[BioC] rtracklayer export method requires unique names

[Samuel Younkin]

BioC,

It seems that the export method in rtracklayer for the GRanges class 
requires that the GRanges object have unique names.  The error message 
given when names are not unique is the following:

Error in export(object, FileForFormat(con), ...) :
   cannot export object of class 'GRanges'

As one can easily make a case that non-unique names may be troublesome, 
I am curious to know whether you intentionally disallowed non-unique names.

For future users, it would be great if the error message was not so 
misleading.  I imagine that others may label ranges by subject ID, as I 
did, and therefore are likely to create a GRanges object with non-unique 
names.

See code below for an example.

Thanks,

Sam

~~

 > foo <- GRangesForUCSCGenome( genome = "hg18", chrom = rep("chr1",10) 
, ranges = IRanges(start = 1:10, width = 5), strand = "*" )
 > names(foo) <- 1:10
 > export(foo, "foo.bed" )
 > foobar <- foo
 > names(foobar) <- c(rep(1,2),3:10)
 > export(foobar, "foobar.bed" )
Error in export(object, FileForFormat(con), ...) :
   cannot export object of class 'GRanges'
 > sessionInfo()
R Under development (unstable) (2013-01-08 r61589)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
  [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
  [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
  [7] LC_PAPER=C                     LC_NAME=C
  [9] LC_ADDRESS=C                   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C

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

other attached packages:
  [1] rtracklayer_1.19.6    CleftCNVAssoc_0.1.0   MinimumDistance_1.3.3
  [4] GWASTools_1.5.5       gdsfmt_0.9.10         sandwich_2.2-9
  [7] zoo_1.7-9             GWASExactHW_1.01      ncdf_1.6.6
[10] Biobase_2.19.2        GenomicRanges_1.11.21 IRanges_1.17.24
[13] BiocGenerics_0.5.6

loaded via a namespace (and not attached):
  [1] affyio_1.27.1         annotate_1.37.3       AnnotationDbi_1.21.9
  [4] BiocInstaller_1.9.6   Biostrings_2.27.8     bit_1.1-9
  [7] bitops_1.0-5          BSgenome_1.27.1       codetools_0.2-8
[10] crlmm_1.17.12         DBI_0.2-5             DNAcopy_1.33.1
[13] ellipse_0.3-7         ff_2.2-10             foreach_1.4.0
[16] genefilter_1.41.1     grid_3.0.0            iterators_1.0.6
[19] lattice_0.20-13       lmtest_0.9-30         Matrix_1.0-10
[22] msm_1.1.4             mvtnorm_0.9-9994      oligoClasses_1.21.6
[25] preprocessCore_1.21.1 quantsmooth_1.25.0    RcppEigen_0.3.1.2
[28] RCurl_1.95-3          Rsamtools_1.11.14     RSQLite_0.11.2
[31] SNPchip_2.5.1         splines_3.0.0         stats4_3.0.0
[34] survival_2.37-2       tools_3.0.0           VanillaICE_1.21.10
[37] XML_3.95-0.1          xtable_1.7-0          zlibbioc_1.5.0
 >