Message-ID: <79d5d56f-8313-499c-bc8d-7d76d7bd947f@fredhutch.org>
Date: 2018-04-02T18:25:28Z
From: Hervé Pagès
Subject: [Bioc-devel] Error: node stack overflow
In-Reply-To: <tencent_65AE734E16F9B95D79982FA7B5B050977E08@qq.com>
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
>
>
--
Herv? Pag?s
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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P.O. Box 19024
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