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 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

[Bioc-devel] cannot git (the package Pi)

2018-02-02 Thread Hai Fang
Dear Lori, I have an issue accessing my package called ‘Pi’. Following the instruction detailed at http://bioconductor.org/developers/how-to/git/maintain-bioc-only/, I have submit my SSH public key (shown in red): $ cat ~/.ssh/id_dsa.pub ssh-dss

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