[BioC] Multiple Errors in the new cummerbund

[Micheal [guest]]

Hi,

I have experianced mutliple errors when plotting using cummerbund 2.0 but only some functions, and it works on the demo dataset.

My is data from replicates and density plots works - dens(), but not the densrep() function, can this be a problem of the cuffdiff version?

Here is also session info:

R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

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

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

other attached packages:
 [1] BiocInstaller_1.8.1  cummeRbund_2.0.0     Gviz_1.2.0           rtracklayer_1.18.0   GenomicRanges_1.10.1
 [6] IRanges_1.16.2       fastcluster_1.1.7    reshape2_1.2.1       ggplot2_0.9.2.1      RSQLite_0.11.2      
[11] DBI_0.2-5            BiocGenerics_0.4.0  

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.20.0   BSgenome_1.26.0        Biobase_2.18.0         Biostrings_2.26.1     
 [5] GenomicFeatures_1.10.0 Hmisc_3.9-3            MASS_7.3-22            RColorBrewer_1.0-5    
 [9] RCurl_1.95-0.1.2       Rsamtools_1.10.1       XML_3.95-0.1           biomaRt_2.14.0        
[13] biovizBase_1.6.0       bitops_1.0-4.1         cluster_1.14.2         colorspace_1.1-1      
[17] dichromat_1.2-4        digest_0.5.2           gtable_0.1.1           labeling_0.1          
[21] lattice_0.20-10        memoise_0.1            munsell_0.4            parallel_2.15.1       
[25] plyr_1.7.1             proto_0.3-9.2          scales_0.2.2           stats4_2.15.1         
[29] stringr_0.6.1          tools_2.15.1           zlibbioc_1.4.0 

 -- output of sessionInfo(): 

> disp<-dispersionPlot(genes(cuff))
> disp
Error in layout_base(data, vars, drop = drop) : 
  Faceting variables must have at least one value

> genes.scv<-fpkmSCVPlot(genes(cuff))
Error in sqliteExecStatement(con, statement, bind.data) : 
  RS-DBI driver: (error in statement: near ")": syntax error)
> isoforms.scv<-fpkmSCVPlot(isoforms(cuff))
Error in sqliteExecStatement(con, statement, bind.data) : 
  RS-DBI driver: (error in statement: near ")": syntax error)

> densRep<-csDensity(genes(cuff),replicates=T)
Error in sqliteExecStatement(con, statement, bind.data) : 
  RS-DBI driver: (error in statement: near ")": syntax err

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