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 <hpa...@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@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: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
