_COLLATE=en_US.UTF-8        LC_MONETARY=en_US.UTF-8 
> LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8          LC_NAME=en_US.UTF-8 
> LC_ADDRESS=en_US.UTF-8
> [10] LC_TELEPHONE=en_US.UTF-8      LC_MEASUREMENT=en_US.UTF-8 
> LC_IDENTIFICATION=en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods base
>
> other attached packages:
> [1] xlsx_0.5.7     xlsxjars_0.6.1 rJava_0.9-8    limma_3.30.7
>
> loaded via a namespace (and not attached):
> [1] tools_3.3.0
> >
> > ma = new("MAList", list(A=matrix(rnorm(300), 30,10), 
> M=matrix(rnorm(300), 30,10)))
> > #sweep(ma, 2, c(1:10), "*")
> >
> > f = match.fun("*")
> > f
> function (e1, e2)  .Primitive("*")
>
> > f(ma, ma$M)
>
> ----> crash to command line with segfault.
>
> Best regards,
> Hilmar
>

-- 
Dr. Hilmar Berger, MD
Max Planck Institute for Infection Biology
Charit?platz 1
D-10117 Berlin
GERMANY

Phone:  + 49 30 28460 430
Fax:    + 49 30 28460 401
  
E-Mail: berger at mpiib-berlin.mpg.de
Web   : www.mpiib-berlin.mpg.de



[Rd] Crash after (wrongly) applying product operator on object from LIMMA package
Hilmar Berger