[Bioc-devel] Error: node stack overflow
Michael Lawrence
lawrence.michael at gene.com
Mon Apr 30 06:04:41 CEST 2018
Just noticed this thread. I will look into this and hopefully fix it.
On Sun, Apr 29, 2018 at 6:12 PM, Hervé Pagès <hpages at fredhutch.org> wrote:
> 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
>>>
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=b4YM1TCcJjPge2siQJS5BQv7g1DMkoCQ-7FvZz89w-E&s=JNrsjIF-swIGjCJUiljVcp0KYi42-z3NNryBT3EZmSg&e=
>>>
>>> <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
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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