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> library("pasilla")
> inDir = system.file("extdata", package="pasilla", mustWork=TRUE)
> dir(inDir)
 [1] "Dmel.BDGP5.25.62.DEXSeq.chr.gff" "geneIDsinsubset.txt"            
 [3] "pasilla_gene_counts.tsv"         "treated1fb.txt"                 
 [5] "treated2fb.txt"                  "treated3fb.txt"                 
 [7] "untreated1fb.txt"                "untreated2fb.txt"               
 [9] "untreated3fb.txt"                "untreated4fb.txt"               
> 
> setwd("/home/korlin/Temp")
> samples<-read.table('fly', header=T, sep="\t")
> rownames(samples)<-samples[,1]
> samples[,1] <- NULL
> print(samples)
             condition       type
treated1fb     treated paired-end
treated2fb     treated paired-end
treated3fb     treated paired-end
untreated1fb untreated paired-end
untreated2fb untreated paired-end
untreated3fb untreated paired-end
untreated4fb untreated paired-end
> #print(rownames(samples))
> annotationfile = file.path(inDir, "Dmel.BDGP5.25.62.DEXSeq.chr.gff")
> library("DEXSeq")
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:stats’:

    xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
    do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
    is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unlist

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GenomicRanges
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: DESeq2
Loading required package: Rcpp
Loading required package: RcppArmadillo
Loading required package: BiocParallel
> ecs = read.HTSeqCounts(countfiles = file.path(inDir, paste(rownames(samples), "txt", sep=".")),design = samples,flattenedfile = annotationfile)
Error in checkAtAssignment("character", "annotationFile", "character") : 
  ‘annotationFile’ is not a slot in class “character”
Calls: read.HTSeqCounts -> checkAtAssignment
In addition: Warning message:
'newExonCountSet' is deprecated.
Use 'DEXSeqDataSet' instead.
See help("Deprecated") 
Execution halted