[Bioc-devel] [Fwd: Problem showing a GRanges with a meta data column of data frame]

[Jialin Ma]

Hi Hervé,

Thanks a lot for addressing it!

Best regards,
Jialin


On Tue, 2018-05-15 at 09:02 -0700, Hervé Pagès wrote:
> Hi Jialin,
> 
> Thanks for the report. This should be fixed in BioC 3.7 (S4Vectors
> 0.18.2 and IRanges 2.14.10) and BioC devel (S4Vectors 0.19.3 and
> IRanges 2.15.11).
> 
> The updated packages will become available via biocLite() in the
> next 24h (if everything goes as expected).
> 
> Best,
> H.
> 
> On 05/14/2018 07:38 PM, Jialin Ma wrote:
> > 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 <marlin- at gmx.cn>
> > To: bioc-devel <bioc-devel at 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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> 
>