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" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > 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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel