[Bioc-devel] Error: node stack overflow
Hervé Pagès
hpages at fredhutch.org
Mon Apr 30 23:14:17 CEST 2018
Excellent! Are you planning to commit this to the 3.5 branch too?
In that case we'll wait a couple more days before installing R 3.5
patched on the build machines for the BioC 3.8 builds.
Thanks,
H.
On 04/30/2018 01:43 PM, Michael Lawrence wrote:
> It's checked into devel now. Thanks for the well documented examples, Hervé.
>
> On Mon, Apr 30, 2018 at 10:26 AM, Michael Lawrence <michafla at gene.com> wrote:
>> I've fixed it and will push to R-devel as soon as it passes checks.
>>
>> Michael
>>
>> On Sun, Apr 29, 2018 at 9:04 PM, Michael Lawrence <michafla at gene.com> wrote:
>>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_uniqueGeneric&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=hI6LWw_u7csv2YoouDZz4PmV3GnTtE0movmB_pZuog8&s=5UWyuXnFrW3P7eeuT0jq8O9gi7BOreYKUmZ0LdDpJ3M&e=
>>>>
>>>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=hI6LWw_u7csv2YoouDZz4PmV3GnTtE0movmB_pZuog8&s=NJsCdpN9A1bsrpPUJSfAS8wTz1sXycGRPlBKr4-2M0E&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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