Hi, I'm running a DEXSEQ differential exon usage analysis on a 152 sample dataset. I've tested a variety of simple and more complex models as such:

full_model <-  ~sample + exon + batch:exon + day:exon + product2:exon 
reduced_model <- ~sample + exon + batch:exon + day:exon

In a sense, the model doesn't seem to matter since I have the same error messages being returned. I am using the standard step-wise analysis from the vignette but with a separate load function for feature counts inputs taken from https://github.com/vivekbhr/Subread_to_DEXSeq

dxd.fc <- DEXSeqDataSetFromFeatureCounts("exon_count.out",
                                         flattenedfile = "flat.gtf",
                                         sampleData = coldata_all,
                                         design = full_model)

dxd_dtu <- dxd.fc
rm(dxd.fc)

dxd_dtu1 = estimateSizeFactors(dxd_dtu)
print("size factors done")
dxd_dtu2 = estimateDispersions(dxd_dtu1, formula = full_model)
print("dispersions done")
dxd_dtu3 = testForDEU(dxd_dtu2, fullModel = design(dxd_dtu2), reducedModel = reduced_model)
print("DEU done")
dxd_dtu3 = estimateExonFoldChanges( dxd_dtu3, fitExpToVar="product2")
print("fold changes done")
dxr = DEXSeqResults(dxd_dtu3, independentFiltering = TRUE)

However, halfway through estimating size dispersions I am encountering this error:

Reading and adding Exon IDs for DEXSeq
converting counts to integer mode
Warning message:
0 aggregate geneIDs were found truncated in featureCounts output 
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA) : 
  replacement has 1 row, data has 0
Calls: estimateDispersions ... colData<- -> makeBigModelFrame -> $<- -> $<-.data.frame
Execution halted

Can anyone help me solve this? Is this a bug or package clash? Here is my session information:

R version 3.6.1 (2019-07-05)
Platform: x86_64-conda_cos6-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     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8      
 [8] LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] DEXSeq_1.32.0               RColorBrewer_1.1-3          AnnotationDbi_1.48.0        DESeq2_1.26.0               SummarizedExperiment_1.16.1 DelayedArray_0.12.3         matrixStats_0.62.0         
 [8] GenomicRanges_1.38.0        GenomeInfoDb_1.22.1         IRanges_2.20.2              S4Vectors_0.24.4            Biobase_2.46.0              BiocGenerics_0.32.0         BiocParallel_1.20.1        

loaded via a namespace (and not attached):
 [1] bitops_1.0-7           bit64_4.0.5            httr_1.4.4             progress_1.2.2         tools_3.6.1            backports_1.4.1        utf8_1.2.2             R6_2.5.1               rpart_4.1.16          
[10] Hmisc_4.7-0            DBI_1.1.3              colorspace_2.0-3       nnet_7.3-17            tidyselect_1.1.2       gridExtra_2.3          prettyunits_1.1.1      curl_4.3.2             bit_4.0.5             
[19] compiler_3.6.1         cli_3.4.1              htmlTable_2.4.0        scales_1.2.1           checkmate_2.1.0        genefilter_1.68.0      askpass_1.1            rappdirs_0.3.3         Rsamtools_2.2.3       
[28] stringr_1.4.1          digest_0.6.29          foreign_0.8-76         XVector_0.26.0         base64enc_0.1-3        jpeg_0.1-9             pkgconfig_2.0.3        htmltools_0.5.2        dbplyr_2.1.1          
[37] fastmap_1.1.0          htmlwidgets_1.5.4      rlang_1.0.2            rstudioapi_0.14        RSQLite_2.2.13         generics_0.1.3         hwriter_1.3.2.1        dplyr_1.0.9            RCurl_1.98-1.6        
[46] magrittr_2.0.3         GenomeInfoDbData_1.2.2 Formula_1.2-4          interp_1.1-3           Matrix_1.4-1           Rcpp_1.0.8.3           munsell_0.5.0          fansi_1.0.3            lifecycle_1.0.1       
[55] yaml_2.3.5             stringi_1.7.6          zlibbioc_1.32.0        BiocFileCache_1.10.2   grid_3.6.1             blob_1.2.3             crayon_1.5.2           deldir_1.0-6           lattice_0.20-45       
[64] Biostrings_2.54.0      splines_3.6.1          annotate_1.64.0        hms_1.1.1              locfit_1.5-9.4         knitr_1.39             pillar_1.8.0           geneplotter_1.64.0     biomaRt_2.42.1        
[73] XML_3.99-0.3           glue_1.6.2             latticeExtra_0.6-30    data.table_1.14.2      png_0.1-8              vctrs_0.4.1            openssl_2.0.0          gtable_0.3.1           purrr_0.3.5           
[82] assertthat_0.2.1       cachem_1.0.6           ggplot2_3.3.6          xfun_0.30              xtable_1.8-4           survival_3.3-1         tibble_3.1.7           memoise_2.0.1          cluster_2.1.3         
[91] statmod_1.4.36         ellipsis_0.3.2