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

[Hervé Pagès]

Yep, moving RMySQL to Suggests makes sense. Will do. Also migrating to
RMariaDB is on the TODO list.

Note that the current problem of RMySQL being hard to install on Mac is
only because CRAN doesn't provide an RMySQL binary for R 3.5 yet:

   https://cran.r-project.org/web/packages/RMySQL/index.html

For the record, we had a similar situation one year ago when R 3.4 was
in development: CRAN started to build package binaries for Mac a few
weeks only before the release of R 3.4.0. Not ideal :-/

H.

On 01/26/2018 07:35 AM, Tim Triche, Jr. wrote:
> Moving it to Suggests: would certainly ease installation on clusters and
> such.
> 
> --t
> 
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_web_packages_RMySQL_index.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=fU7GJM0vRA454YjFLP8edDtDgyvICfjQmxPlT81V6vs&s=VnqaJPDwlPTUg8EwcI-uhm0UISQ6z5Cf7Ml5yb71KOI&e=
>>>
>>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__CRAN.R-2Dproject.org_package-3DRMariaDB&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=fU7GJM0vRA454YjFLP8edDtDgyvICfjQmxPlT81V6vs&s=ENePjXHv_uoxwPiSLsoj0K0M4yAzHXPCDLsnTpoURJ8&e=
>>
>> 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
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>>>
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>>
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-- 
Hervé Pagès

Program in Computational Biology
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