From january.weiner at gmail.com  Mon Apr 24 11:46:35 2017
From: january.weiner at gmail.com (January W.)
Date: Mon, 24 Apr 2017 11:46:35 +0200
Subject: [Rd] Crash after (wrongly) applying product operator on object
 from LIMMA package
In-Reply-To: <9c987df5-1852-56b6-3de5-89358aaffb0a@mpiib-berlin.mpg.de>
References: <e3a03266-b7f3-d5df-6940-906f9bd41104@mpiib-berlin.mpg.de>
 <9c987df5-1852-56b6-3de5-89358aaffb0a@mpiib-berlin.mpg.de>
Message-ID: <CA+A1kV6sNGsNW1-ULZ7-uDOq_M91zr7aJKX4aRaeogfGe_SSPw@mail.gmail.com>

Hi Hilmar,

weird. The memory problem seems be due to recursion (my R, version 3.3.3,
says: Error: evaluation nested too deeply: infinite recursion /
options(expressions=)?, just write traceback() to see how it happens), but
why does it segfault with xlsx? Nb xlsx is the culprit: neither rJava nor
xlsxjars cause the problem.

On the other hand, quick googling for r+xlsx+segfault returns tons of
reports of how xlsx crashes in dozens of situations. See for example
http://r.789695.n4.nabble.com/segfault-in-gplots-heatmap-2-td4641808.html.
Also, the problem might be platform-specific. It would be interesting to
see whether anyone with a Mac can reproduce it.

kind regards,

j.





On 19 April 2017 at 10:01, Hilmar Berger <berger at mpiib-berlin.mpg.de> wrote:

> 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
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>



-- 
-------- January Weiner --------------------------------------

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[Rd] Crash after (wrongly) applying product operator on object from LIMMA package
January W.