Hi,

I was having much trouble trying to install a goseq database in the annotation section.

source("https://bioconductor.org/biocLite.R")
  biocLite("org.Mm.eg.db")

This was not good enough, and I tried following all kinds of advice. Finally I really looked at what the error messages were saying.

It wanted RSQLite, and also needed AnnotationDbi.

 #I had to allow Rstudio to save and reload R, but then I could install
  #RSQLite with the install.packages("RSQLite") command.
  package ‘RSQLite’ successfully unpacked and MD5 sums checked
  
  The downloaded binary packages are in
  C:\Users\Wahl\AppData\Local\Temp\RtmpKmFRSi\downloaded_packages
  #Then I could install AnnotationDbi with biocLite, and then I could install
  #org.Mm.eg.db
  > library("AnnotationDbi", lib.loc="~/R/win-library/3.4")
  > source("https://bioconductor.org/biocLite.R")
  Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
  > biocLite("org.Mm.eg.db")
  GO.wall = goseq(pwf,"mm9","ensGene")
  Fetching GO annotations...

I got what I needed and was able to proceed with the GO.wall function in goseq.