I  have this error:

dHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable=SampleTable,directory="TuttoCount/", design= ~ 1) #
Error in Ops.factor(a$V1, l[[1]]$V1) :
  level sets of factors are different
In addition: Warning message:
  In is.na(e1) | is.na(e2) :
  longer object length is not a multiple of shorter object length

str(SampleTable)
'data.frame':    1235 obs. of  3 variables:
  $ SampleName: int  1 2 3 4 5 6 7 8 9 10 ...
$ fileName  : Factor w/ 1235 levels "0000772b-773d-4cf8-8baf-0e1e6dbf55e8.htseq.counts",..: 1 2 3 4 5 6 7 8 9 10 ...
$ condition : Factor w/ 6 levels "A","B","C",..: 1 1 2 2 1 1 2 1 2 2 ...

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] ggplot2_2.2.0              DESeq2_1.12.4              SummarizedExperiment_1.2.3 Biobase_2.32.0            
[5] GenomicRanges_1.24.3       GenomeInfoDb_1.8.7         IRanges_2.6.1              S4Vectors_0.10.3          
[9] BiocGenerics_0.18.0       

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.8          RColorBrewer_1.1-2   plyr_1.8.4           XVector_0.12.1       bitops_1.0-6         tools_3.3.1         
 [7] zlibbioc_1.18.0      digest_0.6.10        rpart_4.1-10         RSQLite_1.0.0        annotate_1.50.1      tibble_1.2          
[13] gtable_0.2.0         htmlTable_1.7        lattice_0.20-34      Matrix_1.2-7.1       DBI_0.5-1            gridExtra_2.2.1     
[19] genefilter_1.54.2    stringr_1.1.0        cluster_2.0.5        knitr_1.15           locfit_1.5-9.1       grid_3.3.1          
[25] nnet_7.3-12          data.table_1.9.6     AnnotationDbi_1.34.4 XML_3.98-1.5         survival_2.40-1      BiocParallel_1.6.6  
[31] foreign_0.8-67       latticeExtra_0.6-28  Formula_1.2-1        geneplotter_1.50.0   magrittr_1.5         htmltools_0.3.5     
[37] Hmisc_4.0-0          scales_0.4.1         splines_3.3.1        assertthat_0.1       xtable_1.8-2         colorspace_1.3-1    
[43] labeling_0.3         stringi_1.1.2        acepack_1.4.1        RCurl_1.95-4.8       lazyeval_0.2.0       munsell_0.4.3  

Any Suggestion??

Are you sure that all the files exist? Can you check this?

table(file.exists(file.path(dir, sampleTable[,2])))