As an alternative to Suggests, perhaps make a GenomicFeaturesBuildTools. Not sure if it is better or worse, just different
On Fri, Jan 26, 2018 at 2:39 PM, Wolfgang Huber <wolfgang.hu...@embl.de> wrote: > > > 26.1.18 14:59, Martin Morgan scripsit: > >> 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 >> > > I have no problems installing RMariaDB on MacOS (10.13.3) on an R-devel > from source, after installing mariadb-connector-c with homebrew. > > OTOH, I have not figured out a way to install RMySQL neither on my R-devel > from source (various complaints about missing .h files) nor on a binary R > 3.4.2 with the binary package download (complaints about missing system > libraries / wrong versions). > > Thanks and kind regards > Wolfgang > > 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.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 confidential >> information. If you are not the intended recipient(s), or the employee or >> agent responsible for the delivery of this message to the intended >> recipient(s), you are hereby notified that any disclosure, copying, >> distribution, or use of this email message is prohibited. If you have >> received this message in error, please notify the sender immediately by >> e-mail and delete this email message from your computer. Thank you. >> > > -- > 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel