[Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

[Martin Morgan]

On 01/24/2018 03:38 PM, Wolfgang Huber wrote:
> GenomicFeatures_1.31.3 imports RMySQL.
> 
> I'm having great trouble installing RMySQL from source on a recent MacOS 
> (10.13.3) with homebrew.
> 
> The package's homepage says "The 'RMySQL' package contains an old 
> implementation based on legacy code from S-PLUS which being phased out. 
> A modern 'MySQL' client based on 'Rcpp' is available from the 'RMariaDB' 
> package" https://cran.r-project.org/web/packages/RMySQL/index.html
> 
> So is it time to heed that advice and migrate GenomicFeatures to RMariaDB ?

Out of curiosity, is MariaDB easier to install on your system? Its 
system dependencies are described at 
https://CRAN.R-project.org/package=RMariaDB

FWIW MySQL is a relatively recent addition as a dependency to 
GenomicFeatures; it enables `makeTxDbFromEnsembl()`, which is probably a 
much more stable solution than `makeTxDbFromBiomart()`. On the other had 
Johannes does an excellent job on the ensembldb packages, so perhaps 
this code could really be conditional with the RMySQL dependency moved 
to Suggests:

Martin

> 
> With thanks in advance-
> Wolfgang
> 
> -------
> Wolfgang Huber
> Principal Investigator, EMBL Senior Scientist
> European Molecular Biology Laboratory (EMBL)
> Heidelberg, Germany
> 
> wolfgang.huber at embl.de
> http://www.huber.embl.de
> 
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