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??:
?0?2 ?0?2 clusterApply, clusterApplyLB, clusterCall, clusterEvalQ
?0?2 ?0?2 clusterExport, clusterMap, parApply, parCapply, parLapp
?0?2 ?0?2 parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ??package:rJava??:
?0?2 ?0?2 anyDuplicated, duplicated, sort, unique
The following objects are masked from ??package:stats??:
?0?2 ?0?2 IQR, mad, sd, var, xtabs
The following objects are masked from ??package:base??:
?0?2 ?0?2 anyDuplicated, append, as.data.frame, basename, cbind,
?0?2 ?0?2 colnames, colSums, dirname, do.call, duplicated, eval,
?0?2 ?0?2 Filter, Find, get, grep, grepl, intersect, is.unsorted,
?0?2 ?0?2 lengths, Map, mapply, match, mget, order, paste, pmax,
?0?2 ?0?2 pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans
?0?2 ?0?2 rowSums, sapply, setdiff, sort, table, tapply, union, u
?0?2 ?0?2 unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: ??S4Vectors??
The following object is masked from ??package:base??:
?0?2 ?0?2 expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
> gr1 <- GRanges(seqnames=Rle(c("ch1", "chMT"), c(2, 4)),
+?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ranges=IRanges(16:21, 20),
+?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 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
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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