Hello,

I'm trying to replicate this Gene ontology enrichment: https://davetang.org/muse/2010/11/10/gene-ontology-enrichment-analysis/

I have been following instructions line by line. I'm at this point where I have to run the hypergeometric test. But get this error.

> hgOver <- hyperGTest(params)
Error in getGoToEntrezMap_db(p) : could not find function "dbGetQuery"

Also providing my session information. Can anyone tell me what I'm doing wrong ? Thanks, Krithika

> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X Mavericks 10.9.5

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] parallel  stats4    stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
 [1] GOstats_2.40.0         Category_2.40.0        Matrix_1.2-12         
 [4] topGO_2.26.0           SparseM_1.77           GO.db_3.4.0           
 [7] graph_1.52.0           clusterProfiler_3.2.14 BiocInstaller_1.24.0  
[10] DOSE_3.0.10            org.Hs.eg.db_3.4.0     AnnotationDbi_1.36.2  
[13] IRanges_2.8.2          S4Vectors_0.12.2       Biobase_2.34.0        
[16] BiocGenerics_0.20.0   

loaded via a namespace (and not attached):
 [1] genefilter_1.56.0      qvalue_2.6.0           fgsea_1.0.2           
 [4] reshape2_1.4.2         purrr_0.2.4            splines_3.3.3         
 [7] lattice_0.20-35        colorspace_1.3-2       yaml_2.1.15           
[10] survival_2.41-3        RBGL_1.50.0            XML_3.98-1.9          
[13] blob_1.1.0             rlang_0.1.4            glue_1.2.0            
[16] DBI_0.7                BiocParallel_1.8.2     bit64_0.9-7           
[19] matrixStats_0.52.2     plyr_1.8.4             stringr_1.2.0         
[22] munsell_0.4.3          GOSemSim_2.0.4         gtable_0.2.0          
[25] memoise_1.1.0          evaluate_0.10.1        knitr_1.17            
[28] GSEABase_1.36.0        Rcpp_0.12.14           xtable_1.8-2          
[31] scales_0.5.0           DO.db_2.9              annotate_1.52.1       
[34] bit_1.1-12             gridExtra_2.3          fastmatch_1.1-0       
[37] ggplot2_2.2.1          digest_0.6.12          stringi_1.1.6         
[40] grid_3.3.3             bitops_1.0-6           tools_3.3.3           
[43] magrittr_1.5           RCurl_1.95-4.8         lazyeval_0.2.1        
[46] tibble_1.3.4           RSQLite_2.0            tidyr_0.7.2           
[49] pkgconfig_2.0.1        data.table_1.10.4-3    AnnotationForge_1.16.1
[52] igraph_1.1.2        

It should work for you, and it does work for me. The error says that R can't find a particular function that is defined in the DBI package, yet that function should be correctly imported and found by the function that uses it.

Anyway, you are using an old version of R and Bioconductor, so you should update both. We don't support old versions, so you need the release if you expect much help. There may be something weird going on with your installation and updating should fix that, but let us know if the problem persists.