When I try and create the topGOdata object, I get an error warning about a zero-length vector. I've recently moved to a Mac (see session info). Previously I had no issues using topGO on a linux box, under R-3.6.3 (with an up to date bioconductor). I was hoping someone might have gotten a similar error and could help me troubleshoot? I'm not certain where to start looking.
Quick Start Example from the vignette:
> library(topGO) > library(ALL) > data(ALL) > data(geneList) > > affyLib <- paste(annotation(ALL), "db", sep = ".") > library(package = affyLib, character.only = TRUE) > > sampleGOdata <- new("topGOdata", + description = "Simple session", ontology = "BP", + allGenes = geneList, geneSel = topDiffGenes, nodeSize = 10, + annot = annFUN.db, affyLib = affyLib) Building most specific GOs ..... ( 1647 GO terms found. ) Build GO DAG topology .......... Error in if (node == GENE.ONTO.ROOT) return(2) : argument is of length zero
There is also a warning message:
> warnings() Warning message: In result_fetch(res@ptr, n = n) : SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
> sessionInfo() R version 4.0.0 (2020-04-24) 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:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  stats4 parallel stats graphics grDevices  utils datasets methods base other attached packages:  hgu95av2.db_3.2.3 org.Hs.eg.db_3.11.0  ALL_1.29.0 org.Mm.eg.db_3.11.0  topGO_2.40.0 SparseM_1.78  GO.db_3.11.0 AnnotationDbi_1.50.0  IRanges_2.22.1 S4Vectors_0.26.0  Biobase_2.48.0 graph_1.66.0  BiocGenerics_0.34.0 loaded via a namespace (and not attached):  Rcpp_188.8.131.52 bit_1.1-15.2 lattice_0.20-41  rlang_0.4.6 blob_1.2.1 tools_4.0.0  grid_4.0.0 DBI_1.1.0 matrixStats_0.56.0  bit64_0.9-7 digest_0.6.25 vctrs_0.2.4  memoise_1.1.0 RSQLite_2.2.0 compiler_4.0.0  pkgconfig_2.0.3