From tomas.kalibera at gmail.com  Wed Apr 19 15:51:24 2017
From: tomas.kalibera at gmail.com (Tomas Kalibera)
Date: Wed, 19 Apr 2017 15:51:24 +0200
Subject: [Rd] Crash after (wrongly) applying product operator on S4
 object that derives from list
In-Reply-To: <CAOQ5NyeLwEU3vD1W-+615cXzFsY-S3yn4ccyV3BaDSUMOLT9og@mail.gmail.com>
References: <e3a03266-b7f3-d5df-6940-906f9bd41104@mpiib-berlin.mpg.de>
 <9c987df5-1852-56b6-3de5-89358aaffb0a@mpiib-berlin.mpg.de>
 <24e4a410-b5c2-c25a-f31f-3637de4d5b88@embl.de>
 <CAOQ5NyeLwEU3vD1W-+615cXzFsY-S3yn4ccyV3BaDSUMOLT9og@mail.gmail.com>
Message-ID: <bda4738f-92e8-6d30-b3d1-eaa151d0c861@gmail.com>


We're working on a workaround for the JVM issue, it should be available 
in rJava soon.
(the JVM issue is only on Linux and it turns infinite/deep recursion 
into a crash of R; it also effectively reduces the R stack size)

Best
Tomas

On 04/19/2017 02:56 PM, Michael Lawrence wrote:
> I think this is a known issue with Java messing with the stack, see
> e.g. http://r.789695.n4.nabble.com/Error-memory-exhausted-limit-reached-td4729708.html.
>
> I'll fix the infinite recursion caused by the methods package.
>
> Michael
>
> On Wed, Apr 19, 2017 at 1:12 AM, Wolfgang Huber <wolfgang.huber at embl.de> wrote:
>> Dear Hilmar
>>
>> Perhaps this gives an indication of why the infinite recursion happens:
>>
>> ## after calling `*` on ma and a matrix:
>>
>>> showMethods(classes=class(ma), includeDefs=TRUE, inherited = TRUE)
>>
>> Function: * (package base)
>> e1="FOOCLASS", e2="matrix"
>>      (inherited from: e1="vector", e2="structure")
>>      (definition from function "Ops")
>> function (e1, e2)
>> {
>>      value <- callGeneric(e1, e2 at .Data)
>>      if (length(value) == length(e2)) {
>>          e2 at .Data <- value
>>          e2
>>      }
>>      else value
>> }
>>
>>
>>
>>> is(ma, "vector")
>> [1] TRUE
>>
>> I got that in a fresh session of
>>> sessionInfo()
>> R Under development (unstable) (2017-04-18 r72542)
>> Platform: x86_64-apple-darwin16.5.0 (64-bit)
>> Running under: macOS Sierra 10.12.4
>>
>> Best wishes
>> Wolfgang
>>
>> 19.4.17 10:01, Hilmar Berger scripsit:
>>> 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
>>>>
>> ______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/r-devel
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[Rd] Crash after (wrongly) applying product operator on S4 object that derives from list
Tomas Kalibera