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 <ber...@mpiib-berlin.mpg.de
<mailto:ber...@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
Charitéplatz 1
D-10117 Berlin
GERMANY
Phone: + 49 30 28460 430 <tel:%2B%2049%2030%2028460%20430>
Fax: + 49 30 28460 401 <tel:%2B%2049%2030%2028460%20401>
E-Mail: ber...@mpiib-berlin.mpg.de
<mailto:ber...@mpiib-berlin.mpg.de>
Web : www.mpiib-berlin.mpg.de <http://www.mpiib-berlin.mpg.de>
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