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rcavalcante / annotatr

Package Homepage: http://bioconductor.org/packages/devel/bioc/html/annotatr.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=annotatr.
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Problem with obtaining certain annotations #43

Closed jakalssj3 closed 3 years ago

jakalssj3 commented 3 years ago

The below code I use to download annotations with annotatr works only partially:

annotations <- c("hg19_cpgs","hg19_genes_promoters")
promoters.GR <- annotatr::build_annotations(genome='hg19', annotations=c(annotations[2]))
cpgs.GR <- annotatr::build_annotations(genome='hg19', annotations=c(annotations[1]))

Specifically, there is no problem to get annotations of promoters, but when trying to get cpg annotations, the following error occurs:

Error in UseMethod("filter_") : no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"

What could be the reason for this?

I'm using R version 3.6.3 and annotatr version 1.12.1

rcavalcante commented 3 years ago

Hi,

Thanks for using annotatr. I couldn't replicate your error using a Docker image with a similar environment (R 3.6.2 and annotar 1.12.1):

https://hub.docker.com/repository/docker/rcavalcante/bioconductor_docker (RELEASE_3_10 tag)

I wonder if perhaps you have some packages loaded that are causing the error because of NAMESPACE issues... I'm not sure if the code you provided above is after only doing library(annotatr) or if you've loaded other packages too. Do you get the same error with just library(annotatr)?

Here is my devtools::session_info():

> devtools::session_info()
─ Session info ───────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.6.2 (2019-12-12)
 os       Debian GNU/Linux 10 (buster)
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       Etc/UTC                     
 date     2021-06-11                  

─ Packages ───────────────────────────────────────────────────────────────────
 package                           * version  date       lib source        
 AnnotationDbi                     * 1.48.0   2019-10-29 [1] Bioconductor  
 AnnotationHub                       2.18.0   2019-10-29 [1] Bioconductor  
 annotatr                          * 1.12.1   2019-11-12 [1] Bioconductor  
 askpass                             1.1      2019-01-13 [1] CRAN (R 3.6.2)
 assertthat                          0.2.1    2019-03-21 [1] CRAN (R 3.6.2)
 backports                           1.1.5    2019-10-02 [1] CRAN (R 3.6.2)
 Biobase                           * 2.46.0   2019-10-29 [1] Bioconductor  
 BiocFileCache                       1.10.2   2019-11-08 [1] Bioconductor  
 BiocGenerics                      * 0.32.0   2019-10-29 [1] Bioconductor  
 BiocManager                       * 1.30.10  2019-11-16 [1] CRAN (R 3.6.2)
 BiocParallel                        1.20.1   2019-12-21 [1] Bioconductor  
 BiocVersion                         3.10.1   2019-06-06 [1] Bioconductor  
 biomaRt                             2.42.1   2020-03-26 [1] Bioconductor  
 Biostrings                          2.54.0   2019-10-29 [1] Bioconductor  
 bit                                 1.1-15.2 2020-02-10 [1] CRAN (R 3.6.2)
 bit64                               0.9-7    2017-05-08 [1] CRAN (R 3.6.2)
 bitops                              1.0-6    2013-08-17 [1] CRAN (R 3.6.2)
 blob                                1.2.1    2020-01-20 [1] CRAN (R 3.6.2)
 BSgenome                            1.54.0   2019-10-29 [1] Bioconductor  
 callr                               3.4.2    2020-02-12 [1] CRAN (R 3.6.2)
 cli                                 2.0.2    2020-02-28 [1] CRAN (R 3.6.2)
 colorspace                          1.4-1    2019-03-18 [1] CRAN (R 3.6.2)
 crayon                              1.3.4    2017-09-16 [1] CRAN (R 3.6.2)
 curl                                4.3      2019-12-02 [1] CRAN (R 3.6.2)
 DBI                                 1.1.0    2019-12-15 [1] CRAN (R 3.6.2)
 dbplyr                              1.4.2    2019-06-17 [1] CRAN (R 3.6.2)
 DelayedArray                        0.12.2   2020-01-06 [1] Bioconductor  
 desc                                1.2.0    2018-05-01 [1] CRAN (R 3.6.2)
 devtools                            2.2.2    2020-02-17 [1] CRAN (R 3.6.2)
 digest                              0.6.25   2020-02-23 [1] CRAN (R 3.6.2)
 dplyr                               0.8.5    2020-03-07 [1] CRAN (R 3.6.2)
 ellipsis                            0.3.0    2019-09-20 [1] CRAN (R 3.6.2)
 fansi                               0.4.1    2020-01-08 [1] CRAN (R 3.6.2)
 fastmap                             1.0.1    2019-10-08 [1] CRAN (R 3.6.2)
 fs                                  1.3.2    2020-03-05 [1] CRAN (R 3.6.2)
 GenomeInfoDb                      * 1.22.0   2019-10-29 [1] Bioconductor  
 GenomeInfoDbData                    1.2.2    2020-03-27 [1] Bioconductor  
 GenomicAlignments                   1.22.1   2019-11-12 [1] Bioconductor  
 GenomicFeatures                   * 1.38.2   2020-02-15 [1] Bioconductor  
 GenomicRanges                     * 1.38.0   2019-10-29 [1] Bioconductor  
 ggplot2                             3.3.0    2020-03-05 [1] CRAN (R 3.6.2)
 glue                                1.3.2    2020-03-12 [1] CRAN (R 3.6.2)
 gtable                              0.3.0    2019-03-25 [1] CRAN (R 3.6.2)
 hms                                 0.5.3    2020-01-08 [1] CRAN (R 3.6.2)
 htmltools                           0.4.0    2019-10-04 [1] CRAN (R 3.6.2)
 httpuv                              1.5.2    2019-09-11 [1] CRAN (R 3.6.2)
 httr                                1.4.1    2019-08-05 [1] CRAN (R 3.6.2)
 interactiveDisplayBase              1.24.0   2019-10-29 [1] Bioconductor  
 IRanges                           * 2.20.2   2020-01-13 [1] Bioconductor  
 later                               1.0.0    2019-10-04 [1] CRAN (R 3.6.2)
 lattice                             0.20-40  2020-02-19 [2] CRAN (R 3.6.2)
 lifecycle                           0.2.0    2020-03-06 [1] CRAN (R 3.6.2)
 magrittr                            1.5      2014-11-22 [1] CRAN (R 3.6.2)
 Matrix                              1.2-18   2019-11-27 [2] CRAN (R 3.6.2)
 matrixStats                         0.56.0   2020-03-13 [1] CRAN (R 3.6.2)
 memoise                             1.1.0    2017-04-21 [1] CRAN (R 3.6.2)
 mime                                0.9      2020-02-04 [1] CRAN (R 3.6.2)
 munsell                             0.5.0    2018-06-12 [1] CRAN (R 3.6.2)
 openssl                             1.4.1    2019-07-18 [1] CRAN (R 3.6.2)
 org.Hs.eg.db                      * 3.10.0   2020-03-27 [1] Bioconductor  
 pillar                              1.4.3    2019-12-20 [1] CRAN (R 3.6.2)
 pkgbuild                            1.0.6    2019-10-09 [1] CRAN (R 3.6.2)
 pkgconfig                           2.0.3    2019-09-22 [1] CRAN (R 3.6.2)
 pkgload                             1.0.2    2018-10-29 [1] CRAN (R 3.6.2)
 plyr                                1.8.6    2020-03-03 [1] CRAN (R 3.6.2)
 prettyunits                         1.1.1    2020-01-24 [1] CRAN (R 3.6.2)
 processx                            3.4.2    2020-02-09 [1] CRAN (R 3.6.2)
 progress                            1.2.2    2019-05-16 [1] CRAN (R 3.6.2)
 promises                            1.1.0    2019-10-04 [1] CRAN (R 3.6.2)
 ps                                  1.3.2    2020-02-13 [1] CRAN (R 3.6.2)
 purrr                               0.3.3    2019-10-18 [1] CRAN (R 3.6.2)
 R6                                  2.4.1    2019-11-12 [1] CRAN (R 3.6.2)
 rappdirs                            0.3.1    2016-03-28 [1] CRAN (R 3.6.2)
 Rcpp                                1.0.4    2020-03-17 [1] CRAN (R 3.6.2)
 RCurl                               1.98-1.1 2020-01-19 [1] CRAN (R 3.6.2)
 readr                               1.3.1    2018-12-21 [1] CRAN (R 3.6.2)
 regioneR                            1.18.1   2020-01-14 [1] Bioconductor  
 remotes                             2.1.1    2020-02-15 [1] CRAN (R 3.6.2)
 reshape2                            1.4.3    2017-12-11 [1] CRAN (R 3.6.2)
 rlang                               0.4.5    2020-03-01 [1] CRAN (R 3.6.2)
 rprojroot                           1.3-2    2018-01-03 [1] CRAN (R 3.6.2)
 Rsamtools                           2.2.3    2020-02-23 [1] Bioconductor  
 RSQLite                             2.2.0    2020-01-07 [1] CRAN (R 3.6.2)
 rtracklayer                         1.46.0   2019-10-29 [1] Bioconductor  
 S4Vectors                         * 0.24.3   2020-01-18 [1] Bioconductor  
 scales                              1.1.0    2019-11-18 [1] CRAN (R 3.6.2)
 sessioninfo                         1.1.1    2018-11-05 [1] CRAN (R 3.6.2)
 shiny                               1.4.0.2  2020-03-13 [1] CRAN (R 3.6.2)
 stringi                             1.4.6    2020-02-17 [1] CRAN (R 3.6.2)
 stringr                             1.4.0    2019-02-10 [1] CRAN (R 3.6.2)
 SummarizedExperiment                1.16.1   2019-12-19 [1] Bioconductor  
 testthat                            2.3.2    2020-03-02 [1] CRAN (R 3.6.2)
 tibble                              2.1.3    2019-06-06 [1] CRAN (R 3.6.2)
 tidyselect                          1.0.0    2020-01-27 [1] CRAN (R 3.6.2)
 TxDb.Hsapiens.UCSC.hg19.knownGene * 3.2.2    2020-03-27 [1] Bioconductor  
 usethis                             1.5.1    2019-07-04 [1] CRAN (R 3.6.2)
 vctrs                               0.2.4    2020-03-10 [1] CRAN (R 3.6.2)
 withr                               2.1.2    2018-03-15 [1] CRAN (R 3.6.2)
 XML                                 3.99-0.3 2020-01-20 [1] CRAN (R 3.6.2)
 xtable                              1.8-4    2019-04-21 [1] CRAN (R 3.6.2)
 XVector                             0.26.0   2019-10-29 [1] Bioconductor  
 yaml                                2.2.1    2020-02-01 [1] CRAN (R 3.6.2)
 zlibbioc                            1.32.0   2019-10-29 [1] Bioconductor  

[1] /usr/local/lib/R/site-library
[2] /usr/local/lib/R/library
jakalssj3 commented 3 years ago

Do you get the same error with just library(annotatr)?

Unfortunately, I get the same error with a fresh R session and only this single library loaded.

rcavalcante commented 3 years ago

Interesting...

I'd be curious to see the result of your session info (preferably devtools::session_info() because it gets alphabetized). I bet there's some dependency that's different between us.

jakalssj3 commented 3 years ago

Here is a more extensive log:

> library(annotatr)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.
> annotations <- c("hg19_cpgs","hg19_genes_promoters", "hg19_basicgenes")
> promoters.GR <- annotatr::build_annotations(genome='hg19', annotations=c(annotations[2]))
Loading required package: GenomicFeatures
'select()' returned 1:1 mapping between keys and columns
Building promoters...

> cpgs.GR <- annotatr::build_annotations(genome='hg19', annotations=c(annotations[1]))
Error in UseMethod("filter_") :
  no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
> devtools::session_info()
Error in get(genname, envir = envir) : object 'testthat_print' not found
Failed to create bus connection: No such file or directory
─ Session info ──────────────────────────────────────────
 setting  value
 version  R version 3.6.3 (2020-02-29)
 os       Ubuntu 18.04 LTS
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  C.UTF-8
 ctype    C.UTF-8
 tz       Etc/UTC
 date     2021-06-11

─ Packages ───────────────────────────────────────────
 package                           * version  date       lib source
 AnnotationDbi                     * 1.48.0   2019-10-29 [1] Bioconductor
 AnnotationHub                       2.18.0   2019-10-29 [1] Bioconductor
 annotatr                          * 1.12.1   2019-11-12 [1] Bioconductor
 askpass                             1.1      2019-01-13 [2] CRAN (R 3.6.3)
 assertthat                          0.2.1    2019-03-21 [2] CRAN (R 3.6.3)
 Biobase                           * 2.46.0   2019-10-29 [2] Bioconductor
 BiocFileCache                       1.10.2   2019-11-08 [1] Bioconductor
 BiocGenerics                      * 0.32.0   2019-10-29 [1] Bioconductor
 BiocManager                         1.30.15  2021-05-11 [1] CRAN (R 3.6.3)
 BiocParallel                        1.20.1   2019-12-21 [1] Bioconductor
 BiocVersion                         3.10.1   2019-06-06 [2] Bioconductor
 biomaRt                             2.42.1   2020-03-26 [1] Bioconductor
 Biostrings                          2.54.0   2019-10-29 [1] Bioconductor
 bit                                 4.0.4    2020-08-04 [1] CRAN (R 3.6.3)
 bit64                               4.0.5    2020-08-30 [1] CRAN (R 3.6.3)
 bitops                              1.0-6    2013-08-17 [2] CRAN (R 3.6.3)
 blob                                1.2.1    2020-01-20 [1] CRAN (R 3.6.3)
 BSgenome                            1.54.0   2019-10-29 [1] Bioconductor
 callr                               3.7.0    2021-04-20 [1] CRAN (R 3.6.3)
 cli                                 2.5.0    2021-04-26 [1] CRAN (R 3.6.3)
 colorspace                          1.4-1    2019-03-18 [2] CRAN (R 3.6.3)
 crayon                              1.4.1    2021-02-08 [1] CRAN (R 3.6.3)
 curl                                4.3      2019-12-02 [2] CRAN (R 3.6.3)
 DBI                                 1.1.0    2019-12-15 [2] CRAN (R 3.6.3)
 dbplyr                              2.1.1    2021-04-06 [1] CRAN (R 3.6.3)
 DelayedArray                        0.12.3   2020-04-09 [1] Bioconductor
 desc                                1.2.0    2018-05-01 [2] CRAN (R 3.6.3)
 devtools                            2.3.2    2020-09-18 [1] CRAN (R 3.6.3)
 digest                              0.6.25   2020-02-23 [2] CRAN (R 3.6.3)
 dplyr                               1.0.6    2021-05-05 [1] CRAN (R 3.6.3)
 ellipsis                            0.3.2    2021-04-29 [1] CRAN (R 3.6.3)
 fansi                               0.4.2    2021-01-15 [1] CRAN (R 3.6.3)
 fastmap                             1.1.0    2021-01-25 [1] CRAN (R 3.6.3)
 fs                                  1.4.2    2020-06-30 [1] CRAN (R 3.6.3)
 generics                            0.1.0    2020-10-31 [1] CRAN (R 3.6.3)
 GenomeInfoDb                      * 1.22.1   2020-03-27 [1] Bioconductor
 GenomeInfoDbData                    1.2.2    2020-08-23 [2] Bioconductor
 GenomicAlignments                   1.22.1   2019-11-12 [1] Bioconductor
 GenomicFeatures                   * 1.38.2   2020-02-15 [1] Bioconductor
 GenomicRanges                     * 1.38.0   2019-10-29 [1] Bioconductor
 ggplot2                             3.3.3    2020-12-30 [1] CRAN (R 3.6.3)
 glue                                1.4.1    2020-05-13 [2] CRAN (R 3.6.3)
 gtable                              0.3.0    2019-03-25 [2] CRAN (R 3.6.3)
 hms                                 1.1.0    2021-05-17 [1] CRAN (R 3.6.3)
 htmltools                           0.5.1.1  2021-01-22 [1] CRAN (R 3.6.3)
 httpuv                              1.5.3.1  2020-05-26 [1] CRAN (R 3.6.3)
 httr                                1.4.2    2020-07-20 [2] CRAN (R 3.6.3)
 interactiveDisplayBase              1.24.0   2019-10-29 [1] Bioconductor
 IRanges                           * 2.20.2   2020-01-13 [2] Bioconductor
 later                               1.0.0    2019-10-04 [1] CRAN (R 3.6.3)
 lattice                             0.20-41  2020-04-02 [4] CRAN (R 3.6.3)
 lifecycle                           1.0.0    2021-02-15 [1] CRAN (R 3.6.3)
 magrittr                            1.5      2014-11-22 [2] CRAN (R 3.6.3)
 Matrix                              1.2-18   2019-11-27 [4] CRAN (R 3.6.1)
 matrixStats                         0.56.0   2020-03-13 [1] CRAN (R 3.6.3)
 memoise                             1.1.0    2017-04-21 [2] CRAN (R 3.6.3)
 mime                                0.9      2020-02-04 [2] CRAN (R 3.6.3)
 munsell                             0.5.0    2018-06-12 [2] CRAN (R 3.6.3)
 openssl                             1.4.2    2020-06-27 [2] CRAN (R 3.6.3)
 org.Hs.eg.db                      * 3.10.0   2020-07-13 [1] Bioconductor
 pillar                              1.6.1    2021-05-16 [1] CRAN (R 3.6.3)
 pkgbuild                            1.1.0    2020-07-13 [2] CRAN (R 3.6.3)
 pkgconfig                           2.0.3    2019-09-22 [2] CRAN (R 3.6.3)
 pkgload                             1.1.0    2020-05-29 [2] CRAN (R 3.6.3)
 plyr                                1.8.6    2020-03-03 [2] CRAN (R 3.6.3)
 prettyunits                         1.1.1    2020-01-24 [2] CRAN (R 3.6.3)
 processx                            3.5.2    2021-04-30 [1] CRAN (R 3.6.3)
 progress                            1.2.2    2019-05-16 [1] CRAN (R 3.6.3)
 promises                            1.1.0    2019-10-04 [1] CRAN (R 3.6.3)
 ps                                  1.3.4    2020-08-11 [2] CRAN (R 3.6.3)
 purrr                               0.3.4    2020-04-17 [2] CRAN (R 3.6.3)
 R6                                  2.4.1    2019-11-12 [2] CRAN (R 3.6.3)
 rappdirs                            0.3.1    2016-03-28 [2] CRAN (R 3.6.3)
 Rcpp                                1.0.6    2021-01-15 [1] CRAN (R 3.6.3)
 RCurl                               1.98-1.2 2020-04-18 [1] CRAN (R 3.6.3)
 readr                               1.3.1    2018-12-21 [1] CRAN (R 3.6.3)
 regioneR                            1.18.1   2020-01-14 [1] Bioconductor
 remotes                             2.2.0    2020-07-21 [1] CRAN (R 3.6.3)
 reshape2                            1.4.4    2020-04-09 [2] CRAN (R 3.6.3)
 rlang                               0.4.10   2020-12-30 [1] CRAN (R 3.6.3)
 rprojroot                           2.0.2    2020-11-15 [1] CRAN (R 3.6.3)
 Rsamtools                           2.2.3    2020-02-23 [1] Bioconductor
 RSQLite                             2.2.7    2021-04-22 [1] CRAN (R 3.6.3)
 rstudioapi                          0.11     2020-02-07 [2] CRAN (R 3.6.3)
 rtracklayer                         1.46.0   2019-10-29 [1] Bioconductor
 S4Vectors                         * 0.24.4   2020-04-09 [1] Bioconductor
 scales                              1.1.1    2020-05-11 [2] CRAN (R 3.6.3)
 sessioninfo                         1.1.1    2018-11-05 [1] CRAN (R 3.6.3)
 shiny                               1.6.0    2021-01-25 [1] CRAN (R 3.6.3)
 stringi                             1.4.6    2020-02-17 [2] CRAN (R 3.6.3)
 stringr                             1.4.0    2019-02-10 [2] CRAN (R 3.6.3)
 SummarizedExperiment                1.16.1   2019-12-19 [1] Bioconductor
 testthat                            2.3.2    2020-03-02 [2] CRAN (R 3.6.3)
 tibble                              3.1.2    2021-05-16 [1] CRAN (R 3.6.3)
 tidyselect                          1.1.0    2020-05-11 [2] CRAN (R 3.6.3)
 TxDb.Hsapiens.UCSC.hg19.knownGene * 3.2.2    2020-05-29 [1] Bioconductor
 usethis                             2.0.1    2021-02-10 [1] CRAN (R 3.6.3)
 utf8                                1.1.4    2018-05-24 [2] CRAN (R 3.6.3)
 vctrs                               0.3.8    2021-04-29 [1] CRAN (R 3.6.3)
 withr                               2.4.1    2021-01-26 [1] CRAN (R 3.6.3)
 XML                                 3.99-0   2020-07-24 [1] local
 xtable                              1.8-4    2019-04-21 [1] CRAN (R 3.6.3)
 XVector                             0.26.0   2019-10-29 [2] Bioconductor
 yaml                                2.2.1    2020-02-01 [1] CRAN (R 3.6.3)
 zlibbioc                            1.32.0   2019-10-29 [2] Bioconductor
jakalssj3 commented 3 years ago

I've tried several things now, including restarting R, reinstalling annotatr and still on selected annotation classes the same error appears:

> annots = c('hg19_cpgs', 'hg19_basicgenes', 'hg19_genes_intergenic')
> annotations = build_annotations(genome = 'hg19', annotations = annots)
'select()' returned 1:1 mapping between keys and columns
Building promoters...
Building 1to5kb upstream of TSS...
Building intergenic...
Building 5UTRs...
Building 3UTRs...
Building exons...
Building introns...
Error in UseMethod("filter_") : 
  no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
rcavalcante commented 3 years ago

I think this is related to a major version difference in the tibble package. You have 3.1.2 and I have 2.1.3.

I'm going to update my tidyverse install in the image and see if I can then reproduce.

rcavalcante commented 3 years ago

Bingo, that's the issue.

I'll have to wait until next week to look into this in more detail. I'll keep you updated. Thanks for the quick replies.

jakalssj3 commented 3 years ago

Great, thanks for tracking the issue so fast!

rcavalcante commented 3 years ago

Sorry for the delay, but I had to wrap up some work things before going on vacation. I will be able to get to this at the beginning of July.

rcavalcante commented 3 years ago

Upon further investigation, it actually looks like this is an issue with the AnnotationHub package and the updated tibble (or tidyverse) package. In the docker image I have for Bioconductor 3.10, I updated tidyverse to your versions and encountered an issue at the line:

ah = AnnotationHub::AnnotationHub()

So this is a much deeper dependency compatibility issue that falls outside the scope of annotatr proper. I hate when the solution to problems like this is "Update your version of R," but I think that's the solution here. When I use a fresh Bioconductor 3.13 docker image I don't get that error.

For now I'll close this.