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.hu...@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

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