useEnsemblGenomes not found
0
0
Entering edit mode
lessismore ▴ 20
@lessismore
Last seen 10 days ago
Italy

Dear all,

I was constantly using biomaRt for my analyses. Then left for few months. Now I cannot rerun my code as this function is no longer working and giving me the following error:


library(biomaRt)

> ensembl_plants <- useEnsemblGenomes(biomart = "plants_mart")

Error in useEnsemblGenomes(biomart = "plants_mart") : 
  could not find function "useEnsemblGenomes"

Do you have any tip for me?

Thanks

biomaRt • 156 views
ADD COMMENT
0
Entering edit mode

Can you provide the output of sessionInfo() after you've run library(biomaRt)? This will help me see what version of biomaRt you're using.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode

ok solved upgrading R and Rstudio to the latest version R (Kick Things) Rstudio (2021.09.0 Build 351)

ADD REPLY

Login before adding your answer.

Traffic: 298 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6