[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.
Thanks,
Zheng
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’:
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
> 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
locale:
[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
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=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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