Hi Michael,
Thanks for your patience. Here is a self-contained example with comments
https://gist.github.com/PeteHaitch/fdb66d360446ff96ed4b
Thanks,
Pete
On 27/08/2014, at 1:43 AM, Michael Lawrence wrote:
> Do you have the code that actually fails? Then I could use it to reproduce
> the pro
Hi Leo,
So sorry for the late reply, I guess the problem is fixed already? I cannot
see the error anymore, and thanks for the discussion!
cheers
Tengfei
On Wed, Jul 16, 2014 at 2:39 PM, Leonardo Collado Torres
wrote:
> Hi Tengfei and BioC-devel,
>
> ggbio 1.13.11 fails to load due to recent
Hi Kristoffer,
On 08/26/2014 07:40 AM, Kristoffer Vitting-Seerup wrote:
The problem is best illustrated with an example (with comments in bold):
# Load libraries:
library('GenomicFeatures')
library("BSgenome.Hsapiens.UCSC.hg19�)
# Create two test transcripts, one on each strand
testTranscriptP
Gabe is still testing/profiling, but we'll send something randomized along
eventually.
On Tue, Aug 26, 2014 at 11:15 AM, Martin Morgan wrote:
> I didn't see in the original thread a reproducible (simulated, I guess)
> example, to be explicit about what the problem is??
>
> Martin
>
>
> On 08/26
Hi Karim,
- Original Message -
> From: "Karim Mezhoud"
> To: bioc-devel@r-project.org
> Sent: Tuesday, August 26, 2014 11:26:45 AM
> Subject: [Bioc-devel] built BioC packages using RStudio
>
> Dear All,
> I am trying to built for the first time a package. I am following
> this
> tutorial
Dear All,
I am trying to built for the first time a package. I am following this
tutorial:
https://support.rstudio.com/hc/en-us/articles/200486488-Developing-Packages-with-RStudio
I create a new Project (package) and I added 44 .R sources files
(functions).
After, I got error message when I built
I didn't see in the original thread a reproducible (simulated, I guess) example,
to be explicit about what the problem is??
Martin
On 08/26/2014 10:47 AM, Michael Lawrence wrote:
My understanding is that the heap optimization provided marginal gains, and
that we need to think harder about how
My understanding is that the heap optimization provided marginal gains, and
that we need to think harder about how to optimize the all of the string
manipulation in writeVcf. We either need to reduce it or reduce its
overhead (i.e., the CHARSXP allocation). Gabe is doing more tests.
On Tue, Aug 2
Hi Gabe,
Martin responded, and so did Michael,
https://stat.ethz.ch/pipermail/bioc-devel/2014-August/006082.html
It sounded like Michael was ok with working with/around heap
initialization.
Michael, is that right or should we still consider this on the table?
Val
On 08/26/2014 09:34 AM, G
Val,
Has there been any movement on this? This remains a substantial bottleneck
for us when writing very large VCF files (e.g. variants+genotypes for whole
genome NGS samples).
I was able to see a ~25% speedup with 4 cores and an "optimal" speedup of
~2x with 10-12 cores for a VCF with 500k rows
Do you have the code that actually fails? Then I could use it to reproduce
the problem and fix things.
Thanks,
Michael
On Tue, Aug 26, 2014 at 4:25 AM, Peter Hickey wrote:
> Hi Michael,
>
> Sorry for my misunderstanding. Here is some code describing the class
> https://github.com/PeteHaitch/Ge
The problem is best illustrated with an example (with comments in bold):
# Load libraries:
library('GenomicFeatures')
library("BSgenome.Hsapiens.UCSC.hg19�)
# Create two test transcripts, one on each strand
testTranscriptPlus <- GRanges(seqnames='chr1',
ranges=IRanges(start=1e5+c(1,11), end=1e5+
Hi Michael,
Sorry for my misunderstanding. Here is some code describing the class
https://github.com/PeteHaitch/GenomicTuples/blob/master/R/GTuples-class.R(the
package is not yet installable but hopefully the in-progress code shows you
what I'm trying to achieve).
The relevant slot is called "i
hi Dario,
Here's some example behavior of SummarizedExperiment (here in devel).
The renaming behavior is coming from GenomicRanges. Anyway I can't
avoid the duplication of memory in the case of a conflict of colnames
of the matrix and the rownames of colData, unless I internally
overwrite the row
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