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I installed biomaRt after the latest R update and I am having problems. Whenever I try to call library("biomaRt") it gives me the following error:
Error in completeSubclasses(classDef2, class1, obj, where) :
trying to get slot "subclasses" from an object of a basic class ("NULL") with no slots
Error: package or namespace load failed for 'biomaRt':
.onLoad failed in loadNamespace() for 'dbplyr', details:
call: setClass(cl, contains = c(prevClass, "VIRTUAL"), where = where)
error: error in the contained classes ("character") for the class "ident";
class definition removed from 'dbplyr'
I tried to re-install it and update dbplyr as well but the problem is not solved. Any suggestions?
> sessionInfo()
R version 4.2.3 (2023-03-15 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22621)
Matrix products: default
locale:
[1] LC_COLLATE=Italian_Italy.utf8 LC_CTYPE=Italian_Italy.utf8 LC_MONETARY=Italian_Italy.utf8 LC_NUMERIC=C
[5] LC_TIME=Italian_Italy.utf8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] fgsea_1.24.0 colorspace_2.1-0 ggtree_3.6.2 gson_0.1.0 qvalue_2.30.0
[6] XVector_0.38.0 aplot_0.1.10 rstudioapi_0.14 farver_2.1.1 graphlayouts_0.8.4
[11] ggrepel_0.9.3 bit64_4.0.5 AnnotationDbi_1.60.2 fansi_1.0.4 scatterpie_0.1.8
[16] codetools_0.2-19 splines_4.2.3 cachem_1.0.7 GOSemSim_2.24.0 knitr_1.42
[21] polyclip_1.10-4 jsonlite_1.8.4 GO.db_3.16.0 png_0.1-8 ggforce_0.4.1
[26] BiocManager_1.30.20 compiler_4.2.3 httr_1.4.5 Matrix_1.5-3 fastmap_1.1.1
[31] lazyeval_0.2.2 cli_3.6.1 tweenr_2.0.2 htmltools_0.5.5 prettyunits_1.1.1
[36] tools_4.2.3 igraph_1.4.1 gtable_0.3.3 glue_1.6.2 GenomeInfoDbData_1.2.9
[41] reshape2_1.4.4 dplyr_1.1.1 fastmatch_1.1-3 Rcpp_1.0.10 enrichplot_1.18.4
[46] Biobase_2.58.0 vctrs_0.6.1 Biostrings_2.66.0 ape_5.7-1 nlme_3.1-162
[51] ggraph_2.1.0 xfun_0.38 stringr_1.5.0 lifecycle_1.0.3 clusterProfiler_4.6.2
[56] XML_3.99-0.14 DOSE_3.24.2 zlibbioc_1.44.0 MASS_7.3-58.2 scales_1.2.1
[61] tidygraph_1.2.3 hms_1.1.3 parallel_4.2.3 RColorBrewer_1.1-3 yaml_2.3.7
[66] memoise_2.0.1 gridExtra_2.3 ggplot2_3.4.2 downloader_0.4 ggfun_0.0.9
[71] HDO.db_0.99.1 yulab.utils_0.0.6 stringi_1.7.12 RSQLite_2.3.0 S4Vectors_0.36.2
[76] tidytree_0.4.2 BiocGenerics_0.44.0 BiocParallel_1.32.6 GenomeInfoDb_1.34.9 rlang_1.1.0
[81] pkgconfig_2.0.3 bitops_1.0-7 evaluate_0.20 lattice_0.20-45 purrr_1.0.1
[86] treeio_1.22.0 patchwork_1.1.2 cowplot_1.1.1 shadowtext_0.1.2 bit_4.0.5
[91] tidyselect_1.2.0 plyr_1.8.8 magrittr_2.0.3 R6_2.5.1 IRanges_2.32.0
[96] generics_0.1.3 DBI_1.1.3 pillar_1.9.0 withr_2.5.0 KEGGREST_1.38.0
[101] RCurl_1.98-1.12 tibble_3.2.1 crayon_1.5.2 utf8_1.2.3 rmarkdown_2.21
[106] viridis_0.6.2 progress_1.2.2 grid_4.2.3 data.table_1.14.8 blob_1.2.4
[111] digest_0.6.31 tidyr_1.3.0 gridGraphics_0.5-1 stats4_4.2.3 munsell_0.5.0
[116] viridisLite_0.4.1 ggplotify_0.1.0
I don't think this is really a biomaRt issue, as biomaRt doesn't use the dbplyr package directly. It also seems like this error is somewhat common, and not easy to fix e.g. https://github.com/tidyverse/dbplyr/issues/619 and https://github.com/tidyverse/dbplyr/issues/779
Perhaps start a totally new R session and run
BiocManager::valid()
which should give an overview of whether you have packages that need to be updated.If so there will be a section in the output called "create a valid installation with" and some code after that you can copy and paste to update the packages.