When I use EDAseq R package to deal with the counts in RNASEQ.

Error information as followed:

Rscript EDAseq.R --args htseqcount.txt gtfLengthAndGC.txt zz4
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: methods
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,
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

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Loading required package: ShortRead
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: XVector
Loading required package: Biostrings
Loading required package: lattice
Loading required package: Rsamtools
filter
FALSE TRUE
3528 20744
[1] 20744
Error in assayDataNew(counts = counts, normalizedCounts = normalizedCounts, :
argument "counts" is missing, with no default
Calls: newSeqExpressionSet ... .nextMethod -> .local -> checkClass -> is -> assayDataNew
Execution halted

Check one step by step. the error should show in

> data <- newSeqExpressionSet(exprs=as.matrix(geneLevelData[common,]),
+ featureData=feature[common,],
+ phenoData=data.frame(
+ conditions=c(rep("mut",2),rep("wt",2)),
+ row.names=colnames(geneLevelData)))

How to deal with it?