Whereby I'm trying to output cuffdiff data into cummeRbund, but it appears to be having issues with connection to a database (below). Does anyone have any suggestions as to how I can fix this? Thanks! 

 cuff=readCufflinks()
Creating database F:/1Evs1L/cuffData.db
Reading Run Info File F:/1Evs1L/run.info
Writing runInfo Table
Reading Read Group Info  F:/1Evs1L/read_groups.info
Writing replicates Table
Reading Var Model Info  F:/1Evs1L/var_model.info
Writing varModel Table
Reading F:/1Evs1L/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Writing geneData table
Reading F:/1Evs1L/gene_exp.diff
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘make.db.names’ for signature ‘"SQLiteConnection", "numeric"’
In addition: Warning messages:
1: RSQLite::dbGetPreparedQuery() is deprecated, please switch to DBI::dbGetQuery(params = bind.data). 
2: RSQLite::make.db.names() is deprecated, please switch to DBI::dbQuoteIdentifier(). 
3: Column name mismatch, columns will be matched by position. This warning may be converted to an error soon. 
4: attributes are not identical across measure variables; they will be dropped