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Bioconductor / GenomicRanges

Representation and manipulation of genomic intervals
https://bioconductor.org/packages/GenomicRanges
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GRangesList fails with named arguments #9

Closed LTLA closed 6 years ago

LTLA commented 6 years ago

Calling:

GRangesList(a=GRanges())

fails with

Error in `rownames<-`(`*tmp*`, value = "a") : invalid rownames length

I'm pretty sure this was working before, and indeed it works fine with BioC-release versions of all packages. Traceback suggests it may be related to the new use.names=TRUE setting for mcols(), as discussed in Bioconductor/SummarizedExperiment#2.

R version 3.5.0 Patched (2018-04-30 r74679)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS: /home/cri.camres.org/lun01/Software/R/R-3-5-branch/lib/libRblas.so
LAPACK: /home/cri.camres.org/lun01/Software/R/R-3-5-branch/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] GenomicRanges_1.33.6 GenomeInfoDb_1.17.1  IRanges_2.15.13     
[4] S4Vectors_0.19.12    BiocGenerics_0.27.0 

loaded via a namespace (and not attached):
[1] zlibbioc_1.27.0        compiler_3.5.0         XVector_0.21.1        
[4] GenomeInfoDbData_1.1.0 RCurl_1.95-4.10        bitops_1.0-6
hpages commented 6 years ago

Works for me. Make sure you have the latest IRanges (2.15.14, propagated this morning):

> library(GenomicRanges)

> GRangesList(a=GRanges())
GRangesList object of length 1:
$a 
GRanges object with 0 ranges and 0 metadata columns:
   seqnames    ranges strand
      <Rle> <IRanges>  <Rle>

-------
seqinfo: no sequences

> sessionInfo()
R version 3.5.0 Patched (2018-05-03 r74699)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS: /home/hpages/R/R-3.5.r74699/lib/libRblas.so
LAPACK: /home/hpages/R/R-3.5.r74699/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_1.33.6 GenomeInfoDb_1.17.1  IRanges_2.15.14     
[4] S4Vectors_0.19.12    BiocGenerics_0.27.0 

loaded via a namespace (and not attached):
[1] zlibbioc_1.27.0        compiler_3.5.0         XVector_0.21.1        
[4] GenomeInfoDbData_1.1.0 RCurl_1.95-4.10        bitops_1.0-6
LTLA commented 6 years ago

Yep, confirmed. Must have been an issue with using Github versions of some but not all core packages. Sorry for the noise.