biomaRt - NameSpace loading failed
0
0
Entering edit mode
Alessia • 0
@1b283aa4
Last seen 5 months ago
Spain

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 
biomaRt bioma • 2.0k views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 428 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