[BioC] AnnBuilder: ABPkgBuilder gives missing GO and NAs in ACCNUM

[Nianhua Li]

Hi, Chuen,

The purpose of the GenBank-environment (i.e. ACCNUM) is to record the probset 
to GenBank Accession mapping provided by users via the base mapping file. It 
will contain nothing but NAs when the base mapping type is "ll". ABPkgBuilder 
currently doesn't extract GenBank Accessions based on Entrez Gene ID. This is 
due to design choices rather than technical changes as I understood. 

The missing of GO-environments is a real problem. The perl complaints right 
after loading GO in your outputs is abnormal. Not sure whether it relates to 
the GO problem. I know ABPkgBuilder only utilizes the perl scripts when it 
maps probset IDs to Entrez Gene IDs. Everything is pure R when it gets to GO 
annotations. You have already given the mappings as input, and you got most of 
the annotations (PATH, CHR, etc), so it seems the perl problem is not the 
cause of the GO problem. Sorry that I don't have more useful information :(

best

nianhua