On Fri, Jan 26, 2018 at 8:59 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote:
> 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: > I would vote for moving the relationship to Suggests. > > Martin > > >> With thanks in advance- >> Wolfgang >> >> ------- >> Wolfgang Huber >> Principal Investigator, EMBL Senior Scientist >> European Molecular Biology Laboratory (EMBL) >> Heidelberg, Germany >> >> wolfgang.hu...@embl.de >> http://www.huber.embl.de >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > > This email message may contain legally privileged and/or...{{dropped:2}} > > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
