fix some bugs affecting bioc-devel versions

the examples now run properly on a devel install

R> packageVersion('genomation')
[1] '0.99.0.3'

R> biocVersion()
[1] '3.0'

R> sessionInfo()
R version 3.1.0 (2014-04-10)
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=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  grid      stats     graphics  grDevices datasets  utils    
[8] methods   base     

other attached packages:
 [1] genomation_0.99.0.3      GenomicAlignments_1.1.25 Rsamtools_1.17.33       
 [4] Biostrings_2.33.13       XVector_0.5.7            GenomicRanges_1.17.35   
 [7] GenomeInfoDb_1.1.18      IRanges_1.99.24          S4Vectors_0.1.2         
[10] BiocGenerics_0.11.4      BiocInstaller_1.15.5     bigrquery_0.1           
[13] gtools_3.4.1             dplyr_0.2               

loaded via a namespace (and not attached):
 [1] assertthat_0.1       BatchJobs_1.3        BBmisc_1.7          
 [4] BiocParallel_0.99.13 bitops_1.0-6         brew_1.0-6          
 [7] checkmate_1.3        codetools_0.2-9      colorspace_1.2-4    
[10] data.table_1.9.2     DBI_0.2-7            digest_0.6.4        
[13] fail_1.2             foreach_1.4.2        ggplot2_1.0.0       
[16] gridBase_0.4-7       gtable_0.1.2         httr_0.4            
[19] impute_1.39.0        iterators_1.0.7      jsonlite_0.9.10     
[22] MASS_7.3-34          munsell_0.4.2        plyr_1.8.1          
[25] proto_0.3-10         Rcpp_0.11.2          RCurl_1.95-4.3      
[28] reshape2_1.4         RSQLite_0.11.4       rtracklayer_1.25.13 
[31] scales_0.2.4         sendmailR_1.1-2      stats4_3.1.0        
[34] stringr_0.6.2        tools_3.1.0          XML_3.98-1.1        
[37] zlibbioc_1.11.1