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 usage 7969864 is
too close to the limit*
*Error during wrapup: C stack usage 7969656 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] parallel stats4 stats graphics
grDevices 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_0.6.15 rprojroot_1.3-2 [4]
bitops_1.0-6 backports_1.1.2 magrittr_1.5 [7]
evaluate_0.10.1 zlibbioc_1.25.0 stringi_1.1.7 [10]
XVector_0.19.9 tools_3.5.0 stringr_1.3.0 [13]
RCurl_1.95-4.10 compiler_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 <hpa...@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, 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: hpa...@fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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