biomaRt - NameSpace loading failed

Question

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: caricamento pacchetto o namespace fallito per ‘biomaRt’:
 .onLoad fallito in loadNamespace() per 'dbplyr', dettagli:
  chiamata: setClass(cl, contains = c(prevClass, "VIRTUAL"), where = where)
  errore: errore nelle classi contenute ("character") per la classe “ident”; definizione di classe rimossa da ‘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

score 0 · Answer 1 · answered Apr 11 '23 at 20:54

Translating the error message into English (using ChatGPT) I get the following translation:

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'

Based on this message, it appears that the version of dbplyr you are using has had a class definition removed that biomaRt needs to run. Perhaps you need to go back to a previous version of dbplyr? Alternatively, you could post this as a bug on biomaRt and wait for the maintainer to update their package to work with the latest version of dbplyr.

Thank you! Unfortunately even with two older version ofthe package the problem remains unsolved. I will ask in the bioconductor page — Alessia, Apr 12 '23 at 08:00

score 0 · Answer 2 · answered May 08 '23 at 13:20

0

I had the same issue. I dont think this will be an accepted answer, but reinstalling dbplyr and restarting the Rsession fixed the problem for me. I still dont know why the problem occurred in the first place though

answered May 08 '23 at 13:20

user34124

1

biomaRt - NameSpace loading failed

2 Answers2