To Whom It May Concern, 
I am currently working out the pipeline for differential expression on a subset of RNA-seq lists (2 treatments with 2 biological replicates each) and following the pasilla tutorial online. I am encountering an error with the DEXSeq Bioconductor package when creating the object "DEXSeqDataSetFromHTSeq". I have changed a few names (files and paths) for confidentiality and clarity purposes!

Error:
Error in strsplit(rownames(dcounts), ":") : non-character argument

>inDir = "/home/user"

>countFiles = list.files(inDir, pattern="sorted.txt", full.names=TRUE)
>countFiles
[1] "/home/user/x1_pe_align_sorted.txt"
[2] "/home/user/x2_pe_align_sorted.txt" 
[3] "/home/user/y1_pe_align_sorted.txt" 
[4] "/home/user/y2_pe_align_sorted.txt"

>flattenedFile = list.files(inDir, pattern="gff$", full.names=TRUE)
>flattenedFile
[1] "/home/user/GCF_Reference_from_NCBI.gff"

> sampleTable = data.frame(row.names = c( "x1", "x2", "y1","y2"),condition = c("x_tx", "x_tx", "y_tx","y_tx" ), libType = c( "paired-end", "paired-end","paired-end", "paired-end" ) )
> sampleTable
                               condition    libType
/home/user/x1_pe_align_sorted.txt   x_tx paired-end
/home/user/x2_pe_align_sorted.txt   x_tx paired-end
/home/user/y1_pe_align_sorted.tx    y_tx paired-end
/home/user/y2_pe_align_sorted.txt   y_tx paired-end

>dxd = DEXSeqDataSetFromHTSeq(countfiles=countFiles,sampleData=sampleTable,design=~ sample + exon + condition:exon,flattenedfile=flattenedFile )
Error in strsplit(rownames(dcounts), ":") : non-character argument

> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: CentOS release 6.6 (Final)

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] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] DEXSeq_1.14.1             DESeq2_1.8.1             
 [3] RcppArmadillo_0.5.200.1.0 Rcpp_0.12.0              
 [5] GenomicRanges_1.20.5      GenomeInfoDb_1.4.1       
 [7] IRanges_2.2.5             S4Vectors_0.6.3          
 [9] Biobase_2.28.0            BiocGenerics_0.14.0      
[11] BiocParallel_1.2.9        BiocInstaller_1.18.4     

loaded via a namespace (and not attached):
 [1] genefilter_1.50.0    statmod_1.4.21       locfit_1.5-9.1      
 [4] reshape2_1.4.1       splines_3.2.1        lattice_0.20-33     
 [7] colorspace_1.2-6     survival_2.38-3      XML_3.98-1.3        
[10] foreign_0.8-65       DBI_0.3.1            RColorBrewer_1.1-2  
[13] lambda.r_1.1.7       plyr_1.8.3           stringr_1.0.0       
[16] zlibbioc_1.14.0      Biostrings_2.36.1    munsell_0.4.2       
[19] gtable_0.1.2         futile.logger_1.4.1  hwriter_1.3.2       
[22] latticeExtra_0.6-26  geneplotter_1.46.0   biomaRt_2.24.0      
[25] AnnotationDbi_1.30.1 proto_0.3-10         acepack_1.3-3.3     
[28] xtable_1.7-4         scales_0.2.5         Hmisc_3.16-0        
[31] annotate_1.46.1      XVector_0.8.0        Rsamtools_1.20.4    
[34] gridExtra_2.0.0      ggplot2_1.0.1        digest_0.6.8        
[37] stringi_0.5-5        grid_3.2.1           tools_3.2.1         
[40] bitops_1.0-6         magrittr_1.5         RCurl_1.95-4.7      
[43] RSQLite_1.0.0        Formula_1.2-1        cluster_2.0.3       
[46] futile.options_1.0.0 MASS_7.3-43          rpart_4.1-10        
[49] nnet_7.3-10

Thank you in advance,

A. Romney