[BioC] Error in AnnBuilder writeAnnData2Pkg

[Georg Otto]

Dear John,

sorry, I forgot to give this information:

R 2.0.1 on Mac OS 10.2.8
AnnBuilder 1.4.21

Here are the first two lines of the annotation matrix. For reasons that  
I do not understand, the first line is empty. Could this be the reason  
for the error? And is there a way to circumvent this?

 > annotation[1:2,]
                     PROBE                 ACCNUM     LOCUSID UNIGENE
                     ""                    ""         "NA"    "NA"
CGENZEB_456000002_0 "CGENZEB_456000002_0" "AF030031" "30131" "Dr.30326"
                     GENENAME SYMBOL CHR  MAP  PMID                       
    GRIF
                     "NA"     "NA"   "NA" "NA" "NA"                       
    "NA"
CGENZEB_456000002_0 "deltaA" "dla"  "1"  "NA"  
"12890499;12835391;12477932" "NA"
                     SUMFUNC
                     "NA"
CGENZEB_456000002_0 "NA"
                     GO
                     "NA"
CGENZEB_456000002_0  
"GO:0005509 at IEA;GO:0007154 at IEA;GO:0009880 at IMP;GO:0016020 at IEA;GO:0005515@ 
IDA"
                     OMIM REFSEQ
                     "NA" "NA"
CGENZEB_456000002_0 "NA" "NM_130954;NP_571029"


Best,

Georg


>
>>> pkgName<-"test"
>>> pkgPath<-getwd()
>>> createEmptyDPkg(pkgName, pkgPath, force=TRUE)
>>> annotation<-as.matrix(annotation)
>
> What did annotation contain? Did annotation have column names? You  
> need to
> provide us with more information (e. g. R version, AnnBuilder version,  
> more
> example code)
>
>
>>
>> then I get the following error:
>>
>>> writeAnnData2Pkg(annotation, pkgName, pkgPath)
>>
>> Error in assign(x[i], value[[i2]], envir = envir, inherits =  
>> inherits) :
>>         attempt to use zero-length variable name
>>
>>
>> Could someone give me a hint what is wrong here?
>>
>> Best,
>>
>> Georg
>>
>> P.S. I am on digest mode, cc'ing the answer directly to me would be  
>> nice



-- 
Georg Wilhelm Otto
Max-Planck-Institute for Developmental Biology
Spemannstrasse 35/III
D-72076 Tuebingen Germany
phone: +49-7071-601 401
http://www.eb.tuebingen.mpg.de