Re: [Bioc-devel] metadata() in BiocGenerics?

2014-04-17 Thread Hervé Pagès
Hi Vince, On 04/10/2014 08:16 AM, Vincent Carey wrote: seems like something we should use more routinely, and it was not straightforward for me to find it in IRanges I could do that but... Good object design would be that if a developer wants its class to support the metadata() getter and

[Bioc-devel] BiocUpgrades updates to devel instead of stable

2014-04-17 Thread Julian Gehring
Hi, When I run source(http://bioconductor.org/biocLite.R;) biocLite(BiocUpgrade) on a stable R-3.1.0 with bioc 2.14 already installed, bioc wants to upgrade to bioc 3.0 (devel): Bioconductor version 2.14 (BiocInstaller 1.14.1), ?biocLite for help Upgrade all packages to Bioconductor

Re: [Bioc-devel] BiocUpgrades updates to devel instead of stable

2014-04-17 Thread Steve Lianoglou
HI, On Thu, Apr 17, 2014 at 7:09 AM, Julian Gehring julian.gehr...@embl.de wrote: Hi, When I run source(http://bioconductor.org/biocLite.R;) biocLite(BiocUpgrade) on a stable R-3.1.0 with bioc 2.14 already installed, bioc wants to upgrade to bioc 3.0 (devel): Bioconductor version

[Bioc-devel] S4Vectors package

2014-04-17 Thread Hervé Pagès
Hi, The IRanges package is too big and hard to maintain (90 classes, 157 generics, 844 methods, 447 ordinary functions). I'm going to start moving its lowest level stuff to a new package called S4Vectors. The idea is to end up with 2 smaller and more focused packages that should be easier to

Re: [Bioc-devel] Apparent error in illuminaHumanv4.db

2014-04-17 Thread Taku Tokuyasu
Hi Jim, Thank you very much for the detailed response, that's very helpful. And apologies for the delayed response on my part. Cheers, _Taku On Thu, Mar 27, 2014 at 6:38 AM, James W. MacDonald jmac...@uw.edu wrote: Hi Taku, This 'error' is not due to anything in the illuminahumanv4.db