[BioC] cummeRbund errors

[Wang, Li]

Dear list members

I am struggling with cummeRbund. I tried some codes listed here, and am confronted with some errors. 

> cuff_data <- readCufflinks('diff_out')
> csDensity(genes(cuff_data))

Error in dat$fpkm + pseudocount : non-numeric argument to binary operator

> diffGeneIDs <- getSig(cuff_data, level="genes", alpha=0.05)
> diffGenes <- getGenes(cuff_data, diffGeneIDs)

Error in sqliteExecStatement(conn, statement, ...) : 
RS-DBI driver: (RS_SQLite_exec: could not execute1: cannot start a transaction within a transaction)

> 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] cummeRbund_1.2.0 reshape2_1.2.1   ggplot2_0.9.1    RSQLite_0.11.1   DBI_0.2-5       

loaded via a namespace (and not attached):
 [1] colorspace_1.1-1   dichromat_1.2-4    digest_0.5.2       grid_2.15.0       
 [5] labeling_0.1       MASS_7.3-18        memoise_0.1        munsell_0.3       
 [9] plyr_1.7.1         proto_0.3-9.2      RColorBrewer_1.0-5 scales_0.2.1      
[13] stringr_0.6 

I cannot figure out the reason, could anyone give me some hints?

Thanks in advance!

Best wishes
Li