[Bioc-devel] BiocGenerics::unique Bug? Error: node stack overflow

魏征 wei-z14 at mails.tsinghua.edu.cn
Mon Apr 2 13:06:41 CEST 2018

Dear all,

I am a maintainer of package 'esATAC'

I find this error if calling library(rJava) before using BiocGenerics::unique

The code is pasted below. 


> 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’:


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
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