[BioC] RdbiPgSQL problem: SET_VECTOR_ELT() can only be applied to a 'list', not a 'character'

John Zhang jzhang at jimmy.harvard.edu
Sun Apr 26 02:50:41 CEST 2009

I just came back from a vacation. Another user has complained about this. I will 
take a look when I get to the office on Monday.


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>To: Philip Lijnzaad <p.lijnzaad at umcutrecht.nl>
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>Subject: Re: [BioC] RdbiPgSQL problem: SET_VECTOR_ELT() can only be applied to 
a 'list', not a 'character'
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>This is most likely a bug in RdbiPgSQL, related to more stringent  
>check of SET_VECTOR_ELT (C code) in R.
>It is probably easy to fix, but I don't have access to a PostGres  
>database, so I would be unable to check.
>Contact the maintainer and complain :)
>On Apr 25, 2009, at 2:26 , Philip Lijnzaad wrote:
>> Dear all,
>> I'm having difficulty using RdbiPgSQL. This is using R 2.9.1,  
>> RdbiPgSQL
>> 1.18.0, both R client and server at 8.3.
>> If I do
>>  conn=dbConnect(PgSQL(),
>>                 host=db.host,
>>                 dbname=db.name,
>>                 user=db.user,
>>                 password=db.password)
>> I keep getting this:
>>  SET_VECTOR_ELT() can only be applied to a 'list', not a 'character'
>>  Calls: dbConnect ... dbConnectionInfo ->
>> dbConnectionInfo.PgSQL.conn -> .Call
>> This used to work fine under R 2.7
>> I see that the RdbiPgSQL compiles properly, but is the actual  
>> connectivity
>> against a real database really checked? In an ideal world this would  
>> be the
>> case, as the current version is unusuable.
>> This is very unfortunate, since we really rely on this code.
>> Any suggestions are welcome.
>>                                                                       Philip
>> -- 
>> Philip Lijnzaad, PhD
>> Holstege Genomics Laboratory
>> Dept. of Biomedical Genetics
>> University Medical Center (UMC), Utrecht
>> Stratenum room 2.211 (on Mondays and Thursdays not in after 15.00)
>> MSN chat (*NOT* email): philip_lijnzaad at hotmail.com
>> P.O. Box 85060, 3508 AB Utrecht
>> (Universiteitsweg 100, 3584 CG Utrecht)
>> The Netherlands
>> tel: +31 (0)8875 68464
>> fax: +31 (0)8875 68479
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084

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