update: I've updated biomaRt to the latest version. Now I get the following error: > ensembl_plants <- useEnsemblGenomes(biomart = "plants_variations") 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')"

version 3.6.3 (2020-02-29) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets [6] methods base

other attached packages: [1] conflicted_1.0.4 biomaRt_2.48.3 forcats_0.5.1
[4] stringr_1.4.0 dplyr_0.8.0 purrr_0.3.4
[7] readr_2.0.2 tidyr_1.1.4 tibble_3.1.5
[10] ggplot2_3.3.5 tidyverse_1.3.1

loaded via a namespace (and not attached): [1] Biobase_2.46.0 httr_1.4.2
[3] pkgload_1.2.3 bit64_4.0.5
[5] jsonlite_1.7.2 modelr_0.1.8
[7] assertthat_0.2.1 BiocManager_1.30.16 [9] stats4_3.6.3 BiocFileCache_1.10.2 [11] blob_1.2.2 cellranger_1.1.0
[13] remotes_2.4.1 progress_1.2.2
[15] sessioninfo_1.1.1 pillar_1.6.4
[17] RSQLite_2.2.8 backports_1.2.1
[19] glue_1.4.2 digest_0.6.28
[21] rvest_1.0.2 colorspace_2.0-2
[23] XML_3.99-0.3 pkgconfig_2.0.3
[25] devtools_2.4.2 broom_0.7.9
[27] haven_2.4.3 scales_1.1.1
[29] processx_3.5.2 tzdb_0.1.2
[31] generics_0.1.0 IRanges_2.20.2
[33] usethis_2.1.0 ellipsis_0.3.2
[35] cachem_1.0.6 withr_2.4.2
[37] BiocGenerics_0.32.0 cli_3.0.1
[39] magrittr_2.0.1 crayon_1.4.1
[41] readxl_1.3.1 ps_1.6.0
[43] memoise_2.0.0 fs_1.5.0
[45] fansi_0.5.0 xml2_1.3.2
[47] pkgbuild_1.2.0 tools_3.6.3
[49] prettyunits_1.1.1 hms_1.1.1
[51] lifecycle_1.0.1 S4Vectors_0.24.4
[53] munsell_0.5.0 reprex_2.0.1
[55] AnnotationDbi_1.48.0 callr_3.7.0
[57] compiler_3.6.3 rlang_0.4.12
[59] grid_3.6.3 rstudioapi_0.13
[61] rappdirs_0.3.3 testthat_3.1.0
[63] gtable_0.3.0 DBI_1.1.1
[65] curl_4.3.2 R6_2.5.1
[67] lubridate_1.8.0 knitr_1.36
[69] fastmap_1.1.0 bit_4.0.4
[71] utf8_1.2.2 rprojroot_2.0.2
[73] desc_1.4.0 stringi_1.7.5
[75] parallel_3.6.3 Rcpp_1.0.7
[77] vctrs_0.3.8 dbplyr_2.1.1
[79] tidyselect_1.1.1 xfun_0.27