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

[Wolfgang Huber]

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.huber at embl.de
>> http://www.huber.embl.de
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
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-- 
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