When I was using DiffBind, I got the error message below from  dba.plotBox(): 

Error in wilcox.test.default(toplot[[i]], toplot[[j]], paired = FALSE) :

  not enough 'y' observations

Calls: runDiffBind ... pv.plotBoxplot -> pvalMethod -> wilcox.test.default

Could someone tell me the possible reason of this? Thanks in advance. 

The code is shown as below:

    samples = read.csv(input)

    # read the peaks into a DBA object.

    # 1) plot
    # by default, it will plots a correlation heatmap
    #Correlation heatmap using occupacy (peak caller score) data
    #For the peaks of SICER, I used fold change values here
    tamoxifen = dba(sampleSheet=input)

    #calculate a binding matrix with cores based on read counts for every sample.
    # 2) plot
    # correlation heatmap using read count data by default
    tamoxifen = dba.count(tamoxifen, minOverlap=3, bRemoveDuplicates = FALSE)

    # Establishing a contrast.
    tamoxifen<-dba.contrast(tamoxifen, minMembers=2)
    # dba.analyze is the main differential analysis function
    # 3) plot
    # by default, it will plots a correlation heatmap if diff peaks are found
    # correlation heatmap using read count data of diff peaks.
    cat("-dba.analyze", "\n")
    tamoxifen<-dba.analyze(tamoxifen, bSubControl = FALSE)

    cat("-dba.report", "\n")
    tamoxifen.DB<-dba.report(tamoxifen, th = thrd)

    # MA plot of comparison: Sites identified as significantly differentially bound shown in red.
    # 4) plot:
    cat("dba.plotMA", "\n")
    dba.plotMA(tamoxifen)

    cat("dba.fold", "\n")
    tamoxifen.DB[tamoxifen.DB$Fold<0,]

    length(tamoxifen.DB[tamoxifen.DB$Fold<0,])
    length(tamoxifen.DB[tamoxifen.DB$Fold>0,])

    # 4) plot PCA
    cat("dba.plotPCA", "\n")
    dba.plotPCA(tamoxifen, label = DBA_REPLICATE)

    cat("dba.plotPCA", "\n")
    # 5) plot PCA using count data for only differentailly bound sites.
    dba.plotPCA(tamoxifen, contrast=1, th = thrd, label = DBA_REPLICATE)

    #cat("dba.plotBox", "\n")
    # 6) Boxplot of read distribution for differential peaks
    #dba.plotBox(tamoxifen)

    cat("dba.plotHeatmap", "\n")
    # 7) Heatmap showing binding affinities for differentially peaks
    dba.plotHeatmap(tamoxifen, contrast=1, correlations=FALSE)

    ## we need elementMetadata to
    library("GenomicRanges")
     cat("Write the table", "\n")
     df <- data.frame(seqnames=seqnames(tamoxifen.DB), starts=start(tamoxifen.DB),  ends=end(tamoxifen.DB),elementMetadata(tamoxifen.DB))
    write.table(df, file=out, quote=F, sep="\t", row.names = F)

Here is the session information:

> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.9 (Santiago)

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

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

loaded via a namespace (and not attached):
 [1] Biobase_2.32.0             edgeR_3.14.0
 [3] bit64_0.9-7                splines_3.3.0
 [5] gtools_3.5.0               assertthat_0.2.0
 [7] stats4_3.3.0               latticeExtra_0.6-28
 [9] amap_0.8-14                RBGL_1.48.1
[11] blob_1.1.0                 Rsamtools_1.24.0
[13] Category_2.38.0            RSQLite_2.0
[15] backports_1.1.0            lattice_0.20-35
[17] glue_1.1.1                 limma_3.28.21
[19] digest_0.6.12              GenomicRanges_1.24.3
[21] RColorBrewer_1.1-2         XVector_0.12.1
[23] checkmate_1.7.4            colorspace_1.3-2
[25] Matrix_1.2-6               plyr_1.8.4
[27] GSEABase_1.34.1            XML_3.98-1.9
[29] pkgconfig_2.0.1            pheatmap_1.0.8
[31] ShortRead_1.30.0           biomaRt_2.28.0
[33] genefilter_1.54.2          zlibbioc_1.18.0
[35] xtable_1.8-2               GO.db_3.3.0
[37] scales_0.5.0               brew_1.0-6
[39] gdata_2.18.0               BiocParallel_1.6.6
[41] tibble_1.3.4               annotate_1.50.1
[43] IRanges_2.6.1              ggplot2_2.2.1.9000
[45] SummarizedExperiment_1.2.3 GenomicFeatures_1.24.2
[47] BiocGenerics_0.18.0        lazyeval_0.2.0
[49] survival_2.41-3            magrittr_1.5
[51] memoise_1.1.0              systemPipeR_1.6.2
[53] fail_1.3                   gplots_3.0.1
[55] hwriter_1.3.2              DiffBind_2.0.2
[57] GOstats_2.38.0             graph_1.50.0
[59] tools_3.3.0                BBmisc_1.9
[61] stringr_1.2.0              sendmailR_1.2-1
[63] S4Vectors_0.10.3           munsell_0.4.3
[65] locfit_1.5-9.1             bindrcpp_0.2
[67] AnnotationDbi_1.34.4       Biostrings_2.40.2
[69] GenomeInfoDb_1.8.7         caTools_1.17.1
[71] rlang_0.1.2                grid_3.3.0
[73] RCurl_1.95-4.8             rjson_0.2.15
[75] AnnotationForge_1.14.2     bitops_1.0-6
[77] base64enc_0.1-3            gtable_0.2.0
[79] DBI_0.7                    R6_2.2.2
[81] GenomicAlignments_1.8.4    dplyr_0.7.2
[83] rtracklayer_1.32.0         bit_1.1-12
[85] bindr_0.1                  KernSmooth_2.23-15
[87] stringi_1.1.5              parallel_3.3.0
[89] BatchJobs_1.6              Rcpp_0.12.12

Hello-

I tried running your script with the samplesheet and data from the vignette and it works fine. This is using the current version of DiffBind (2.4), I see that you are using a somewhat older version. (Also, I wasn't sure what the value of the variable thrd is, I used thrd <- 3, but it doesn't really matter as your call to dba.plotBox() did not specify a contrast and hence uses the default contrast=1.)

If you could email me your DBA object tamoxifen I can try the call to see if I can reproduce the problem with the current released version of DiffBind.

Cheers-

Rory