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

[Wolfgang Huber]

Thanks Hervé!

This seems to take a long time to propagate. As of now, 
https://bioconductor.org/packages/devel/bioc/html/GenomicFeatures.html 
still shows 1.31.3.

( Btw, there's also an error in the build report which seems to come 
from a rather excessive-looking example in the makeTxDbFromBiomart man 
page - that maybe could better live in a vignette, not least for 
reducing brittleness? )

	Best wishes
		Wolfgang

30.1.18 19:00, Hervé Pagès scripsit:
> 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
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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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> 

-- 
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