Re: [Bioc-devel] biocLite malfunctioning? and mzR package not working on R 3.0.0?

2013-04-03 Thread Steffen Neumann
Hi, On Wed, 2013-04-03 at 13:15 +0200, Andreas Heider wrote: ... Besides this I was not able to install the mzR package correctly on both Mac OS X and Windows already some weeks ago. Was there some changes I am not aware about? On Windows where mzR comes as precompiled package, which requires

Re: [Bioc-devel] biocLite malfunctioning? and mzR package not working on R 3.0.0?

2013-04-03 Thread Andreas Heider
OK, but I am not able to install a single package right now. Can you confirm it works for you? Cheers, Andreas 2013/4/3 Steffen Neumann sneum...@ipb-halle.de Hi, On Wed, 2013-04-03 at 13:15 +0200, Andreas Heider wrote: ... Besides this I was not able to install the mzR package correctly

[Bioc-devel] GLX extension missing on petty

2013-04-03 Thread Jiří Hon
Hi, the latest bioc build of my new package 'triplex' on petty ended with this error message: Warning in rgl.init(initValue) : RGL: GLX extension missing on server Warning in fun(libname, pkgname) : error in rgl_init For full report see

Re: [Bioc-devel] RFC: IntervalTrees for GRanges objects

2013-04-03 Thread Michael Lawrence
Hi Hector, That's interesting, thanks for passing this along. I'm still wishing that somehow GRanges itself could abstract the way it stores ranges. I know that Herve/Patrick had some reasons for depending specifically on GRanges. One reason was probably convenience at the C level, but it

Re: [Bioc-devel] RFC: IntervalTrees for GRanges objects

2013-04-03 Thread Michael Lawrence
Some ideas: - Turn the IntervalTree into a list/array of nodes that can be subset/reordered with shallow copying (just copy the pointers to the nodes), and the index would be secondary. The index in the array could be stored in each node, for lookup during overlap queries. Right now, as far as I

[Bioc-devel] BioC 2.12 branch created

2013-04-03 Thread Dan Tenenbaum
The BioC 2.12 branch is now ready. Remember, you always have access to 2 versions of your package: the release and the devel versions. Right now the release version of your package (which is not officially released yet but will be in the next 72 hours if everything goes well) is in the 2.12