[BioC] annotate incompatible with RdbiPgSQL !?!

Philip Lijnzaad p.lijnzaad at umcutrecht.nl
Tue Apr 28 12:42:09 CEST 2009

[ sorry, my reply was intended to go to BioC (I realize BioC-devel would 
prolly have been more approppriate) ]
On Monday 27 April 2009 19:14:40 you wrote:
> Hi Philip,
>   Please upgrade to R 2.9.x and relevant packages.  

I am sorry that I forgot to mention that I had actually tested it there as 
well, and the issue is identical (see below).  I had to downgrade to a 
previous release because RdbiPgSQL is broken in 2.9.x 
(see thread 'RdbiPgSQL problem: SET_VECTOR_ELT() can only be applied to 
a 'list', not a 'character'). 

(The 'unable to find an inherited method for function "dbConnect", for 
signature "PgSQL"' bug occurs only in combination with library(DBI), and is 
triggered by the PgSQL() call. The SET_VECTOR_ELT() problem comes after 

> We are not able to provide assistance for 
> people that do not follow the guidelines.

My apologies for this. At the same time (since this basically is caused by the 
database connection package being broken), I would (kindly!) suggest that, in 
an ideal world, RdbiPgSQL ought to have been tested more thoroughly 
(especially connecting with an actual database) before the release; after all 
this is an infrastructure package. Anyways, kind regards,



platform       i686-pc-linux-gnu                                               
arch           i686                                                            
os             linux-gnu                                                       
system         i686, linux-gnu                                                 
status         Under development (unstable)                                    
major          2                                                               
minor          9.0                                                             
year           2009                                                            
month          01                                                              
day            22                                                              
svn rev        47686                                                           
language       R                                                               
version.string R version 2.9.0 Under development (unstable) (2009-01-22 

> library(RdbiPgSQL)
Loading required package: Rdbi

> package.version("Rdbi")
[1] "1.8.0"

> package.version("RdbiPgSQL")
[1] "1.18.0"

> library(DBI)

Attaching package: 'DBI'

        The following object(s) are masked from package:RdbiPgSQL :


        The following object(s) are masked from package:Rdbi :


> package.version("DBI")
[1] "0.2-4"

> conn=dbConnect(PgSQL(), host=db.host, dbname=db.name, user=db.user, 
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "dbConnect", for 
signature "PgSQL"
Calls: dbConnect -> .valueClassTest -> is -> <Anonymous>

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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