[Bioc-devel] dbApply name collision, RMySQL and RPostgreSQL, no direct call to either
paul.thurmond.shannon at gmail.com
Wed Apr 25 22:01:25 CEST 2018
Many thanks, Herve’ - this worked nicely.
Thanks for the MariaDB tip. I’ll take a look.
> 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
> 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:
> BTW have you considered using RMariaDB instead of RMySQL?
> 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?
>> - Paul
>> Bioc-devel at r-project.org mailing list
> 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
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