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

2018-02-02 Thread Vincent Carey
It is important but not completely clear how to address. I think it has been written that bioc package checking should make minimal use of the internet, and most checking concerning manipulation of net-derived objects should use "mocks". One possible approach is to test with calls to the external

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

2018-02-02 Thread Wolfgang Huber
Thanks Mike and Hervé! Somehow, errors in examples that are caused by the state (or absence) of things on the internet should have a different status in my view than ones that reflect local state of R and packages - and distinguishing this could make maintenance of the package corpus & builds

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

2018-02-02 Thread Hervé Pagès
Hi Wolfgang, Mike, We didn't have a successful build of GenomicFeatures in devel for many days because of all kinds of problems with the examples that try to access the Ensembl marts. The latest of which being: https://support.bioconductor.org/p/105565/ (which also affects GenomicFeatures in

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

2018-02-02 Thread Mike Smith
The error TxDbFromBiomart looks like it might be related to a biomaRt change I made recently to submit queries using httr rather than RCurl. Others have reported something similar (e.g https://support.bioconductor.org/p/104502/) and I raised the timeout from 10 to 60 seconds. I guess with the old

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

2018-02-02 Thread 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 makeTxDbFromBio

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

2018-01-30 Thread Hervé Pagès
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

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

2018-01-26 Thread Kasper Daniel Hansen
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 wrote: > > > 26.1.18 14:59, Martin Morgan scripsit: > >> On 01/24/2018 03:38 PM, Wolfgang Huber wrote: >> >>> GenomicFeature

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

2018-01-26 Thread Wolfgang Huber
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 i

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

2018-01-26 Thread Hervé Pagès
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.ht

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

2018-01-26 Thread Tim Triche, Jr.
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 ins

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

2018-01-26 Thread Vincent Carey
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 pa

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

2018-01-26 Thread Martin Morgan
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-

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

2018-01-24 Thread Wolfgang Huber
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'