Hi,

After updating Bioconductor(v.3.20) and simplifyEnrichment(v.2.0.0) today, I'm encountering an error when trying to use the term_similarity_from_KEGG function from the simplifyEnrichment package. Has this function been renamed or moved to a different location in a recent update?

Error: 'term_similarity_from_KEGG' is not exported by 'namespace:simplifyEnrichment'

> sessionInfo()
R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] BiocManager_1.30.25      simplifyEnrichment_2.0.0

loaded via a namespace (and not attached):
  [1] later_1.3.2                 tibble_3.2.1               
  [3] polyclip_1.10-7             preprocessCore_1.68.0      
  [5] graph_1.84.0                XML_3.99-0.17              
  [7] lifecycle_1.0.4             topGO_2.58.0               
  [9] doParallel_1.0.17           NLP_0.3-0                  
 [11] lattice_0.22-6              MASS_7.3-61                
 [13] MultiAssayExperiment_1.32.0 magrittr_2.0.3             
 [15] openxlsx_4.2.7.1            limma_3.62.0               
 [17] rmarkdown_2.28              yaml_2.3.10                
 [19] remotes_2.5.0               httpuv_1.6.15              
 [21] flexmix_2.3-19              zip_2.3.1                  
 [23] MsCoreUtils_1.18.0          pbapply_1.7-2              
 [25] DBI_1.2.3                   RColorBrewer_1.1-3         
 [27] abind_1.4-8                 zlibbioc_1.52.0            
 [29] GenomicRanges_1.58.0        purrr_1.0.2                
 [31] AnnotationFilter_1.30.0     ggraph_2.2.1               
 [33] BiocGenerics_0.52.0         nnet_7.3-19                
 [35] tweenr_2.0.3                circlize_0.4.16            
 [37] GenomeInfoDbData_1.2.13     IRanges_2.40.0             
 [39] S4Vectors_0.44.0            tm_0.7-14                  
 [41] ggrepel_0.9.6               masstools_1.0.13           
 [43] MSnbase_2.32.0              annotate_1.84.0            
 [45] ggwordcloud_0.6.2           ncdf4_1.23                 
 [47] codetools_0.2-20            DelayedArray_0.32.0        
 [49] xml2_1.3.6                  ggforce_0.4.2              
 [51] tidyselect_1.2.1            shape_1.4.6.1              
 [53] UCSC.utils_1.2.0            farver_2.1.2               
 [55] viridis_0.6.5               massdataset_1.0.29         
 [57] matrixStats_1.4.1           stats4_4.4.1               
 [59] jsonlite_1.8.9              GetoptLong_1.0.5           
 [61] tidygraph_1.3.1             iterators_1.0.14           
 [63] foreach_1.5.2               tools_4.4.1                
 [65] Rcpp_1.0.13                 glue_1.8.0                 
 [67] gridExtra_2.3               Rttf2pt1_1.3.12            
 [69] SparseArray_1.6.0           xfun_0.48                  
 [71] MatrixGenerics_1.18.0       GenomeInfoDb_1.42.0        
 [73] dplyr_1.1.4                 withr_3.0.2                
 [75] fastmap_1.2.0               fansi_1.0.6                
 [77] SparseM_1.84-2              digest_0.6.37              
 [79] R6_2.5.1                    mime_0.12                  
 [81] colorspace_2.1-1            GO.db_3.20.0               
 [83] RSQLite_2.3.7               utf8_1.2.4                 
 [85] tidyr_1.3.1                 generics_0.1.3             
 [87] corpcor_1.6.10              graphlayouts_1.2.0         
 [89] PSMatch_1.10.0              httr_1.4.7                 
 [91] S4Arrays_1.6.0              scatterplot3d_0.3-44       
 [93] pkgconfig_2.0.3             gtable_0.3.6               
 [95] modeltools_0.2-23           blob_1.2.4                 
 [97] ComplexHeatmap_2.22.0       impute_1.80.0              
 [99] XVector_0.46.0              htmltools_0.5.8.1          
[101] RBGL_1.82.0                 MALDIquant_1.22.3          
[103] ProtGenerics_1.38.0         clue_0.3-65                
[105] scales_1.3.0                Biobase_2.66.0             
[107] png_0.1-8                   knitr_1.48                 
[109] rstudioapi_0.17.1           tzdb_0.4.0                 
[111] reshape2_1.4.4              rjson_0.2.23               
[113] org.Hs.eg.db_3.20.0         cachem_1.1.0               
[115] GlobalOptions_0.1.2         Polychrome_1.5.1           
[117] stringr_1.5.1               parallel_4.4.1             
[119] extrafont_0.19              AnnotationDbi_1.68.0       
[121] mzID_1.44.0                 vsn_3.74.0                 
[123] pillar_1.9.0                grid_4.4.1                 
[125] vctrs_0.6.5                 pcaMethods_1.98.0          
[127] slam_0.1-54                 promises_1.3.0             
[129] xtable_1.8-4                cluster_2.1.6              
[131] extrafontdb_1.0             evaluate_1.0.1             
[133] readr_2.1.5                 cli_3.6.3                  
[135] compiler_4.4.1              rlang_1.1.4                
[137] crayon_1.5.3                simona_1.4.0               
[139] QFeatures_1.16.0            affy_1.84.0                
[141] plyr_1.8.9                  stringi_1.8.4              
[143] viridisLite_0.4.2           BiocParallel_1.40.0        
[145] munsell_0.5.1               Biostrings_2.74.0          
[147] lazyeval_0.2.2              Matrix_1.7-1               
[149] GOSim_1.42.0                hms_1.1.3                  
[151] patchwork_1.3.0             bit64_4.5.2                
[153] ggplot2_3.5.1               KEGGREST_1.46.0            
[155] statmod_1.5.0               shiny_1.9.1                
[157] SummarizedExperiment_1.36.0 gridtext_0.1.5             
[159] mzR_2.40.0                  igraph_2.1.1               
[161] memoise_2.0.1               affyio_1.76.0              
[163] bit_4.5.0

term_similarity_from_KEGG() and some other functions are removed from the package. Now the package only focuses on the gene set resources that have ontology structures.

If you still want to use it, you can use the package in its lower versions.