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

[Hervé Pagès]

This is done in GenomicFeatures 1.31.6.

Note that I also made a few changes to makeTxDbFromUCSC() to make it
a little bit faster (about 2x).

@Kasper: moving the makeTxDb* functions to a GenomicFeaturesBuildTools
or GenomicFeaturesForge package is maybe an idea to explore...

H.

On 01/26/2018 06:09 PM, Kasper Daniel Hansen wrote:
> 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.huber at 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://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=jUD3XGyxapAK8nfWvxbR_9Rz7RBxP592NO0nWz_wyr0&s=0neTB2BJghm4wF-LnEZ9V9sV_AbF1botcOeTb_bWk-w&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=jUD3XGyxapAK8nfWvxbR_9Rz7RBxP592NO0nWz_wyr0&s=55tLfrRpaigMug-pW7L1AhpsD1A830xw1f9d1FZEANo&e=
>>>
>>
>> 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
>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.huber.embl.de&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=jUD3XGyxapAK8nfWvxbR_9Rz7RBxP592NO0nWz_wyr0&s=Vp0j7sKJXiZSWHn3LVWSECRS-f-AFZZSSh0mq5rvJ-0&e=
>>>>
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>>>>
>>>
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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
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-- 
Hervé Pagès

Program in Computational Biology
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