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