Unable to find an inherited method for function ‘species’ for signature ‘"character"’

[gerardq675]

Updated R to 4.0 and now am getting an error with the following code:

OrgDb = 'org.Hs.eg.db'
res@organism <- AnnotationDbi::species(OrgDb)
Unable to find an inherited method for function ‘species’ for signature ‘"character"’

Guessing it has something to do with stringtofactor changes?

[hpages]

sessionInfo() please?

I don't think this was ever meant to work.

I get the same thing with R 3.6 and BioC 3.10:

library(AnnotationDbi)
AnnotationDbi::species('org.Hs.eg.db')
# Error in (function (classes, fdef, mtable)  : 
#   unable to find an inherited method for function ‘species’ for signature ‘"character"’

Note that the following works though, in both BioC 3.10 (no longer supported) and BioC 3.11 (current release):

library(org.Hs.eg.db)
AnnotationDbi::species(org.Hs.eg.db)
# [1] "Homo sapiens"

[hbandukw]

Hello,

I am having the same problem with many of the AnnotationDbi functions.
library(org.Mm.eg.db) AnnotationDbi::species(org.Mm.eg.db)

Error:
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘species’ for signature ‘"character"’

I have been trying to use AnnotationDbi to get map EntrezIDs to GeneIDs but I keep running into this problem.

Mm <- org.Mm.eg.db gene_annos <- AnnotationDbi::select(Mm, keys = f_peakAnno_mappings$Genes, columns = c("ENTREZID", "SYMBOL"), keytype = "ENTREZID")
Where 'f_peakAnno_mappings' is a data frame with a column called 'Genes' that contains EntrezIDs that need to be mapped.

Genes
1	497097
2	497097
3	497097
4	497097
5	497097
6	497097

Error:
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘mapIds’ for signature ‘"character"’.

My sessionInfo() is:

`R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.4

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] biomaRt_2.44.1 org.Mm.eg.db_3.11.4 AnnotationDbi_1.50.3 IRanges_2.22.2 S4Vectors_0.26.1 Biobase_2.48.0 BiocGenerics_0.34.0 dplyr_1.0.1

loaded via a namespace (and not attached):
[1] reticulate_1.16 tidyselect_1.1.0 RSQLite_2.2.0 htmlwidgets_1.5.1
[5] grid_4.0.2 BiocParallel_1.22.0 Rtsne_0.15 scatterpie_0.1.4
[9] munsell_0.5.0 codetools_0.2-16 ica_1.0-2 future_1.18.0
[13] miniUI_0.1.1.1 colorspace_1.4-1 GOSemSim_2.14.1 knitr_1.29
[17] rstudioapi_0.11 Seurat_3.2.0 ROCR_1.0-11 tensor_1.5
[21] DOSE_3.14.0 listenv_0.8.0 urltools_1.7.3 GenomeInfoDbData_1.2.3
[25] polyclip_1.10-0 bit64_4.0.2 farver_2.0.3 downloader_0.4
[29] vctrs_0.3.2 generics_0.0.2 xfun_0.16 BiocFileCache_1.12.0
[33] R6_2.4.1 GenomeInfoDb_1.24.2 graphlayouts_0.7.0 rsvd_1.0.3
[37] bitops_1.0-6 spatstat.utils_1.17-0 fgsea_1.14.0 gridGraphics_0.5-0
[41] DelayedArray_0.14.1 assertthat_0.2.1 promises_1.1.1 scales_1.1.1
[45] ggraph_2.0.3 enrichplot_1.8.1 gtable_0.3.0 globals_0.12.5
[49] goftest_1.2-2 tidygraph_1.2.0 rlang_0.4.7 splines_4.0.2
[53] rtracklayer_1.48.0 lazyeval_0.2.2 europepmc_0.4 BiocManager_1.30.10
[57] reshape2_1.4.4 abind_1.4-5 GenomicFeatures_1.40.1 httpuv_1.5.4
[61] qvalue_2.20.0 clusterProfiler_3.16.0 tools_4.0.2 ggplotify_0.0.5
[65] ggplot2_3.3.2 gplots_3.0.4 ellipsis_0.3.1 RColorBrewer_1.1-2
[69] ggridges_0.5.2 Rcpp_1.0.5 plyr_1.8.6 progress_1.2.2
[73] zlibbioc_1.34.0 purrr_0.3.4 RCurl_1.98-1.2 prettyunits_1.1.1
[77] rpart_4.1-15 openssl_1.4.2 deldir_0.1-28 pbapply_1.4-2
[81] viridis_0.5.1 cowplot_1.0.0 zoo_1.8-8 SummarizedExperiment_1.18.2
[85] ggrepel_0.8.2 cluster_2.1.0 magrittr_1.5 data.table_1.13.0
[89] DO.db_2.9 lmtest_0.9-37 triebeard_0.3.0 RANN_2.6.1
[93] fitdistrplus_1.1-1 matrixStats_0.56.0 hms_0.5.3 patchwork_1.0.1
[97] mime_0.9 xtable_1.8-4 XML_3.99-0.5 gridExtra_2.3
[101] compiler_4.0.2 tibble_3.0.3 KernSmooth_2.23-17 crayon_1.3.4
[105] htmltools_0.5.0 mgcv_1.8-31 later_1.1.0.1 tidyr_1.1.1
[109] DBI_1.1.0 tweenr_1.0.1 ChIPseeker_1.24.0 dbplyr_1.4.4
[113] MASS_7.3-51.6 rappdirs_0.3.1 boot_1.3-25 Matrix_1.2-18
[117] gdata_2.18.0 igraph_1.2.5 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicRanges_1.40.0
[121] pkgconfig_2.0.3 rvcheck_0.1.8 GenomicAlignments_1.24.0 plotly_4.9.2.1
[125] xml2_1.3.2 XVector_0.28.0 stringr_1.4.0 digest_0.6.25
[129] sctransform_0.2.1 RcppAnnoy_0.0.16 spatstat.data_1.4-3 Biostrings_2.56.0
[133] leiden_0.3.3 fastmatch_1.1-0 uwot_0.1.8 curl_4.3
[137] gtools_3.8.2 shiny_1.5.0 Rsamtools_2.4.0 lifecycle_0.2.0
[141] nlme_3.1-148 jsonlite_1.7.0 viridisLite_0.3.0 askpass_1.1
[145] pillar_1.4.6 lattice_0.20-41 plotrix_3.7-8 fastmap_1.0.1
[149] httr_1.4.2 survival_3.2-3 GO.db_3.11.4 glue_1.4.1
[153] spatstat_1.64-1 png_0.1-7 bit_4.0.4 ggforce_0.3.2
[157] stringi_1.4.6 blob_1.2.1 caTools_1.18.0 memoise_1.1.0
[161] irlba_2.3.3 future.apply_1.6.0 ape_5.4 `

Any help will be greatly appreciated.
Hina

[mjsteinbaugh]

Argh, I seem to be hitting this error now with clusterProfiler gseGO():

gseGO(
    geneList = gene_list,
    ont = "BP",
    OrgDb = "org.Hs.eg.db",
    keyType = "ENSEMBL"
)

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'species' for signature '"character"'

I'll work on posting a bug report on the Bioconductor support forum as well.
@GuangchuangYu any thoughts on how to fix this?

sessionInfo()

R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
 [1] grid      parallel  stats4    stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
 [1] org.Hs.eg.db_3.11.4         AnnotationDbi_1.50.3       
 [3] pathview_1.28.1             DOSE_3.14.0                
 [5] clusterProfiler_3.16.1      acidgsea_0.3.2             
 [7] tximport_1.16.1             DESeqAnalysis_0.3.5        
 [9] DESeq2_1.28.1               acidplots_0.2.32           
[11] bcbioRNASeq_0.3.35          basejump_0.12.12           
[13] SummarizedExperiment_1.18.2 DelayedArray_0.14.1        
[15] matrixStats_0.56.0          Biobase_2.48.0             
[17] GenomicRanges_1.40.0        GenomeInfoDb_1.24.2        
[19] IRanges_2.22.2              S4Vectors_0.26.1           
[21] BiocGenerics_0.34.0         forcats_0.5.0              
[23] stringr_1.4.0               dplyr_1.0.1                
[25] purrr_0.3.4                 readr_1.3.1                
[27] tidyr_1.1.1                 tibble_3.0.3               
[29] ggplot2_3.3.2               tidyverse_1.3.0            
[31] magrittr_1.5                bb8_0.2.27                 

loaded via a namespace (and not attached):
  [1] tidyselect_1.1.0              RSQLite_2.2.0                
  [3] BiocParallel_1.22.0           scatterpie_0.1.4             
  [5] munsell_0.5.0                 withr_2.2.0                  
  [7] colorspace_1.4-1              GOSemSim_2.14.1              
  [9] pipette_0.4.13                knitr_1.29                   
 [11] rstudioapi_0.11               SingleCellExperiment_1.10.1  
 [13] labeling_0.3                  KEGGgraph_1.48.0             
 [15] urltools_1.7.3                GenomeInfoDbData_1.2.3       
 [17] polyclip_1.10-0               bit64_4.0.2                  
 [19] farver_2.0.3                  pheatmap_1.0.12              
 [21] downloader_0.4                vctrs_0.3.2                  
 [23] generics_0.0.2                acidgenerics_0.3.10          
 [25] xfun_0.16                     BiocFileCache_1.12.1         
 [27] R6_2.4.1                      graphlayouts_0.7.0           
 [29] locfit_1.5-9.4                acidbase_0.1.13              
 [31] AnnotationFilter_1.12.0       gridGraphics_0.5-0           
 [33] bitops_1.0-6                  fgsea_1.14.0                 
 [35] assertthat_0.2.1              promises_1.1.1               
 [37] scales_1.1.1                  vroom_1.2.1                  
 [39] ggraph_2.0.3                  enrichplot_1.8.1             
 [41] gtable_0.3.0                  tidygraph_1.2.0              
 [43] ensembldb_2.12.1              rlang_0.4.7                  
 [45] genefilter_1.70.0             splines_4.0.2                
 [47] rtracklayer_1.48.0            lazyeval_0.2.2               
 [49] europepmc_0.4                 broom_0.7.0                  
 [51] BiocManager_1.30.10           yaml_2.2.1                   
 [53] reshape2_1.4.4                modelr_0.1.8                 
 [55] GenomicFeatures_1.40.1        backports_1.1.8              
 [57] httpuv_1.5.4                  qvalue_2.20.0                
 [59] syntactic_0.4.2               tools_4.0.2                  
 [61] ggplotify_0.0.5               ellipsis_0.3.1               
 [63] RColorBrewer_1.1-2            goalie_0.4.8                 
 [65] sessioninfo_1.1.1             ggridges_0.5.2               
 [67] Rcpp_1.0.5                    plyr_1.8.6                   
 [69] progress_1.2.2                zlibbioc_1.34.0              
 [71] RCurl_1.98-1.2                prettyunits_1.1.1            
 [73] openssl_1.4.2                 viridis_0.5.1                
 [75] cowplot_1.0.0                 haven_2.3.1                  
 [77] ggrepel_0.8.2                 fs_1.5.0                     
 [79] data.table_1.13.0             DO.db_2.9                    
 [81] triebeard_0.3.0               reprex_0.3.0                 
 [83] ProtGenerics_1.20.0           evaluate_0.14                
 [85] hms_0.5.3                     mime_0.9                     
 [87] xtable_1.8-4                  XML_3.99-0.5                 
 [89] readxl_1.3.1                  gridExtra_2.3                
 [91] compiler_4.0.2                biomaRt_2.44.1               
 [93] crayon_1.3.4                  htmltools_0.5.0              
 [95] later_1.1.0.1                 geneplotter_1.66.0           
 [97] lubridate_1.7.9               DBI_1.1.0                    
 [99] tweenr_1.0.1                  dbplyr_1.4.4                 
[101] MASS_7.3-51.6                 rappdirs_0.3.1               
[103] Matrix_1.2-18                 cli_2.0.2                    
[105] igraph_1.2.5                  pkgconfig_2.0.3              
[107] rvcheck_0.1.8                 GenomicAlignments_1.24.0     
[109] xml2_1.3.2                    annotate_1.66.0              
[111] XVector_0.28.0                rvest_0.3.6                  
[113] digest_0.6.25                 graph_1.66.0                 
[115] Biostrings_2.56.0             rmarkdown_2.3                
[117] cellranger_1.1.0              fastmatch_1.1-0              
[119] edgeR_3.30.3                  curl_4.3                     
[121] shiny_1.5.0                   Rsamtools_2.4.0              
[123] lifecycle_0.2.0               jsonlite_1.7.0               
[125] viridisLite_0.3.0             askpass_1.1                  
[127] limma_3.44.3                  fansi_0.4.1                  
[129] pillar_1.4.6                  lattice_0.20-41              
[131] KEGGREST_1.28.0               fastmap_1.0.1                
[133] httr_1.4.2                    survival_3.2-3               
[135] GO.db_3.11.4                  interactiveDisplayBase_1.26.3
[137] glue_1.4.1                    UpSetR_1.4.0                 
[139] png_0.1-7                     Rgraphviz_2.32.0             
[141] BiocVersion_3.11.1            bit_4.0.4                    
[143] ggforce_0.3.2                 stringi_1.4.6                
[145] bcbioBase_0.6.14              blob_1.2.1                   
[147] AnnotationHub_2.20.2          memoise_1.1.0