[Bioc-devel] Error: node stack overflow
Hervé Pagès
hpages at fredhutch.org
Mon Apr 30 03:12:44 CEST 2018
Hi,
I made progress on this. This has actually nothing to do with Java.
You get the same thing with the flexmix package. What rJava and flexmix
have in common is that they both define a method on the base::unique()
implicit S4 generic.
The issue actually originates in the methods package. In order to remove
rJava, BiocGenerics and IRanges from the equation, I made 2 minimalist
packages, uniqueMethod and uniqueGeneric, that can be used to reproduce
the issue. See:
https://github.com/Bioconductor/uniqueGeneric
I committed a workaround in S4Vectors (0.17.44). With this version of
S4Vectors:
library(rJava)
library(IRanges)
unique(IRanges())
# IRanges object with 0 ranges and 0 metadata columns:
# start end width
# <integer> <integer> <integer>
Let me know if you still run into problems with this.
Cheers,
H.
> sessionInfo()
R Under development (unstable) (2018-02-26 r74306)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS
Matrix products: default
BLAS: /home/hpages/R/R-3.5.r74306/lib/libRblas.so
LAPACK: /home/hpages/R/R-3.5.r74306/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] IRanges_2.13.29 S4Vectors_0.17.44 BiocGenerics_0.25.3
[4] rJava_0.9-9
loaded via a namespace (and not attached):
[1] compiler_3.5.0
On 04/14/2018 03:11 AM, Hervé Pagès wrote:
> Hi Zheng,
>
> I can totally reproduce this on my Ubuntu laptop:
>
> library(rJava)
> library(IRanges)
> unique(IRanges())
> # Error in validObject(.Object) :
> # invalid class “MethodWithNext” object: Error : C stack usage
> 7969396 is too close to the limit
>
> See my seesionInfo() at the end of this email.
>
> Probably related to this (but not 100% sure) loading rJava seems
> to break selectMethod().
>
> More precisely: The rJava package defines some "unique" S4 methods
> and the BiocGenerics package defines (and exports) the unique() S4
> generic with the following statement:
>
> setGeneric("unique", signature="x")
>
> Here is what happens when loading the rJava package first:
>
> library(rJava)
> library(BiocGenerics)
>
> setClass("A", slots=c(a="integer"))
> setMethod("unique", "A",
> function(x, incomparables=FALSE, ...) {x at a <- unique(x at a); x}
> )
>
> selectMethod("unique", "A")
> # Method Definition (Class "derivedDefaultMethod"):
> #
> # function (x, incomparables = FALSE, ...)
> # UseMethod("unique")
> # <bytecode: 0x4127140>
> # <environment: namespace:base>
> #
> # Signatures:
> # x
> # target "A"
> # defined "ANY"
>
> selectMethod() doesn't find the method for A objects!
>
> It seems that selectMethod() is looking in the method table for
> the implicit unique() generic defined in rJava instead of the
> explicit unique() generic defined in BiocGenerics. If we tell
> selectMethod() which generic to consider, then it finds the method
> for A objects:
>
> selectMethod(BiocGenerics::unique, "A")
> # Method Definition:
> #
> # function (x, incomparables = FALSE, ...)
> # {
> # x at a <- unique(x at a)
> # x
> # }
> #
> # Signatures:
> # x
> # target "A"
> # defined "A"
>
> In order to reproduce the above problem without the BiocGenerics
> package in the equation, it's not enough to do:
>
> library(rJava)
> setGeneric("unique", signature="x")
> etc...
>
> The setGeneric("unique", signature="x") statement must be put in
> a package. I've created a minimalist package on GitHub that just
> wraps this statement:
>
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_uniqueGeneric&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=b4YM1TCcJjPge2siQJS5BQv7g1DMkoCQ-7FvZz89w-E&s=P9-WHLV4FmY9PQcNjkZ4Cgc24Oi1QTNVBqTaQ1iS-kg&e=
>
>
> This package can be used instead of BiocGenerics to reproduce the
> problem above.
>
> I'm not 100% sure that this problem is related to the issue you
> reported originally but it seems very likely to me.
>
> Not quite sure what the next step should be. I've been told by
> some R core developers that there are known interaction issues
> between Java, rJava and R that are currently being worked on.
> Someone should ask on the R-devel mailing list or directly to
> Simon Urbanek, the rJava author, for more information about this.
>
> H.
>
> > sessionInfo()
> R Under development (unstable) (2018-02-26 r74306)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 16.04.4 LTS
>
> Matrix products: default
> BLAS: /home/hpages/R/R-3.5.r74306/lib/libRblas.so
> LAPACK: /home/hpages/R/R-3.5.r74306/lib/libRlapack.so
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] BiocGenerics_0.25.3 rJava_0.9-9
>
> loaded via a namespace (and not attached):
> [1] compiler_3.5.0 parallel_3.5.0
>
>
> On 04/02/2018 11:47 AM, Vincent Carey wrote:
>> I get the following on MacOSX, after library(rJava);
>> library(GenomicRanges) -- take rJava out of the mix and
>> there is no error. I ran into this originally as an interaction
>> between rJava and Gviz, and have reported to
>> Florian. That seemed to be MacOSX-specific.
>>
>>> gr1 <- GRanges(seqnames=Rle(c("ch1", "chMT"), c(2, 4)),
>>
>> +ranges=IRanges(16:21, 20),
>>
>> +strand=rep(c("+", "-", "*"), 2))
>>
>>> unique(gr1)
>>
>> *Error in validObject(.Object) :*
>>
>> *invalid class "MethodWithNext" object: Error : C stack usage7969864
>> is too close to the limit*
>>
>> *Error during wrapup: C stack usage7969656 is too close to the limit*
>>
>> *
>> *
>>
>> **
>>
>> *> sessionInfo()*
>>
>> *
>>
>> R Under development (unstable) (2018-02-14 r74250)
>>
>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>>
>> Running under: macOS Sierra 10.12.6
>>
>>
>> Matrix products: default
>>
>> BLAS:
>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
>>
>>
>> LAPACK:
>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
>>
>>
>>
>> locale:
>>
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>>
>> attached base packages:
>>
>> [1] parallelstats4stats graphicsgrDevices utils datasets
>>
>> [8] methods base
>>
>>
>> other attached packages:
>>
>> [1] GenomicRanges_1.31.23 GenomeInfoDb_1.15.5 IRanges_2.13.28
>>
>> [4] S4Vectors_0.17.38 BiocGenerics_0.25.3 rJava_0.9-9
>>
>> [7] rmarkdown_1.9
>>
>>
>> loaded via a namespace (and not attached):
>>
>> [1] Rcpp_0.12.16 digest_0.6.15rprojroot_1.3-2
>>
>> [4] bitops_1.0-6 backports_1.1.2magrittr_1.5
>>
>> [7] evaluate_0.10.1zlibbioc_1.25.0stringi_1.1.7
>>
>> [10] XVector_0.19.9 tools_3.5.0stringr_1.3.0
>>
>> [13] RCurl_1.95-4.10compiler_3.5.0 htmltools_0.3.6
>>
>> [16] knitr_1.20 GenomeInfoDbData_1.1.0
>>
>>
>> *
>>
>>
>>
>> On Mon, Apr 2, 2018 at 2:25 PM, Hervé Pagès <hpages at fredhutch.org
>> <mailto:hpages at fredhutch.org>> wrote:
>>
>> Hi Zheng,
>>
>> Thanks for the report. I will look into this and will let you know.
>>
>> H.
>>
>> On 04/01/2018 02:38 AM, Zheng Wei wrote:
>>
>> Dear all,
>>
>> I find this error if calling library(rJava) before using
>> BiocGenerics::unique
>>
>> The code is pasted below.
>>
>> Thanks,
>> Zheng
>>
>> > library(rJava)
>> > library(GenomicRanges)
>> Loading required package: stats4
>> Loading required package: BiocGenerics
>> Loading required package: parallel
>>
>> Attaching package: ‘BiocGenerics’
>>
>> The following objects are masked from ‘package:parallel’:
>>
>> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ
>> clusterExport, clusterMap, parApply, parCapply, parLapp
>> parLapplyLB, parRapply, parSapply, parSapplyLB
>>
>> The following objects are masked from ‘package:rJava’:
>>
>> anyDuplicated, duplicated, sort, unique
>>
>> The following objects are masked from ‘package:stats’:
>>
>> IQR, mad, sd, var, xtabs
>>
>> The following objects are masked from ‘package:base’:
>>
>> anyDuplicated, append, as.data.frame, basename, cbind,
>> colnames, colSums, dirname, do.call, duplicated, eval,
>> Filter, Find, get, grep, grepl, intersect, is.unsorted,
>> lengths, Map, mapply, match, mget, order, paste, pmax,
>> pmin, pmin.int
>>
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__pmin.int&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=WuplCAfYBn5Cq3N946mtZUi0612IchE0DfGaLDRFWTg&s=Km1Jhe0uxvMMuNveRSNtoTyFaOBZRO2jL8kmCFQd8Ec&e=>,
>>
>> Position, rank, rbind, Reduce, rowMeans
>> rowSums, sapply, setdiff, sort, table, tapply, union, u
>> unsplit, which, which.max, which.min
>>
>> Loading required package: S4Vectors
>>
>>
>> Attaching package: ‘S4Vectors’
>>
>> The following object is masked from ‘package:base’:
>>
>> expand.grid
>>
>> Loading required package: IRanges
>> Loading required package: GenomeInfoDb
>> > gr1 <- GRanges(seqnames=Rle(c("ch1", "chMT"), c(2, 4)),
>> + ranges=IRanges(16:21, 20),
>> + strand=rep(c("+", "-", "*"), 2))
>> > unique(gr1)
>> Error: node stack overflow
>> > BiocGenerics::unique(gr1)
>> Error: node stack overflow
>>
>>
>>
>> -- Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpages at fredhutch.org <mailto:hpages at fredhutch.org>
>> Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>> Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>>
>> _______________________________________________
>> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org> mailing
>> list
>>
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>>
>>
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=WuplCAfYBn5Cq3N946mtZUi0612IchE0DfGaLDRFWTg&s=Lw0PlsxUz2dbA2mDa_e4vZrNZ2FfjaNNQ-abMHuIMNY&e=>
>>
>>
>>
>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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