JFI: Also we must be aware of how often these tools are updating their databases (I am not talking about KEGGREST, it is about other available tools for functional enrichment analysis). Otherwise the information we get from these tools might be misleading.
These articles explains the problems associated with outdated source.
Nature methods, correspodence Impact of outdated gene annotations on pathway enrichment analysis
Complete article from the same author in bioRxiv Impact of knowledge accumulation on pathway enrichment analysis
Also checkout this link
There is an linux based real-time tool GeneSCF, (Not R)