[BioC] R --vanilla and Annotation pkg

[Saurin Jani]

Hi BioC,

I just recently installed rae230a cdf, probe and
rae230a pkg from bioconductor metadata website.

When I run my script through R --vanilla < script1.R 

I have below problem. 
-------------------------------
chiptype <- rae230a;

All_Annotations <-
aafTableAnn(myGenes,chiptype,c("Symbol","Description","Function","GenBank","UniGene"));
[1] "You are missing rgu34a looking to see if it is
available."
Package rgu34a version 1.6.5 is available for
download, would you like to install? [yes/y/no/n]
All_Genes_Annotation <-
merge(All_Genes_Annotation,All_Annotations);
All_Genes_Annotation <-
merge(All_Genes_Annotation,All_Annotations); is not a
valid response, try again.
-------------------------------

But WHEN.....I run my script1.R by copy and paste  and
then I do R --vanilla , I DON'T get above error. 

has anyone had this problem..?

Thank you,

Saurin