Hi Mike, based on https://www.biostars.org/p/9559740/#9559740 I made this MRE which errors in R 4.3 - Bioc 3.17 and latest DESeq2. I just checked that it runs fine in the Bioc 3.16 Docker container but errors in the 3.17 one. Hope that helps tracking it down.

suppressMessages(library(DESeq2))
set.seed(1)
dds <- makeExampleDESeqDataSet(n=50000, m=20)
dds <- DESeq(dds, quiet=TRUE)
res <- lfcShrink(dds, coef=2, type="apeglm", quiet=TRUE)
#> Warning in nbinomGLM(x = x, Y = YNZ, size = size, weights = weightsNZ, offset =
#> offsetNZ, : the line search routine failed, possibly due to insufficient
#> numeric precision
#> Error in optimHess(par = init, fn = nbinomFn, gr = nbinomGr, x = x, y = y, : nicht endlicher Wert von optim angegeben
sessionInfo()
#> R version 4.3.0 (2023-04-21 ucrt)
#> Platform: x86_64-w64-mingw32/x64 (64-bit)
#> Running under: Windows 11 x64 (build 22000)
#> 
#> Matrix products: default
#> 
#> 
#> locale:
#> [1] LC_COLLATE=German_Germany.utf8  LC_CTYPE=German_Germany.utf8   
#> [3] LC_MONETARY=German_Germany.utf8 LC_NUMERIC=C                   
#> [5] LC_TIME=German_Germany.utf8    
#> 
#> time zone: Etc/GMT-1
#> tzcode source: internal
#> 
#> attached base packages:
#> [1] stats4    stats     graphics  grDevices utils     datasets  methods  
#> [8] base     
#> 
#> other attached packages:
#>  [1] DESeq2_1.40.1               SummarizedExperiment_1.30.1
#>  [3] Biobase_2.60.0              MatrixGenerics_1.12.0      
#>  [5] matrixStats_0.63.0          GenomicRanges_1.52.0       
#>  [7] GenomeInfoDb_1.36.0         IRanges_2.34.0             
#>  [9] S4Vectors_0.38.1            BiocGenerics_0.46.0        
#> 
#> loaded via a namespace (and not attached):
#>  [1] utf8_1.2.3              bitops_1.0-7            lattice_0.21-8         
#>  [4] digest_0.6.31           magrittr_2.0.3          evaluate_0.21          
#>  [7] grid_4.3.0              mvtnorm_1.1-3           fastmap_1.1.1          
#> [10] plyr_1.8.8              Matrix_1.5-4            fansi_1.0.4            
#> [13] scales_1.2.1            numDeriv_2016.8-1.1     codetools_0.2-19       
#> [16] emdbook_1.3.12          cli_3.6.1               bbmle_1.0.25           
#> [19] rlang_1.1.1             crayon_1.5.2            XVector_0.40.0         
#> [22] munsell_0.5.0           reprex_2.0.2            withr_2.5.0            
#> [25] DelayedArray_0.26.2     yaml_2.3.7              S4Arrays_1.0.1         
#> [28] tools_4.3.0             parallel_4.3.0          BiocParallel_1.34.1    
#> [31] coda_0.19-4             bdsmatrix_1.3-6         colorspace_2.1-0       
#> [34] ggplot2_3.4.2           locfit_1.5-9.7          GenomeInfoDbData_1.2.10
#> [37] vctrs_0.6.2             R6_2.5.1                lifecycle_1.0.3        
#> [40] zlibbioc_1.46.0         fs_1.6.2                MASS_7.3-58.4          
#> [43] pkgconfig_2.0.3         pillar_1.9.0            gtable_0.3.3           
#> [46] glue_1.6.2              Rcpp_1.0.10             xfun_0.39              
#> [49] tibble_3.2.1            rstudioapi_0.14         knitr_1.42             
#> [52] htmltools_0.5.5         apeglm_1.22.0           rmarkdown_2.21         
#> [55] compiler_4.3.0          RCurl_1.98-1.12
Created on 2023-05-10 with reprex v2.0.2

Thanks ATpoint !

Yeah weird, i still have the previous release and it's fine, I needed to update anyway, so will check this once I have it set up.

set.seed(1)
dds <- makeExampleDESeqDataSet(n=50000, m=20)
dds <- DESeq(dds, quiet=TRUE)
res <- lfcShrink(dds, coef=2, type="apeglm", quiet=TRUE)
packageVersion("DESeq2")
[1] 1.38.3