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.