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
>>>
>>
>>
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>
> --
> 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
>
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