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
Hello BioC developers,
We will be creating the Bioconductor 2.12 branch today at 2:00 PM
Seattle time. (21:00 UTC).
Please stop all commits to trunk before 2:00PM and do not resume until
further notice.
We will send another email when it is OK to resume commits. The
process should not take more
On 2013-04-03 19:28, Kasper Daniel Hansen wrote:
Making IntervalTree chromosome would also be a great addition for organisms
with many sequences, like bee (due to an incomplete genome; 10,000s of
sequences). It does not matter for humans, but findOverlaps is
excruciatingly slow for bee's. I hav
Yes, we could use this offset-based approach. Though we would want to just
use the seqlengths for calculating the offsets, so that every query will be
compatible with the index. This would usually mean doubles, instead of
integers. The hash approach might be a tiny bit faster, as we wouldn't need
t
On 04/03/2013 10:28 AM, Kasper Daniel Hansen wrote:
Making IntervalTree chromosome would also be a great addition for organisms
with many sequences, like bee (due to an incomplete genome; 10,000s of
sequences). It does not matter for humans, but findOverlaps is
excruciatingly slow for bee's. I
This is a build system problem, and I am looking into it.
The build system runs under Xvfb, but I have no problem building your
package when logged into the console of petty.
Thank you a lot for your immediate reaction and please let me know if I
could help with anything.
Jirka
Dne Wed, 03
Making IntervalTree chromosome would also be a great addition for organisms
with many sequences, like bee (due to an incomplete genome; 10,000s of
sequences). It does not matter for humans, but findOverlaps is
excruciatingly slow for bee's. I have a couple of posts on this in the
archive.
I am p
Hi Jirka,
On Wed, Apr 3, 2013 at 9:06 AM, Jiří Hon wrote:
> 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 f
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 c
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 wouldn't
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
http://bioconductor.org/checkResults/devel/bioc-LATEST
Yep, I didn't comment on that, but I agree that abstracting how
GRanges stores ranges would make this more elegant. Right now
ranges(GRanges) is specified to be of IRanges class instead of the
abstract Ranges class.
If it were the latter then GIntervalTree can be a subclass of
GenomicRanges, in a
On Wed, Apr 3, 2013 at 7:15 AM, Andreas Heider
wrote:
> OK, but I am not able to install a single package right now. Can you
> confirm it works for you?
>
I assume you are on a Mac? You need a newer version of R 3.0.
Mac packages live in a different part of the CRAN-style repository
(bin/macosx/c
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
> 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
> >
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 requ
Dear bioc-devel mailing list,
I have problems installing packages lately. I used to source the "biocLite"
function from the web and install packages using this function. But
apperantly, this does not work anymore:
> source("http://bioconductor.org/biocLite.R";)
Bioconductor version 2.12 (BiocInsta
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