To add to Henrik's comments, it is also worthwhile to recognize that
mclapply() does not deliver statistically sound random numbers even within
the apply "loop" unless you use RNGkind("L'Ecuyer-CMRG") which is not set
as default. This is because mclapply will initialize random streams with
differen
Agreed. And the BioC build system doesn’t even CHECK workflow packages, so
r75944 actually wouldn’t have an effect at all.
P.S. simpleSingleCell has successfully built on the BioC-devel with my custom
inter-vignette compilation set-up, so that’s a relief.
> On 7 Jan 2019, at 20:13, Pages, Herve
On Mon, Jan 7, 2019 at 4:09 AM Martin Morgan wrote:
>
> I hope for 1. to have a 'local socket' (i.e., not using ports) implementation
> shortly.
>
> I committed a patch in 1.17.6 for the wrong-seeming behavior of 2. We now have
>
> > library(BiocParallel)
> > set.seed(1); p = bpparam(); rnorm(1)
This changes the default for _R_CHECK_BUILD_VIGNETTES_SEPARATELY_ from
false to true so only affects the re-built of the vignettes during 'R
CMD check'. While this is a step in the right direction, it would be
good if 'R CMD build' was modified accordingly i.e. to also build
vignettes in separ
The main problem I’ve described refers to changes in the random seed due to the
MulticoreParam() constructor, prior to dispatch to workers. For the
related-but-separate problem of obtaining consistent random results within each
worker, we’ve been discussing the possible solutions on another Bioc
Hello all,
In the next 24-48 hrs we will be making updates to Bioconductor Support Site
found at https://support.bioconductor.org/. During this update the Support
site may experience intermittent downtime. We hope to keep this to a minimum
and appreciate your understanding.
Thank you
Lori
I don't know if this is helpful for BiocParallel, but there's an extension
for the foreach package that ensures reproducible RNG behavior for all
parallel backends: https://cran.r-project.org/web/packages/doRNG/index.html
Perhaps some of the principles from that package can be re-used?
On Mon, Ja
> I hope for 1. to have a 'local socket' (i.e., not using ports) implementation
> shortly.
Yes, that would be helpful.
> I committed a patch in 1.17.6 for the wrong-seeming behavior of 2. We now have
>
>> library(BiocParallel)
>> set.seed(1); p = bpparam(); rnorm(1)
> [1] -0.6264538
>> set.seed
I hope for 1. to have a 'local socket' (i.e., not using ports) implementation
shortly.
I committed a patch in 1.17.6 for the wrong-seeming behavior of 2. We now have
> library(BiocParallel)
> set.seed(1); p = bpparam(); rnorm(1)
[1] -0.6264538
> set.seed(1); p = bpparam(); rnorm(1)
[1] -0.626453
Hello.
I have a question regarding how to set qnameSuffixStart and qnamePrefixEnd to
be able to read paired reads from bam files:
Many .bam files I worked with have qnames in the format SAMPLENAME.READID.1 and
SAMPLENAME.READID.2 .
I was wondering how I can set qnameSuffixStart and qnamePre
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