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

[Hervé Pagès]

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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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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