[Bioc-devel] BiocGenerics::unique Bug? "Error: node stack overflow" in package esATAC

Zheng Wei wei-z14 at mails.tsinghua.edu.cn
Mon Apr 2 13:55:39 CEST 2018

Dear all,

I am a maintainer of package 'esATAC'.

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

This error makes esATAC under bioc_3_7 check error because esATAC has to import rJava.

The error reproduce-able code and session information is pasted below. 


R Under development (unstable) (2018-03-12 r74392) -- "Unsuffered Consequences"
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> 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, parLapply,
    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, colMeans,
    colnames, colSums, dirname, do.call, duplicated, eval, evalq,
    Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
    lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
    rowSums, sapply, setdiff, sort, table, tapply, union, unique,
    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
> sessionInfo()
R Under development (unstable) (2018-03-12 r74392)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.2 (Maipo)

Matrix products: default
BLAS: /home/software/R/R-devel/lib64/R/lib/libRblas.so
LAPACK: /home/software/R/R-devel/lib64/R/lib/libRlapack.so

 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C             
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8    
 [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8   
 [7] LC_PAPER=en_US.utf8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           

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          

loaded via a namespace (and not attached):
[1] zlibbioc_1.25.0        compiler_3.5.0         XVector_0.19.9        
[4] GenomeInfoDbData_1.1.0 RCurl_1.95-4.10        bitops_1.0-6   
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