Re: [Bioc-devel] ggbio 1.13.11 fails to load due to namespace change in IRanges

2014-08-26 Thread Tengfei Yin
Hi Leo, So sorry for the late reply, I guess the problem is fixed already? I cannot see the error anymore, and thanks for the discussion! cheers Tengfei On Wed, Jul 16, 2014 at 2:39 PM, Leonardo Collado Torres lcoll...@jhu.edu wrote: Hi Tengfei and BioC-devel, ggbio 1.13.11 fails to load

Re: [Bioc-devel] ggbio 1.13.11 fails to load due to namespace change in IRanges

2014-07-16 Thread Martin Morgan
On 07/16/2014 11:39 AM, Leonardo Collado Torres wrote: Hi Tengfei and BioC-devel, ggbio 1.13.11 fails to load due to recent changes in IRanges' namespace as shown further below. Basically, some of IRanges previous code now lives in S4Vectors. On a recent thread Hervé exposed his view on

Re: [Bioc-devel] ggbio 1.13.11 fails to load due to namespace change in IRanges

2014-07-16 Thread Michael Lawrence
I think it's a per-dependency judgement call. If you're making broad use of a package, then it makes sense to import(), but if the dependency on some package is minimal, it makes sense to specify symbols with importFrom(), as the link is more tenuous and there is less risk to things moving around.

Re: [Bioc-devel] ggbio 1.13.11 fails to load due to namespace change in IRanges

2014-07-16 Thread Hervé Pagès
Basically I agree with Stephanie, Martin, and Michael. I'm probably a little biased when I'm advocating the import all approach. I must also admit that I use a few selective imports in the packages I maintain, exactly in the situations you guys describe, that is, when I just need very few things