goplot encountered an error

[Long-zhe]

Dear Uncle Y, hello！

I encountered some issues while using the R package (clusterProfiler) you developed. When using goplot, the following error message appeared：

Error in AnnotationDbi::mget(id, GOANCESTOR) : second argument must be an environment

Subsequently, I followed the user manual you wrote（https://yulab-smu.top/biomedical-knowledge-mining-book/clusterprofiler-go.html） and tried using the example code above（https://yulab-smu.top/biomedical-knowledge-mining-book/clusterprofiler-go.html#clusterprofiler-go-ora）, but still encountered the same problem

 library(clusterProfiler)
data(geneList, package="DOSE")
gene <- names(geneList)[abs(geneList) > 2]

ego <- enrichGO(gene          = gene,
                universe      = names(geneList),
                OrgDb         = org.Hs.eg.db,
                ont           = "CC",
                pAdjustMethod = "BH",
                pvalueCutoff  = 0.01,
                qvalueCutoff  = 0.05,
        readable      = TRUE)

 goplot(ego)

At first, I thought it might be a problem caused by the server, so I ran the example code in the manual in R studio on my local Windows computer, but the same problem still occurred.

But I use barplot and dotplot, both of which can run normally.

I really couldn't find a solution before coming to you for help. I'm very sorry to disturb you and look forward to your suggestions to help me solve the problem. Thank you very much!

sessionInfo()

R version 4.4.1 (2024-06-14)
Platform: x86_64-redhat-linux-gnu
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblaso-r0.3.15.so;  LAPACK version 3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Asia/Shanghai
tzcode source: system (glibc)

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

other attached packages:
 [1] enrichplot_1.24.4      yulab.utils_0.1.7      GOSemSim_2.30.2        org.Hs.eg.db_3.19.1    mirrorselect_0.0.3    
 [6] lubridate_1.9.3        forcats_1.0.0          stringr_1.5.1          dplyr_1.1.4            purrr_1.0.2           
[11] readr_2.1.5            tidyr_1.3.1            tibble_3.2.1           ggplot2_3.5.1          tidyverse_2.0.0       
[16] data.table_1.16.0      org.My.eg.db_1.0       AnnotationDbi_1.66.0   IRanges_2.38.1         S4Vectors_0.42.1      
[21] Biobase_2.64.0         BiocGenerics_0.50.0    clusterProfiler_4.12.6

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3      rstudioapi_0.16.0       jsonlite_1.8.9          magrittr_2.0.3          farver_2.1.2           
  [6] rmarkdown_2.28          fs_1.6.4                zlibbioc_1.50.0         vctrs_0.6.5             memoise_2.0.1          
 [11] ggtree_3.12.0           htmltools_0.5.8.1       curl_5.2.3              gridGraphics_0.5-1      desc_1.4.3             
 [16] plyr_1.8.9              httr2_1.0.5             cachem_1.1.0            igraph_2.0.3            lifecycle_1.0.4        
 [21] pkgconfig_2.0.3         Matrix_1.7-0            R6_2.5.1                fastmap_1.2.0           gson_0.1.0             
 [26] GenomeInfoDbData_1.2.12 digest_0.6.37           aplot_0.2.3             colorspace_2.1-1        ps_1.8.0               
 [31] patchwork_1.3.0         RSQLite_2.3.7           fansi_1.0.6             timechange_0.3.0        httr_1.4.7             
 [36] polyclip_1.10-7         compiler_4.4.1          remotes_2.5.0           bit64_4.5.2             withr_3.0.1            
 [41] BiocParallel_1.38.0     viridis_0.6.5           DBI_1.2.3               pkgbuild_1.4.4          ggforce_0.4.2          
 [46] R.utils_2.12.3          MASS_7.3-61             rappdirs_0.3.3          tools_4.4.1             ape_5.8                
 [51] scatterpie_0.2.4        R.oo_1.26.0             glue_1.8.0              callr_3.7.6             nlme_3.1-166           
 [56] grid_4.4.1              shadowtext_0.1.4        reshape2_1.4.4          fgsea_1.30.0            generics_0.1.3         
 [61] gtable_0.3.5            tzdb_0.4.0              R.methodsS3_1.8.2       hms_1.1.3               tidygraph_1.3.1        
 [66] utf8_1.2.4              XVector_0.44.0          ggrepel_0.9.6           pillar_1.9.0            splines_4.4.1          
 [71] tweenr_2.0.3            treeio_1.28.0           lattice_0.22-6          bit_4.5.0               tidyselect_1.2.1       
 [76] GO.db_3.19.1            Biostrings_2.72.1       knitr_1.48              gridExtra_2.3           xfun_0.48              
 [81] graphlayouts_1.2.0      stringi_1.8.4           UCSC.utils_1.0.0        lazyeval_0.2.2          ggfun_0.1.6            
 [86] yaml_2.3.10             evaluate_1.0.1          codetools_0.2-20        ggraph_2.2.1            qvalue_2.36.0          
 [91] BiocManager_1.30.25     ggplotify_0.1.2         cli_3.6.3               processx_3.8.4          munsell_0.5.1          
 [96] Rcpp_1.0.13             GenomeInfoDb_1.40.1     png_0.1-8               parallel_4.4.1          blob_1.2.4             
[101] DOSE_3.30.5             viridisLite_0.4.2       tidytree_0.4.6          scales_1.3.0            crayon_1.5.3           
[106] rlang_1.1.4             cowplot_1.1.3           fastmatch_1.1-4         KEGGREST_1.44.1  

[mhasoon]

I am also getting the same error. I have recently updated to R 4.4 and when I revert back to R4.3.3 I don't get the error occurring anymore. Not a great fix, but you could try reverting back to R4.3.3 and see if you still get the same error?

[Long-zhe]

I am also getting the same error. I have recently updated to R 4.4 and when I revert back to R4.3.3 I don't get the error occurring anymore. Not a great fix, but you could try reverting back to R4.3.3 and see if you still get the same error?

Thanks, When I use the R 4.2.2，don't get the error occurring！

[mhasoon]

No problem! Seems to be some incompatibility between clusterProfiler 4.12.6 and R 4.4 - hopefully it'll get fixed soon!

[GuangchuangYu]

fixed.