Hi, I was trying to import the count result from HTSeq Count into DESeq2. 

# inside of "HTSeq_Count_ChIPpeak_H3K27ac_geneX.csv"
"Samplename", "countfile", "genotype", "compartment"
"H3K27ac_WTCellB","ChIPpeakWTCellB","WT","CellB"
"H3K27ac_geneXcKOCellA","ChIPpeakgeneXcKOCellA","geneXcKO","CellA"
"H3K27ac_geneXcKOCellC","ChIPpeakgeneXcKOCellC","geneXcKO","CellC"
"H3K27ac_WTCellC","ChIPpeakWTCellC","WT","CellC"
"H3K27ac_geneXcKOCellB","ChIPpeakgeneXcKOCellB","geneXcKO","CellB"
"H3K27ac_WTCellA","ChIPpeakWTCellA","WT","CellA"

> sampleTable <- read.csv(file="HTSeq_Count_ChIPpeak_H3K27ac_geneX.csv")
> ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable,
+                                       directory = directory,
+                                        design= ~ genetype + compartment)

met error: 

Error in DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory,  : 
  Gene IDs (first column) differ between files.
In addition: Warning messages:
1: In is.na(e1) | is.na(e2) :
  longer object length is not a multiple of shorter object length
  ....
  ....
10: In `==.default`(a$V1, l[[1]]$V1) :
  longer object length is not a multiple of shorter object length

"Gene IDs (first column) differ between files." 

What is "Gene IDs" indicated here? I have only gff file without "gene_id" 

Any suggestion ? 

Update: 

I checked the example : 

recreated sample like:

> sampleTable
               Samplename             countfile  genotype compartment
1         ChIPpeakWTCellB       ChIPpeakWTCellB        WT       CellB
2   ChIPpeakgeneXcKOCellA ChIPpeakgeneXcKOCellA  geneXcKO       CellA
3   ChIPpeakgeneXcKOCellC ChIPpeakgeneXcKOCellC  geneXcKO       CellC
4         ChIPpeakWTCellC       ChIPpeakWTCellC        WT       CellC
5   ChIPpeakgeneXcKOCellB ChIPpeakgeneXcKOCellB  geneXcKO       CellB
6         ChIPpeakWTCellA       ChIPpeakWTCellA        WT       CellA​

but re run the process, did not make any difference. 

I also run the example  with the package "papilla" with no problem. So I guess R or R studio is OK...

PSS: the count file was generated by HTSeq Count: 

gt bed_to_gff3 -o ChIPpeak.gff ChIPpeak.bed # convert ChIPpeak.bed file into gff by genometools http://genometools.org/tools.html
# count ChIP reads fall into genomic regions defined by ChIPpeak.gff                                   
python -m HTSeq.scripts.count -f bam -s no -t BED_feature -i Name -o ChIPpeakGeneXcKOCellA  H3K27ac_GeneXcKOCellA.bam ChIPpeak.gff

​here is R information:
​

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X El Capitan 10.11.4

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] DESeq2_1.12.4              RColorBrewer_1.1-2         DiffBind_2.0.9         
[4] SummarizedExperiment_1.2.3 Biobase_2.32.0             GenomicRanges_1.24.3   
[7] GenomeInfoDb_1.8.7         IRanges_2.6.1              S4Vectors_0.10.3       
[10] BiocGenerics_0.18.0       

loaded via a namespace (and not attached):
[1] Category_2.38.0         bitops_1.0-6            tools_3.3.2         
[4] backports_1.0.5         R6_2.2.0                rpart_4.1-10        
[7] KernSmooth_2.23-15      Hmisc_4.0-2             DBI_0.5-1           
[10] lazyeval_0.2.0          colorspace_1.3-2        nnet_7.3-12         
[13] gridExtra_2.2.1         sendmailR_1.2-1         graph_1.50.0        
[16] htmlTable_1.9           rtracklayer_1.32.2      caTools_1.17.1      
[19] scales_0.4.1            checkmate_1.8.2         BatchJobs_1.6       
[22] genefilter_1.54.2       RBGL_1.48.1             stringr_1.1.0       
[25] digest_0.6.12           Rsamtools_1.24.0        foreign_0.8-67      
[28] AnnotationForge_1.14.2  XVector_0.12.1          base64enc_0.1-3     
[31] htmltools_0.3.5         limma_3.28.21           htmlwidgets_0.8     
[34] RSQLite_1.1-2           BBmisc_1.10             GOstats_2.38.1      
[37] hwriter_1.3.2           BiocParallel_1.6.6      gtools_3.5.0        
[40] acepack_1.4.1           dplyr_0.5.0             RCurl_1.95-4.8      
[43] magrittr_1.5            GO.db_3.3.0             Formula_1.2-1       
[46] Matrix_1.2-8            Rcpp_0.12.9             munsell_0.4.3       
[49] stringi_1.1.2           edgeR_3.14.0            zlibbioc_1.18.0     
[52] gplots_3.0.1            fail_1.3                plyr_1.8.4          
[55] grid_3.3.2              gdata_2.17.0            lattice_0.20-34     
[58] Biostrings_2.40.2       splines_3.3.2           GenomicFeatures_1.24.5
[61] annotate_1.50.1         locfit_1.5-9.1          knitr_1.15.1        
[64] rjson_0.2.15            systemPipeR_1.6.4       geneplotter_1.50.0     

I did not figure out how to using DESeqDataSetFromHTSeqCount to input my data into DESeq2, 

but tried "DESeqDataSetFromMatrix", and it worked out, I put it here, in case someone met similar issue:

source("https://bioconductor.org/biocLite.R")
biocLite("Rsubread") 
library("Rsubread")
# count the reads using featureCounts from "Rsubread"
ChIPpeakK27ac_Count <- featureCounts(files=c("H3K27ac_geneXcKOCellA.bam",
                      "H3K27ac_geneXcKOCellC.bam",
                      "H3K27ac_WTCellB.bam",
                      "H3K27ac_geneXcKOCellB.bam",
                      "H3K27ac_WTCellA.bam",
                      "H3K27ac_WTCellC.bam"),annot.ext="ChIPpeak.gtf",
                       isGTFAnnotationFile=TRUE,
                       GTF.featureType="peak",
                       GTF.attrType="gene_id",
                       nthreads=4)

# you need to create a file "H3K27ac_geneX_sampletable.csv"
H3K27ac_geneXcKOCellA.bam    
H3K27ac_geneXcKOCellC.bam        
H3K27ac_WTCellB.bam
H3K27ac_geneXcKOCellB.bam        
H3K27ac_WTCellA.bam        
H3K27ac_WTCellC.bam

sample.table <- read.csv("H3K27ac_geneX_sample.csv",header=T)
dds.fc <- DESeqDataSetFromMatrix(ChIPpeakK27ac_Count$counts,
                                 colData=sample.table, 
                                 design=~ genotype + compartment)

The error says that the count files have different length. Do they?