[BioC] Gviz: UcscTrack function error

[Michael Morley [guest]]

I recently upgraded to R 3.0 and BioC 2.12. I upgraded all my BioC packages and having an error with Gviz

If I try:

chr="chr12" 
start=57591600
end=57637895
conservation <- UcscTrack(genome = 'mm9', chromosome = chr,
                          track = "Conservation", table = "phyloP30wayPlacental",
                          from = start-2000, to = end+2000, trackType = "DataTrack",
                          start = "start", end = "end", data = "score",
                          type = "hist", window = "auto", col.histogram = "darkblue",
                          fill.histogram = "darkblue", ylim = c(-.5, 4),
                          name = "Conservation")


I receive the following error:

Error in makeNewSeqnames(x, new2old = new2old, seqlevels(value)) : 
  when 'new2old' is NULL, the first elements in the
  supplied 'seqlevels' must be identical to 'seqlevels(x)'

> traceback()
9: stop("when 'new2old' is NULL, the first elements in the\n", "  supplied 'seqlevels' must be identical to 'seqlevels(x)'")
8: makeNewSeqnames(x, new2old = new2old, seqlevels(value))
7: `seqinfo<-`(`*tmp*`, value = <S4 object of class "Seqinfo">)
6: `seqinfo<-`(`*tmp*`, value = <S4 object of class "Seqinfo">)
5: normGenomeRange(range, x, single = FALSE)
4: .local(x, ...)
3: ucscTableQuery(sessionInfo$session, sessionInfo$track, gr)
2: ucscTableQuery(sessionInfo$session, sessionInfo$track, gr)
1: UcscTrack(genome = "mm9", chromosome = chr, track = "Conservation", 
       table = "phyloP30wayPlacental", from = start - 2000, to = end + 
           2000, trackType = "DataTrack", start = "start", end = "end", 
       data = "score", type = "hist", window = "auto", col.histogram = "darkblue", 
       fill.histogram = "darkblue", ylim = c(-0.5, 4), name = "Conservation")


Any suggestions?

Thank you,

Mike



 -- output of sessionInfo(): 

R version 3.0.0 (2013-04-03)
Platform: x86_64-pc-linux-gnu (64-bit)

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=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] Gviz_1.4.1

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.22.3   Biobase_2.20.0         BiocGenerics_0.6.0    
 [4] biomaRt_2.16.0         Biostrings_2.28.0      biovizBase_1.8.0      
 [7] bitops_1.0-5           BSgenome_1.28.0        cluster_1.14.4        
[10] colorspace_1.2-2       DBI_0.2-6              dichromat_2.0-0       
[13] GenomicFeatures_1.12.1 GenomicRanges_1.12.2   Hmisc_3.10-1          
[16] IRanges_1.18.0         labeling_0.1           lattice_0.20-15       
[19] munsell_0.4            parallel_3.0.0         plyr_1.8              
[22] RColorBrewer_1.0-5     RCurl_1.95-4.1         Rsamtools_1.12.2      
[25] RSQLite_0.11.3         rtracklayer_1.20.1     scales_0.2.3          
[28] stats4_3.0.0           stringr_0.6.2          tools_3.0.0           
[31] XML_3.96-1.1           zlibbioc_1.6.0        


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