Sorry, forgot to attach the session info:
sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-suse-linux-gnu (64-bit)
Running under: openSUSE Tumbleweed
Matrix products: default
BLAS: /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices
utils datasets
[8] methods base
other attached packages:
[1] GenomicRanges_1.32.2 GenomeInfoDb_1.16.0 IRanges_2.14.8
[4] S4Vectors_0.18.1 BiocGenerics_0.26.0 magrittr_1.5
loaded via a namespace (and not attached):
[1]
zlibbioc_1.26.0 compiler_3.5.0 XVector_0.20.0
[4] tools_3.5.0 GenomeInfoDbData_1.1.0 RCurl_1.95-
4.10
[7] yaml_2.1.19 bitops_1.0-6
-------- Forwarded Message --------
From: Jialin Ma <marl...@gmx.cn>
To: bioc-devel <bioc-devel@r-project.org>
Subject: Problem showing a GRanges with a meta data column of data
frame
Date: Tue, 15 May 2018 10:17:35 +0800
Mailer: Evolution 3.24.4
> Hi all,
>
> I recently upgraded R to 3.5 and use the new release of Bioconductor.
> The new version of S4Vectors seems to have problem showing a GRanges
> with a meta-data column of a data frame. One simplified example is:
>
> gr <- GRanges('chr2', IRanges(1, 11))
> gr$df <- data.frame(a = 32)
>
> rep(gr, 11) ## No error
>
> rep(gr, 12) ## Error when printing
> # GRanges object with 12 ranges and 1 metadata column:
> # Error in .Call2("vector_OR_factor_extract_ranges", x, start, width,
> PACKAGE = "S4Vectors") :
> # 'end' must be <= 'length(x)'
>
> Any help would be appreciated!
>
> Best regards,
> Jialin
>
>
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