[BioC] Problems with ggbio

[Michael Muratet]

Greetings

I installed a development version of bioconductor to get the  
distanceToNearest functionality (sessionInfo below). I am trying to  
plot a GRanges object with ggbio

 > is(hits)
[1] "GRanges"                    "GenomicRanges"               
"Vector"                     "GenomicRangesORmissing"      
"GenomicRangesORGRangesList"
[6] "RangedDataORGenomicRanges"  "Annotated"

 > p <- qplot(hits)
 > print(p)
Error in as.data.frame.default(x[[i]], optional = TRUE) :
   cannot coerce class 'structure("GRanges", package =  
"GenomicRanges")' into a data.frame

I haven't been able to track down the problem. Have I created a  
compatibility issue with the development version? Is it operator  
error? I could save the object and go back to release versions.

Thanks for the help

Mike

 > sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
  [1] ggbio_1.5.6            ggplot2_0.9.1           
BiocInstaller_1.5.11   rtracklayer_1.17.11    GenomicFeatures_1.9.19  
AnnotationDbi_1.19.16
  [7] Biobase_2.17.6         GenomicRanges_1.9.29    
IRanges_1.15.17        BiocGenerics_0.3.0

loaded via a namespace (and not attached):
  [1] biomaRt_2.13.1           Biostrings_2.25.6         
biovizBase_1.5.2         bitops_1.0-4.1            
BSgenome_1.25.3          cluster_1.14.2
  [7] colorspace_1.1-1         DBI_0.2-5                 
dichromat_1.2-4          digest_0.5.2              
grid_2.15.0              gridExtra_0.9
[13] Hmisc_3.9-3              labeling_0.1              
lattice_0.20-6           MASS_7.3-19               
Matrix_1.0-6             memoise_0.1
[19] munsell_0.3              plyr_1.7.1                
proto_0.3-9.2            RColorBrewer_1.0-5        
RCurl_1.91-1             reshape2_1.2.1
[25] Rsamtools_1.9.19         RSQLite_0.11.1            
scales_0.2.1             snpStats_1.7.2            
splines_2.15.0           stats4_2.15.0
[31] stringr_0.6              survival_2.36-14          
tools_2.15.0             VariantAnnotation_1.3.16  
XML_3.9-4                zlibbioc_1.3.0



Michael Muratet, Ph.D.
Senior Scientist
HudsonAlpha Institute for Biotechnology
mmuratet at hudsonalpha.org
(256) 327-0473 (p)
(256) 327-0966 (f)

Room 4005
601 Genome Way
Huntsville, Alabama 35806