Hi,

I was trying the code in the reference manual to get the GC content but it's giving errors. All the parameters appear to be correct (I checked with UCSC) - here is the code, as given in the manual:

###############

from <- 65921878 
to <- 65980988
gcContent <- UcscTrack(genome = "mm9", chromosome = "chrX",    track = "GC Percent", table = "gc5Base", from = from,
         to = to, trackType = "DataTrack", start = "start", end = "end", data = "score", 
         type = "hist", window = -1, windowSize = 1500, fill.histogram = "black",
         "darkblue",col.histogram = "black", ylim = c(30, 70), name = "GC Percent")

##############

The errors that I get:


Error in UcscTrack(genome = "mm9", chromosome = "chrX", track = "GC Percent",  : 
  Error fetching data from UCSC
In addition: Warning message:
In UcscTrack(genome = "mm9", chromosome = "chrX", track = "GC Percent",  :
  Error in try(track(query), silent = TRUE) : 
  could not find function "track"



thanks!!


My sessioninfo:



> 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] grid      stats     graphics  grDevices utils     datasets 
[7] methods   base     

other attached packages:
 [1] IRanges_1.14.2        Gviz_1.0.1           
 [3] xtable_1.7-0          GenomeGraphs_1.16.0  
 [5] quantsmooth_1.22.0    lodplot_1.1          
 [7] quantreg_4.79         SparseM_0.96         
 [9] seqLogo_1.18.0        hash_2.1.0.2         
[11] impute_1.30.0         ggdendro_0.1-05      
[13] ggplot2_0.9.0         XML_3.9-4            
[15] hgu133a.db_2.7.1      affy_1.34.0          
[17] genefilter_1.38.0     biomaRt_2.12.0       
[19] org.Hs.eg.db_2.7.1    GOstats_2.22.0       
[21] graph_1.34.0          Category_2.22.0      
[23] GO.db_2.7.1           RSQLite_0.11.1       
[25] DBI_0.2-5             AnnotationDbi_1.18.0 
[27] Biobase_2.16.0        BiocGenerics_0.2.0   
[29] fExtremes_2100.77     fTrading_2100.76     
[31] fGarch_2110.80        fBasics_2160.81      
[33] MASS_7.3-18           timeSeries_2160.94   
[35] timeDate_2160.95      lattice_0.20-6       
[37] gap_1.1-6             plotrix_3.4          
[39] som_0.3-5             gplots_2.10.1        
[41] KernSmooth_2.23-7     caTools_1.12         
[43] bitops_1.0-4.1        gdata_2.8.2          
[45] pvclust_1.2-2         reshape_0.8.4        
[47] plyr_1.7.1            zoo_1.7-7            
[49] data.table_1.8.0      foreach_1.4.0        
[51] foreign_0.8-49        languageR_1.4        
[53] preprocessCore_1.18.0 gtools_2.6.2         
[55] BiocInstaller_1.4.7  

loaded via a namespace (and not attached):
 [1] affyio_1.24.0       annotate_1.34.0     Biostrings_2.24.1  
 [4] BSgenome_1.24.0     codetools_0.2-8     colorspace_1.1-1   
 [7] dichromat_1.2-4     digest_0.5.2        GenomicRanges_1.8.5
[10] GSEABase_1.18.0     iterators_1.0.6     memoise_0.1        
[13] munsell_0.3         proto_0.3-9.2       RBGL_1.32.0        
[16] RColorBrewer_1.0-5  RCurl_1.91-1        reshape2_1.2.1     
[19] Rsamtools_1.8.4     rtracklayer_1.16.1  scales_0.2.0       
[22] splines_2.15.0      stabledist_0.6-3    stats4_2.15.0      
[25] stringr_0.6         survival_2.36-14    tools_2.15.0       
[28] zlibbioc_1.2.0     
> 

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