[Bioc-devel] Error: node stack overflow

I just pushed it to the 3.5 branch.

On Mon, Apr 30, 2018 at 2:14 PM, Herv? Pag?s <hpages at fredhutch.org> wrote:

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,
Herv?.

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, Herv? Pag?s <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, Herv? Pag?s 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, Herv? Pag?s <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



      --     Herv? Pag?s

      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>

--
Herv? Pag?s

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

--
Herv? Pag?s

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