[Bioc-devel] Error: node stack overflow

[Hervé Pagès]

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
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