I discovered that several AnnotationHub objects corresponding to genome assemblies are no longer available after updating to R 3.6.0. Specifically:
> hub = AnnotationHub() snapshotDate(): 2019-04-29 > hub[["AH134"]] Error: Defunct > hub[["AH188"]] Error: Defunct > hub[["AH47190"]] Error: Defunct > hub[["AH80"]] Error: Defunct
The above objects correspond to the hg19, mm10, danRer10, and dm5 genome assemblies. My lab relies on these assemblies, which are still pretty commonly used. I'm unsure of when these objects became unavailable, but as of R 3.5.3 (and correspond updated versions of Bioconductor packages), I was able to access them via my cached copies. However, after upgrading to R 3.6.0, I am unable to access them even though I have copies in my local cache.
I searched AnnotationHub() to see if I could find equivalents under other names, but was unable to.
Here is my sessionInfo():
> sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.4 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib locale:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  parallel grDevices utils datasets stats graphics methods base other attached packages:  AnnotationHub_2.15.15 BiocFileCache_1.7.10 dbplyr_1.4.0 BiocGenerics_0.29.2 readr_1.3.1 dplyr_0.8.0.1 tibble_2.1.1 magrittr_1.5 loaded via a namespace (and not attached):  Rcpp_1.0.1 pillar_1.3.1 compiler_3.6.0 BiocManager_1.30.4 later_0.8.0  tools_3.6.0 digest_0.6.18 bit_1.1-14 RSQLite_2.1.1 memoise_1.1.0  pkgconfig_2.0.2 rlang_0.3.4 shiny_1.3.2 DBI_1.0.0 curl_3.3  yaml_2.2.0 httr_1.4.0 IRanges_2.17.5 S4Vectors_0.21.24 rappdirs_0.3.1  hms_0.4.2 stats4_3.6.0 bit64_0.9-7 tidyselect_0.2.5 Biobase_2.43.1  glue_1.3.1 R6_2.4.0 AnnotationDbi_1.45.1 purrr_0.3.2 blob_1.1.1  promises_1.0.1 htmltools_0.3.6 assertthat_0.2.1 mime_0.6 interactiveDisplayBase_1.21.0  xtable_1.8-4 httpuv_1.5.1 crayon_1.3.4