Hello, I'm having trouble using DESeq2 and I'm not sure why because the code was working before. I think maybe some packages got updated or something that aren't compatible? But not sure how to fix it. For example, I can't making a DESeq2 object, such as with the code below (when before today it was fine).

# previously I made a DESeqDataSet object without issue using this code
dds <- DESeqDataSetFromMatrix(countData = round(genecounts), 
                              colData = metadata,
                              design = ~ genotype + treatment + genotype:treatment)

When I do try to run it, I get the following error: Error in MatrixGenerics:::.load_next_suggested_package_to_search(x) : Failed to find a rowRanges() method for RangedSummarizedExperiment objects.

I also cannot run other functions such as:

vsd <- vst(dds, blind=TRUE) # I have a dds object saved to the environment

When I try, I get a similar error message: Error in MatrixGenerics:::.load_next_suggested_package_to_search(x) : Failed to find a rowRanges() method for DESeqDataSet objects.

Does anyone know how to fix this? It seems like there's an error with rowRanges() missing, but I can't find much information on it. Thank you.

sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] forcats_0.5.1               stringr_1.4.0              
 [3] dplyr_1.0.6                 purrr_0.3.4                
 [5] readr_1.4.0                 tidyr_1.1.3                
 [7] tibble_3.1.2                ggplot2_3.3.3              
 [9] tidyverse_1.3.1             DESeq2_1.28.1              
[11] EDASeq_2.22.0               ShortRead_1.46.0           
[13] GenomicAlignments_1.24.0    SummarizedExperiment_1.18.2
[15] DelayedArray_0.16.3         MatrixGenerics_1.2.1       
[17] matrixStats_0.58.0          Matrix_1.3-3               
[19] Rsamtools_2.4.0             GenomicRanges_1.40.0       
[21] GenomeInfoDb_1.24.2         Biostrings_2.56.0          
[23] XVector_0.28.0              IRanges_2.24.1             
[25] S4Vectors_0.28.1            BiocParallel_1.24.1        
[27] Biobase_2.48.0              BiocGenerics_0.36.1        
[29] edgeR_3.30.3                limma_3.44.3               

loaded via a namespace (and not attached):
 [1] colorspace_2.0-1          hwriter_1.3.2            
 [3] ellipsis_0.3.2            fs_1.5.0                 
 [5] rstudioapi_0.13           bit64_4.0.5              
 [7] AnnotationDbi_1.50.3      fansi_0.5.0              
 [9] lubridate_1.7.10          xml2_1.3.2               
[11] sparseMatrixStats_1.2.1   splines_4.0.5            
[13] R.methodsS3_1.8.1         cachem_1.0.5             
[15] DESeq_1.39.0              geneplotter_1.66.0       
[17] knitr_1.33                jsonlite_1.7.2           
[19] broom_0.7.6               annotate_1.66.0          
[21] dbplyr_2.1.1              png_0.1-7                
[23] R.oo_1.24.0               compiler_4.0.5           
[25] httr_1.4.2                backports_1.2.1          
[27] assertthat_0.2.1          fastmap_1.1.0            
[29] cli_2.5.0                 htmltools_0.5.1.1        
[31] prettyunits_1.1.1         tools_4.0.5              
[33] gtable_0.3.0              glue_1.4.2               
[35] GenomeInfoDbData_1.2.3    rappdirs_0.3.3           
[37] Rcpp_1.0.6                cellranger_1.1.0         
[39] vctrs_0.3.8               rtracklayer_1.48.0       
[41] DelayedMatrixStats_1.12.3 xfun_0.23                
[43] rvest_1.0.0               lifecycle_1.0.0          
[45] XML_3.99-0.6              zlibbioc_1.34.0          
[47] scales_1.1.1              aroma.light_3.18.0       
[49] hms_1.1.0                 RColorBrewer_1.1-2       
[51] curl_4.3.1                memoise_2.0.0            
[53] biomaRt_2.44.4            latticeExtra_0.6-29      
[55] stringi_1.6.2             RSQLite_2.2.7            
[57] genefilter_1.70.0         GenomicFeatures_1.40.1   
[59] rlang_0.4.11              pkgconfig_2.0.3          
[61] bitops_1.0-7              evaluate_0.14            
[63] lattice_0.20-44           bit_4.0.4                
[65] tidyselect_1.1.1          magrittr_2.0.1           
[67] R6_2.5.0                  generics_0.1.0           
[69] DBI_1.1.1                 pillar_1.6.1             
[71] haven_2.4.1               withr_2.4.2              
[73] survival_3.2-11           RCurl_1.98-1.3           
[75] modelr_0.1.8              crayon_1.4.1             
[77] utf8_1.2.1                BiocFileCache_1.12.1     
[79] rmarkdown_2.8             jpeg_0.1-8.1             
[81] progress_1.2.2            locfit_1.5-9.4           
[83] grid_4.0.5                readxl_1.3.1             
[85] blob_1.2.1                reprex_2.0.0             
[87] digest_0.6.27             xtable_1.8-4             
[89] R.utils_2.10.1            openssl_1.4.4            
[91] munsell_0.5.0             askpass_1.1

Try:

BiocManager::valid()

This will help you to spot installation issues (when you have mixed packages from different and incompatible versions of Bioconductor).