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

[Vincent Carey]

On Fri, Jan 26, 2018 at 8:59 AM, Martin Morgan <
martin.morgan at 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.huber at embl.de
>> http://www.huber.embl.de
>>
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