Crash after (wrongly) applying product operator on S4 object that derives from list

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