[Bioc-devel] dbApply name collision, RMySQL and RPostgreSQL, no direct call to either

[Paul Shannon]

Many thanks, Herve’ - this worked nicely.

Thanks for the MariaDB tip.  I’ll take a look.

 - Paul

> On Apr 23, 2018, at 4:50 PM, Hervé Pagès <hpages at fredhutch.org> wrote:
> 
> Hi Paul,
> 
> trena imports RMySQL and RPostgreSQL. Both packages define and export
> dbApply() so by importing all the symbols from both packages you get a
> name clash. You can get around this by importing only the things you
> need. It seems that you only call the following generic functions in
> trena:
> 
>  dbConnect
>  dbListTables
>  dbGetQuery
>  dbListConnections
>  dbDisconnect
> 
> These are S4 generic functions that are defined in the DBI package so
> they should be imported from there. Also import the corresponding
> methods defined in RMySQL and RPostgreSQL. Your NAMESPACE file will
> look something like this:
> 
> importFrom(DBI,
>    dbConnect,
>    dbListTables,
>    dbGetQuery,
>    dbListConnections,
>    dbDisconnect)
> 
> 
> importMethodsFrom(RMySQL,
>    dbConnect,
>    dbListTables,
>    dbGetQuery,
>    dbListConnections,
>    dbDisconnect)
> 
> importMethodsFrom(RPostgreSQL,
>    dbConnect,
>    dbListTables,
>    dbGetQuery,
>    dbListConnections,
>    dbDisconnect)
> 
> BTW have you considered using RMariaDB instead of RMySQL?
> 
>  https://cran.r-project.org/web/packages/RMariaDB/
> 
> Cheers,
> H.
> 
> On 04/23/2018 11:12 AM, Paul Shannon wrote:
>>     Warning: replacing previous import ‘RMySQL::dbApply’ by ‘RPostgreSQL::dbApply’ when loading ‘trena’
>> We do not call dbApply directly anywhere in the package. I imagine it is called routinely by functions that we do call.
>> Any suggestions on how to clear this warning?
>> Thanks.
>>  - Paul
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=MeyA9WrkJOQDYGySOlgR8QARzH-hSAPwc5-b4mJ5E9A&s=njLygKe4nxHzP911sM3TIgYMkMHsNWR97p3ZFIr0Voc&e=
> 
> -- 
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319