
Hi,

I'm trying to create a custom annotation package for arabidopsis using RefSeq identifiers with AnnotationDbi's function makeDBPackage. Everything runs smoothly but the generated package is empty with 0 mappings for everything and I cannot figure out what I'm doing wrong.

My map file looks like:

AT1G01010-TAIR-G        NM_099983
AT1G01020-TAIR-G        NM_001035846
AT1G01030-TAIR-G        NM_099985
AT1G01040-TAIR-G        NM_099986
AT1G01046-TAIR-G        NR_022015
AT1G01050-TAIR-G        NM_099987
AT1G01060-TAIR-G        NM_001035847
AT1G01070-TAIR-G        NM_099989
AT1G01073-TAIR-G        NM_001160824
AT1G01080-TAIR-G        NM_099990
...

My function call  is the following:

makeDBPackage(
  schema="ARABIDOPSISCHIP_DB",
  affy=FALSE, 
  prefix="arabidopsis.anno", 
  fileName="doc/map_reseq.txt",
  #baseMapType=baseMapType, ## id type present in the fileName gb/ug/eg/refseq/gbNRef
  outputDir="doc/arabidopsis.anno", 
  version="1.0.0", 
  chipName="arabidopsis"
)

One strange thing here is that if I try to use parameter baseMapType I get an error message complaining about an unnecessary parameter. So how can I be sure the function assumes the correct database type?

# after installing and loading the package:

qcdata <- capture.output(arabidopsis.anno())  
> qcdata
 [1] "Quality control information for arabidopsis.anno:"             
 [2] ""                                                              
 [3] ""                                                              
 [4] "This package has the following mappings:"                      
 [5] ""                                                              
 [6] "arabidopsis.annoACCNUM has 0 mapped keys (of 28130 keys)"      
 [7] "arabidopsis.annoARACYC has 0 mapped keys (of 28130 keys)"      
 [8] "arabidopsis.annoARACYCENZYME has 0 mapped keys (of 28130 keys)"
 [9] "arabidopsis.annoCHR has 0 mapped keys (of 28130 keys)"         
[10] "arabidopsis.annoCHRLENGTHS has 7 mapped keys (of 7 keys)"      
[11] "arabidopsis.annoCHRLOC has 0 mapped keys (of 28130 keys)"      
[12] "arabidopsis.annoCHRLOCEND has 0 mapped keys (of 28130 keys)"   
[13] "arabidopsis.annoENZYME has 0 mapped keys (of 28130 keys)"      
[14] "arabidopsis.annoENZYME2PROBE has 0 mapped keys (of 631 keys)"  
[15] "arabidopsis.annoGENENAME has 0 mapped keys (of 28130 keys)"    
[16] "arabidopsis.annoGO has 0 mapped keys (of 28130 keys)"          
[17] "arabidopsis.annoGO2ALLPROBES has 0 mapped keys (of 5861 keys)" 
[18] "arabidopsis.annoGO2PROBE has 0 mapped keys (of 3962 keys)"     
[19] "arabidopsis.annoPATH has 0 mapped keys (of 28130 keys)"        
[20] "arabidopsis.annoPATH2PROBE has 0 mapped keys (of 120 keys)"    
[21] "arabidopsis.annoPMID has 0 mapped keys (of 28130 keys)"        
[22] "arabidopsis.annoPMID2PROBE has 0 mapped keys (of 13671 keys)"  
[23] "arabidopsis.annoSYMBOL has 0 mapped keys (of 28130 keys)"      
[24] ""                                                              
[25] ""                                                              
[26] "Additional Information about this package:"                    
[27] ""                                                              
[28] "DB schema: ARABIDOPSISCHIP_DB"                                 
[29] "DB schema version: 2.1"                                        
[30] "Organism: Arabidopsis thaliana"                                
[31] "Date for NCBI data: 2010-Mar1"                                 
[32] "Date for GO data: 20100320"                                    
[33] "Date for KEGG data: 2010-Feb28"                                
[34] "Data for TAIR data: 2010-Mar12"       

and the session info:
> sessionInfo()
R version 2.11.1 (2010-05-31) 
i386-apple-darwin9.8.0 

locale:
[1] C

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

other attached packages:
[1] org.At.tair.db_2.4.3  RSQLite_0.9-2         DBI_0.2-5             arabidopsis.db0_2.4.3 AnnotationDbi_1.10.2 
[6] Biobase_2.8.0  

I'd be very grateful for any advice!
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