I have been failing to build a DDS object using the function DESeqDataSetFromMatrix()

Here is some randomly generated matrix I am using to test out if my DEseq2 package is working properly:

x <- round(matrix(rexp(480 * 10, rate=.1), ncol=12), 0)
rownames(x) <- paste("gene", 1:nrow(x))
colnames(x) <- paste("sample", 1:ncol(x))

coldata <- data.frame(condition = factor(c(rep("ctl", 3), rep("A", 3), rep("B", 3), rep("C", 3))))

coldata$condition <- relevel(coldata$condition, ref = "ctl")

library(DESeq2)
dds <- DESeqDataSetFromMatrix(countData = x, colData = coldata, design= ~ condition)

The dds object shows up as <object with="" null="" pointer="">

Here is my SessionInfo()

> R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

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] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] DESeq2_1.24.0               SummarizedExperiment_1.14.0 DelayedArray_0.10.0        
 [4] BiocParallel_1.18.0         matrixStats_0.54.0          Biobase_2.44.0             
 [7] GenomicRanges_1.36.0        GenomeInfoDb_1.20.0         IRanges_2.18.1             
[10] S4Vectors_0.22.0            BiocGenerics_0.30.0        

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1             locfit_1.5-9.1         lattice_0.20-38       
 [4] assertthat_0.2.1       digest_0.6.19          R6_2.4.0              
 [7] backports_1.1.4        acepack_1.4.1          RSQLite_2.1.1         
[10] ggplot2_3.2.0          pillar_1.4.1           zlibbioc_1.30.0       
[13] rlang_0.3.4            lazyeval_0.2.2         annotate_1.62.0       
[16] rstudioapi_0.10        data.table_1.12.2      blob_1.1.1            
[19] rpart_4.1-15           Matrix_1.2-17          checkmate_1.9.3       
[22] splines_3.6.0          geneplotter_1.62.0     stringr_1.4.0         
[25] foreign_0.8-71         htmlwidgets_1.3        bit_1.1-14            
[28] RCurl_1.95-4.12        munsell_0.5.0          compiler_3.6.0        
[31] xfun_0.7               pkgconfig_2.0.2        base64enc_0.1-3       
[34] htmltools_0.3.6        nnet_7.3-12            tidyselect_0.2.5      
[37] tibble_2.1.3           gridExtra_2.3          htmlTable_1.13.1      
[40] GenomeInfoDbData_1.2.1 Hmisc_4.2-0            XML_3.98-1.20         
[43] crayon_1.3.4           dplyr_0.8.1            bitops_1.0-6          
[46] grid_3.6.0             DBI_1.0.0              xtable_1.8-4          
[49] gtable_0.3.0           magrittr_1.5           scales_1.0.0          
[52] stringi_1.4.3          XVector_0.24.0         genefilter_1.66.0     
[55] latticeExtra_0.6-28    Formula_1.2-3          RColorBrewer_1.1-2    
[58] tools_3.6.0            bit64_0.9-7            glue_1.3.1            
[61] purrr_0.3.2            survival_2.44-1.1      AnnotationDbi_1.46.0  
[64] colorspace_1.4-1       cluster_2.1.0          BiocManager_1.30.4    
[67] memoise_1.1.0          knitr_1.23

I have tried to uninstall the DESeq2 and SummarisedExperiment packages, and reinstalled them, but still cannot build a proper object.

Can someone tell me what is broken?

Updated answer:

This is not an R or Bioconductor bug. It’s just an “artifact” from RStudio’s interface. There is nothing wrong and you can use your Bioconductor packages while ignoring this “artifact” of what it shows in the Environment pane.

See here:

https://github.com/rstudio/rstudio/issues/4741