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

[Jialin Ma]

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
> 
>