Re: [Bioc-devel] Struggles with correct import .....

2013-12-03 Thread Martin Maechler
Kasper Daniel Hansen kasperdanielhan...@gmail.com on Wed, 20 Nov 2013 15:37:00 -0500 writes: Ok, I analyzed the package using codetoolsBioC and there were a number of missing imports, including what Leonardo has described. I have fixed those in bumphunter 1.3.3 Kasper

Re: [Bioc-devel] GenomicRanges: Storing 'seqlengths' as numeric

2013-12-03 Thread Martin Morgan
On 12/03/2013 02:29 AM, Julian Gehring wrote: Hi, Some of the chromosomes out in the world are fairly large (e.g. wheat chr 3B with 995 Mbp [1]). Currently, the 'seqlengths' of the reference sequence are stored as 'integers' which do not allow to store lengths of this size. Are there any

Re: [Bioc-devel] GenomicRanges: Storing 'seqlengths' as numeric

2013-12-03 Thread Hervé Pagès
Hi, Agreed with Martin that until someone comes up with a chromosome that is longer than .Machine$integer.max I don't see the need for switching to double or int64 to represent the seqlengths. Furthermore, since the seqlengths are used in many range operations like checking the validity of the

[Bioc-devel] Conflict between BiocStyle and the verbatim package

2013-12-03 Thread Nicolas Delhomme
Hej Martin! I’d like to have multi-line comments in my vignette and the easiest way I know is to use the “comment” environment from the verbatim package - i.e. \begin{comment}…\end{comment}. However, when I do this, i.e. load the verbatim package after having “sourced” the BiocStyle package,

Re: [Bioc-devel] Conflict between BiocStyle and the verbatim package

2013-12-03 Thread Martin Morgan
On 12/03/2013 12:30 PM, Nicolas Delhomme wrote: Hej Martin! I’d like to have multi-line comments in my vignette and the easiest way I know is to use the “comment” environment from the verbatim package - i.e. \begin{comment}…\end{comment}. However, when I do this, i.e. load the verbatim

Re: [Bioc-devel] Struggles with correct import .....

2013-12-03 Thread Kasper Daniel Hansen
It is super super super useful for NAMESPACE issues. I don't really use the other stuff. Kasper On Tue, Dec 3, 2013 at 11:34 AM, Dan Tenenbaum dtene...@fhcrc.org wrote: - Original Message - From: Martin Maechler maech...@stat.math.ethz.ch To: Kasper Daniel Hansen