I check that common is not a 0-length vector.

> length(common)
[1] 4604

The detail as followed:

> geneLevelData=read.table("htseqcount.txt",sep="\t",header=T,check.names=F)
> head(geneLevelData)
    gene_id s1 s2 s3 s4
1 0610005C13Rik  3  5  6 11
2 0610007P14Rik 33 47 10  4
3 0610009B22Rik 31 50  6  8
4 0610009L18Rik  1  3  7  3
5 0610009O20Rik 42 67 33 20
6 0610010B08Rik  1  3 16  7
> rownames(geneLevelData)=geneLevelData[,1]                                                                                 
> geneLevelData=geneLevelData[,2:ncol(geneLevelData)] 
> head(geneLevelData)                                
              s1 s2 s3 s4
0610005C13Rik  3  5  6 11
0610007P14Rik 33 47 10  4
0610009B22Rik 31 50  6  8
0610009L18Rik  1  3  7  3
0610009O20Rik 42 67 33 20
0610010B08Rik  1  3 16  7
> yeast=read.table("LengthAndGC.txt",sep="\t",header=T)                
> head(yeast)
     Gene length        gc
1   Itm2a   1632 0.4264706
2  Sergef   1460 0.5589041
3 Fam109a   2335 0.6197002
4    Dhx9   4613 0.4454802
5 Fam71e2   2686 0.5193596
6   Ssu72   1451 0.5348036
> rownames(yeast)=yeast[,1]
> colnames(yeast)[2:3]=c("length","gc")
> colnames(yeast)[2:3]
[1] "length" "gc"    
> yeastGC=data.frame(yeast[,3])
> rownames(yeastGC)=rownames(yeast)
> colnames(yeastGC)="gc"
> head(yeastGC)         
               gc
Itm2a   0.4264706
Sergef  0.5589041
Fam109a 0.6197002
Dhx9    0.4454802
Fam71e2 0.5193596
Ssu72   0.5348036
> yeastLength=data.frame(yeast[,2])
> rownames(yeastLength)=rownames(yeast)
> colnames(yeastLength)="length"
> head(yeastLength)                    
        length
Itm2a     1632
Sergef    1460
Fam109a   2335
Dhx9      4613
Fam71e2   2686
Ssu72     1451
> filter <- apply(geneLevelData,1,function(x) mean(x)>3)
> table(filter)
filter
FALSE  TRUE 
  395  4604 
> common <- intersect(rownames(yeastGC),rownames(geneLevelData[filter,]))
> length(common)
[1] 4604
> feature=yeast[,2:3]
> head(feature)
        length        gc
Itm2a     1632 0.4264706
Sergef    1460 0.5589041
Fam109a   2335 0.6197002
Dhx9      4613 0.4454802
Fam71e2   2686 0.5193596
Ssu72     1451 0.5348036
> library(EDASeq)
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,
    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: 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
> data <- newSeqExpressionSet(exprs=as.matrix(geneLevelData[common,]),featureData=feature[common,],phenoData=data.frame(conditions=colnames(geneLevelData),row.names=colnames(geneLevelData),check.names=F))
Error in assayDataNew(counts = counts, normalizedCounts = normalizedCounts,  : 
  argument "counts" is missing, with no default
> length(common)
[1] 4604
> newlwb=length(common)
> newlen=length(common)  
> head(common)
[1] "Bcl7a"  "Bnip3l" "Capzb"  "Cachd1" "B9d2"   "Ap5s1" 
> data <- newSeqExpressionSet(exprs=as.matrix(geneLevelData[newlen,]),featureData=feature[newlen,],phenoData=data.frame(conditions=colnames(geneLevelData),row.names=colnames(geneLevelData),check.names=F))
Error in assayDataNew(counts = counts, normalizedCounts = normalizedCounts,  : 
  argument "counts" is missing, with no default