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> 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 > Fax: + 49 30 28460 401 > E-Mail: ber...@mpiib-berlin.mpg.de > Web : www.mpiib-berlin.mpg.de > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- -------- January Weiner -------------------------------------- [[alternative HTML version deleted]] ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
