10 weeks ago by
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
You don't explain which genome build or what annotation you have used, so I am going to make some guesses.
I am guessing that you are using the Oe6 de novo olive genome build http://denovo.cnag.cat/olive published by the Spanish CNAG team just a couple of years ago.
I am also guessing that you have used the Oe6 GFF3 gene annotation file from the same site, which provides gene Ids using their own system.
Since CNAG's genome build is so recent, and since they use their own gene Ids unique to the Oe6 project, there is no way that you can expect Bioconductor or KEGG to know what the gene Ids mean. You need to obtain gene annotation information from CNAG's own website. If they don't cross reference their own Gene Ids to NCBI or Ensembl or GO then no one else will be able to do so.
In my opinion, you should make sure that you know what the Gene Ids themselves mean before you try to do any functional analysis such as GO or KEGG. CNAG provides a directory of functional annotation files, and these files are presumably what you need to use. You have to explore the files for yourself and contact the CNAG people if you need help.