Hi,

I am trying to read cuffdiff results into my R session using the following command:

cuffDB1 <- readCufflinks(dir='./myCuffDiff/', rebuild=TRUE, genome='hg19', dbFile='cuffData1.db',
                         gtfFile='/home/ngs/genome.hs/gencode.v21.annotation.gff3') 

the genome gtf was downloaded from Gencode, and was used for alignment with STAR, and for running cufflinks/cuffdiff.  But I got following error:

....
Writing varModel Table
Reading GTF file
Writing GTF features to 'features' table...
Error in sqliteSendQuery(conn, statement, bind.data) :
  RAW() can only be applied to a 'raw', not a 'character'

I googled aroung and could not find a solution.  Please help.  Very much appreciated.

Below is my sessionInfo:

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] grid      stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] spliceR_1.8.0        plyr_1.8.1           RColorBrewer_1.1-2   VennDiagram_1.6.9    cummeRbund_2.8.2    
 [6] Gviz_1.10.10         rtracklayer_1.26.2   GenomicRanges_1.18.4 GenomeInfoDb_1.2.4   IRanges_2.0.1       
[11] S4Vectors_0.4.0      fastcluster_1.1.16   reshape2_1.4.1       ggplot2_1.0.0        RSQLite_1.0.0       
[16] DBI_0.3.1            BiocGenerics_0.12.1

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3          AnnotationDbi_1.28.1     base64enc_0.1-2          BatchJobs_1.5           
 [5] BBmisc_1.9               Biobase_2.26.0           BiocParallel_1.0.3       biomaRt_2.22.0          
 [9] Biostrings_2.34.1        biovizBase_1.14.1        bitops_1.0-6             brew_1.0-6              
[13] BSgenome_1.34.1          checkmate_1.5.1          cluster_2.0.1            codetools_0.2-10        
[17] colorspace_1.2-5         dichromat_2.0-0          digest_0.6.8             fail_1.2                
[21] foreach_1.4.2            foreign_0.8-63           Formula_1.2-0            GenomicAlignments_1.2.2
[25] GenomicFeatures_1.18.3   gtable_0.1.2             Hmisc_3.15-0             iterators_1.0.7         
[29] lattice_0.20-30          latticeExtra_0.6-26      MASS_7.3-39              matrixStats_0.14.0      
[33] munsell_0.4.2            nnet_7.3-9               proto_0.3-10             Rcpp_0.11.4             
[37] RCurl_1.95-4.5           rpart_4.1-9              Rsamtools_1.18.3         scales_0.2.4            
[41] sendmailR_1.2-1          splines_3.1.2            stringr_0.6.2            survival_2.38-1         
[45] tcltk_3.1.2              tools_3.1.2              VariantAnnotation_1.12.9 XML_3.98-1.1            
[49] XVector_0.6.0            zlibbioc_1.12.0