Trying to run the "airway" RNA-seq workflow, I get an error when creating the the DESeqDataSet, on both release and devel (example from release below). It seems to be related to the renaming of GenomicRangesORGRangesList to GenomicRanges_OR_GRangesList:

> suppressPackageStartupMessages(library(DESeq2))
> library(airway)
> data("airway")
> dds <- DESeqDataSet(airway, design = ~cell + dex)
Error in checkSlotAssignment(object, name, value) : 
  assignment of an object of class “GRangesList” is not valid for slot ‘rowRanges’ in an object of class “DESeqDataSet”; is(value, "GenomicRangesORGRangesList") is not TRUE
> is(rowRanges(airway))
[1] "GRangesList"                  "CompressedList"              
[3] "GenomicRangesList"            "GenomicRanges_OR_GRangesList"
[5] "List"                         "Vector"                      
[7] "Annotated"                   
> sessionInfo()
R version 3.4.0 Patched (2017-06-02 r72758)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.5

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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    
[7] datasets  methods   base     

other attached packages:
 [1] airway_0.111.0             DESeq2_1.17.3             
 [3] SummarizedExperiment_1.7.5 DelayedArray_0.3.16       
 [5] matrixStats_0.52.2         Biobase_2.37.2            
 [7] GenomicRanges_1.29.6       GenomeInfoDb_1.13.4       
 [9] IRanges_2.11.5             S4Vectors_0.15.4          
[11] BiocGenerics_0.23.0       

loaded via a namespace (and not attached):
 [1] genefilter_1.59.0       locfit_1.5-9.1         
 [3] splines_3.4.0           lattice_0.20-35        
 [5] colorspace_1.3-2        htmltools_0.3.6        
 [7] base64enc_0.1-3         blob_1.1.0             
 [9] survival_2.41-3         XML_3.98-1.9           
[11] rlang_0.1.1             DBI_0.7                
[13] foreign_0.8-69          BiocParallel_1.11.2    
[15] bit64_0.9-7             RColorBrewer_1.1-2     
[17] GenomeInfoDbData_0.99.1 plyr_1.8.4             
[19] stringr_1.2.0           zlibbioc_1.23.0        
[21] munsell_0.4.3           gtable_0.2.0           
[23] htmlwidgets_0.8         memoise_1.1.0          
[25] latticeExtra_0.6-28     knitr_1.16             
[27] geneplotter_1.55.0      AnnotationDbi_1.39.1   
[29] htmlTable_1.9           Rcpp_0.12.11           
[31] acepack_1.4.1           xtable_1.8-2           
[33] scales_0.4.1            backports_1.1.0        
[35] checkmate_1.8.2         Hmisc_4.0-3            
[37] annotate_1.55.0         XVector_0.17.0         
[39] bit_1.1-12              gridExtra_2.2.1        
[41] ggplot2_2.2.1           digest_0.6.12          
[43] stringi_1.1.5           grid_3.4.0             
[45] tools_3.4.0             bitops_1.0-6           
[47] magrittr_1.5            RSQLite_2.0            
[49] lazyeval_0.2.0          RCurl_1.95-4.8         
[51] tibble_1.3.3            Formula_1.2-1          
[53] cluster_2.0.6           Matrix_1.2-10          
[55] data.table_1.10.4       rpart_4.1-11           
[57] nnet_7.3-12             compiler_3.4.0     

> 

Try re-installing DESeq2; it seems like there is a stale cached class definition.

Hi Levi,

Thanks for reporting this. I'll bump DESeq2's version and also the version of other packages that define RangedSummarizedExperiment derivatives. This will help getting rid of the stale class definitions that are cached on the user machines.

BTW are you sure you also got this problem in release? I only renamed GenomicRangesORGRangesList -> GenomicRanges_OR_GRangesList in devel (in GenomicRanges 1.29.6 to be precised) so I'm surprised that this also affects release.

Thanks,

H.