Hi Martin and Herve,
thanks for the quick responses and the clarification.
It's not an issue now that I know this happens, and can just load DelayedArray
outside of the function.
Best,
Steffi
> On April 12, 2019 at 1:10 AM Martin Morgan wrote:
>
>
> That easy strategy wouldn't work, for inst
That easy strategy wouldn't work, for instance two successive calls to
MulticoreParam() would get the same port assigned, rather than the contract of
a 'random' port in a specific range; the port can be assigned by the
manager.port= argument if the user wants to avoid random assignment. I could
Hi Steffi,
Any code that gets called between your calls to set.seed() and runif()
could potentially use the random number generator. So the sequence
set.seed(123); runif(1) is only guaranteed to be deterministic if no
other code is called in between, or if the code called in between does
not u
This is actually from a dependency DelayedArray which, on load, calls
DelayedArray::setAutoBPPARAM, which calls BiocParallel::MulticoreParam(), which
uses the random number generator to select a random port for connection.
A different approach would be for DelayedArray to respect the user's
con
Dear Hervé,
thank you for your reply and the explanations. I have checked the R CMD
check on my system (MacOS Mojave) and the whole check does not exceed 1Gb
of RAM. I am also surprised why it would need that much, because all the
examples are pretty slim, so even if all objects are kept, I am won
Please ignore this ERROR for now. It is a known issue in VariantAnnotation and
we are working on the patch. You can ignore this for now.
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York
Hi,
I am puzzled by the current check failure of GWASTools on tokay (but not
any other platform). I have a unit test that writes a VCF file, which is
then read in using VariantAnnotation::readVcf. This is the header of the
VCF file:
##fileformat=VCFv4.1
##fileDate=2019-04-11
##source=GWASTools:
Dear Bioconductor,
We are deprecating part of a package. I am following the guidelines in
the "Function Deprecation Guidelines" page at bioconductor.org and I
have a few questions:
(i) Deprecating a S4 method which has the same name in another S4 class.
We have two DelayedArray backends. Fun
Hi all,
I found out that example code for my package GOfuncR yields a different result
the first time it's executed, despite setting a seed. All the following
executions are identical.
It turned out that loading the database package 'Homo.sapiens' changed the
random numbers:
set.seed(123)
runif
The package adds structural variant functionality on top of
VariantAnnotation. It's been pretty stable for the last 18 months and
getting more users so I thought it was time to bit the bullet and get it
into BioConductor. install_github() isn't the ideal distribution mechanism
for a package with so
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