[Bioc-devel] Problem loading Rdbi (again)

[Sean Davis]

Benno Puetz wrote:
> Herve Pages wrote:
>   
>> Hi Benno,
>>
>>
>> Benno Puetz wrote:
>>   
>>     
>>> After successfully installing and using Rdbi (1.12.0, on R 2.6.0) 
>>> yesterday, I started getting error messages when trying to load the 
>>> library today (... cyclic dependencies ...).
>>>     
>>>       
>> On my system 'library(Rdbi)' is desperately quiet ;-)
>>
>> It's hard to believe that Rdbi has a circular dep problem since it depends
>> on nothing except R >= 1.2. What message do you get _exactly_? and after doing
>> what? Please show us the full session.
>>
>> Also, we need your sessionInfo(). Here is mine:
>>
>>   
>>     
>>> sessionInfo()
>>>     
>>>       
>> R version 2.6.0 (2007-10-03)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>> LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] Rdbi_1.12.0
>>
>> loaded via a namespace (and not attached):
>> [1] rcompgen_0.1-17 tools_2.6.0
>>
>>
>>   
>>     
> I thought I had a clean R when doing:
>
> [Workspace restored from /Volumes/User/bpuetz/.RData]
>
>  > sessionInfo()
> R version 2.6.0 (2007-10-03)
> powerpc-apple-darwin8.10.1
>
> locale:
> de_DE.UTF-8/de_DE.UTF-8/de_DE.UTF-8/C/de_DE.UTF-8/de_DE.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets
> [6] methods   base    
>  > library(Rdbi)
> Lade nötiges Paket: Rdbi
> Error in loadNamespace(package, c(which.lib.loc, lib.loc), keep.source = 
> keep.source) :
>   zyklische Abhängigkeiten von Namensräumen werden nicht unterstützt
> Error : Paket 'Rdbi' konnte nicht geladen werden
> Error : .onLoad in 'loadNamespace' für 'Rdbi' fehlgeschlagen
> Fehler: Laden von Paket/Namensraum für 'Rdbi' fehlgeschlagen
>  >
>
> then I noticed the first line and wanted to make sure it was. After
>
> rm (list=ls())
>
> library(Rdbi)
>
> is quiet as it should be... although I seem to have to load RdbiPgSQL 
> manually -
>
>     primer.conn <- dbConnect(PgSQL(),
>                              host='localhost',
>                              dbname='primer')
>
> yields
>
> Fehler in dbConnect(PgSQL(), host = "localhost", dbname = "primer") :
>   konnte Funktion "PgSQL" nicht finden
>
> But I can live with that ...
>
> Thanks for helping me remove the culprit - whatever it may have been
>   

I think if one has a previous connection saved in the workspace, this 
will cause the problem.  After rm(list=ls()), the connection is removed; 
hence, no further problems.  I have simply gotten in the habit of not 
saving connections in the workspace.

Sean