From berger at mpiib-berlin.mpg.de  Tue Apr 18 18:57:08 2017
From: berger at mpiib-berlin.mpg.de (Hilmar Berger)
Date: Tue, 18 Apr 2017 18:57:08 +0200
Subject: [Rd] Crash after (wrongly) applying product operator on object from
 LIMMA package
Message-ID: <e3a03266-b7f3-d5df-6940-906f9bd41104@mpiib-berlin.mpg.de>

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