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.mor...@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.hu...@embl.de
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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