I am using rGREAT to annotate my Chip Seq peaks but suddenly the "availableOntologies(job)" has changed to: [1] "GO Molecular Function" "GO Biological Process"
[3] "GO Cellular Component" "Mouse Phenotype"
[5] "Mouse Phenotype Single KO" "Human Phenotype"
[7] "Ensembl Genes"

and "getEnrichmentTables(job, ontology = c("HGNC Gene Families")) and getEnrichmentTables(job, ontology = c("MSigDB Oncogenic Signatures"))" has stopped working. Does anybody has any clue why is it happening so and how can I see the enrich signaling pathways in my list of genes?

The release notes for GREAT state that some of the ontologies have been removed in the latest version:

Ontologies of the MSigDB, pathways, gene expression, regulatory motifs, and gene families have been dropped in GREAT4.0 but are still available in version 3.0.

http://great.stanford.edu/help/display/GREAT/Version+History

It looks like you can still use the older version of GREAT to get this information, but it isn't something that the author of the rGREAT package has control over.

I updated rGREAT for the GREAT version 4.0.4 which is default in current rGREAT. For GREAT version 4.0.4, less ontologies are supported and also note it works with hg38. So if you want to use the ontologies in version 3, specify as submitGreatJob(..., version = '3.0.0')