[Bioc-devel] Biostrings: XStringViews subsetting operator does not reduce element metadata

2013-02-21 Thread Jiří Hon
Hi, I found out, that XStringViews/Views subsetting operator does not reduce element metadata as I would expect. See the following example. It is reproducible in both stable (2.11) and development (2.12) versions of Bioconductor.

Re: [Bioc-devel] Section~\ref{sec:bla} idiom in vignettes

2013-02-21 Thread Dan Tenenbaum
Hi Wolfgang, Martin, On Sun, Feb 3, 2013 at 8:01 AM, Martin Morgan mtmor...@fhcrc.org wrote: On 02/03/2013 03:35 AM, Wolfgang Huber wrote: Hi, In LaTeX, I like to use the tilde in connection with equation or section references, e.g. Equation~(\ref{eq:bla}) or Section~\ref{sec:blo}, to make

Re: [Bioc-devel] Biostrings: XStringViews subsetting operator does not reduce element metadata

2013-02-21 Thread Hervé Pagès
Hi Jirka, Clearly a bug. Thanks for the catch! The regression was introduced a couple of years ago when the definition of the Views class was modified. Should be fixed in IRanges release (1.16.6) and devel (1.17.34). Both should become available via biocLite() in the next 24 hours or so. FWIW

Re: [Bioc-devel] Request to add 'normalize' to BiocGenerics

2013-02-21 Thread Hervé Pagès
Hi Laurent, Robert, and others, On 02/20/2013 01:33 PM, Laurent Gautier wrote: On 2013-02-20 22:02, Hervé Pagès wrote: Hi Robert, Nice to hear from you! I'm just a little bit worried that if we put normalize() in BiocGenerics without at the same time have a take it or leave it policy, then

Re: [Bioc-devel] Request to add 'normalize' to BiocGenerics

2013-02-21 Thread Wolfgang Huber
Hi Herve I have absolutely no objections against 'normalize' in BiocGenerics, I think it is a good idea. However, the concept of a 'universal namespace' and that no package can mask symbols defined in other packages I find objectionable. There is no 'redefining' of functions as you suggest