[Bioc-devel] IRanges should support long vectors

[Pariksheet Nanda]

Hello,

R 3.0 added support for long vectors, but it's not yet possible to use them
with IRanges.  Without long vector support it's not possible to construct
an IRanges object with more than 2^31 elements:


> ir <- IRanges(start = 1:(2^31 - 1), width = 1)
> ir <- IRanges(start = 1:2^31, width = 1)
Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
:
  long vectors not supported yet: memory.c:3715
In addition: Warning message:
In .normargSEW0(start, "start") :
  NAs introduced by coercion to integer range
>


This is true when using the latest version from GitHub


> BiocManager::install("Bioconductor/IRanges")
> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.7 (Santiago)

Matrix products: default
BLAS:
/home/pan14001/spack/opt/spack/linux-rhel6-x86_64/gcc-7.4.0/r-3.6.0-r7m53dthhqtxyrrdghjuiw2otasowvbl/rlib/R/lib/libRblas.so
LAPACK:
/home/pan14001/spack/opt/spack/linux-rhel6-x86_64/gcc-7.4.0/r-3.6.0-r7m53dthhqtxyrrdghjuiw2otasowvbl/rlib/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] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] IRanges_2.19.5      S4Vectors_0.22.0    BiocGenerics_0.30.0

loaded via a namespace (and not attached):
 [1] ps_1.3.0           prettyunits_1.0.2  withr_2.1.2        crayon_1.3.4

 [5] rprojroot_1.3-2    assertthat_0.2.1   R6_2.4.0
backports_1.1.4
 [9] magrittr_1.5       cli_1.1.0          curl_3.3           remotes_2.0.4

[13] callr_3.2.0        tools_3.6.0        compiler_3.6.0
processx_3.3.1
[17] pkgbuild_1.0.3     BiocManager_1.30.4
>


Pariksheet

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