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
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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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