R devel - Apr 2017 - Crash after (wrongly) applying product operator on object from LIMMA package

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

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

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
>>
>

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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