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

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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-- 
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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