[BioC] MakeDBPackage fails with SQL error

[Scott Presnell [guest]]

Hi Folks,
  I've been trying to create a DB package for the Affymetrix Primeview micro array chip.  I found the vignette called 'Creating a New Annotation Package using SQLForge'  I created a mapping of probes to entrez gene ids.  And I installed the requisite packages.  And ran the following:

> library(AnnotationForge)
> library("human.db0")
> tmpout = tempdir()
> makeDBPackage("HUMANCHIP_DB",
affy=FALSE,
prefix="primeview", fileName="primeviewHumanGeneExprs2.txt",
baseMapType="gb",
outputDir = tmpout,
version="1.0.0",
manufacturer = "Affymetrix",
chipName="Primeview MicroArray",
manufacturerUrl = "http://www.affymetrix.com")
baseMapType is gb or gbNRef
Prepending Metadata
Creating Genes table
Error in sqliteExecStatement(con, statement, bind.data) : 
  RS-DBI driver: (RS_SQLite_exec: could not execute1: genes.gene_id may not be NULL)

But as you can see, I get an SQL based error.  Thinking it was complaining about probes that don't have a corresponding entrez gene Id, I removed them from the file (they originally had a '---' as an entrez gene id), and tried again, but the result is the same.

Can someone provide me with some guidance on where to look to fix or avoid this error?

(alternatively, if anyone is willing to share a primeview.db package, that would also be great!)

 -- output of sessionInfo(): 

> sessionInfo();
R version 2.15.2 (2012-10-26)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] human.db0_2.8.0       AnnotationForge_1.0.3 org.Hs.eg.db_2.8.0   
[4] RSQLite_0.11.2        DBI_0.2-5             AnnotationDbi_1.20.7 
[7] Biobase_2.18.0        BiocGenerics_0.4.0   

loaded via a namespace (and not attached):
[1] IRanges_1.16.6  parallel_2.15.2 stats4_2.15.2  


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