Annotation database not working with topGO

[felixlaguna]

When creating an annotation database like in the vignette:

makeOrgPackage(gene_info=fSym, chromosome=fChr, go=fGO,
               version="0.1",
               maintainer="bla",
               author="bla",
               outputDir = ".",
               tax_id="559292",
               genus="Saccharomyces",
               species="cerevisiae",
               goTable="go")

The package is generated, it is imported without a problem, but then it fails to be used with topGO, with the error of "missing table: go_cc":

install.packages("./org.Scerevisiae.eg.db",repos = NULL)
library("org.Scerevisiae.eg.db")
GODefault <- new("topGOdata",
                    description = "Simple session",
                    ontology = "CC",
                    allGenes = geneListOwn,
                    annot = annFUN.org,
                    mapping = "org.Scerevisiae.eg.db"
                 )

[dvantwisk]

Apologies for the delay.

First off, I'm not sure sure what the values of fSym, fChar, and fGO are in your example. I am assuming these values are from the MakingNewOrganismPackages vignette, however, these tables are for the zebra finch and not applicable to building a yeast orgdb package so the resulting package is not going to be useful.

You are right in pointing out that the user-generate orgdb packages do not include the go_cc table (among other go_ tables it was missing). We found that the org.Sc.sgd.db that we maintain does contain these tables, so one option may be to use this package instead of generating a new one.

We have pushed changes to the master (devel) branch of AnnotationForge that will create the needed go_ tables in user generated orgdb packages, so the package you build should now work with topGO.