I tried to reproduce the commands reported by the build system. So on a fresh
git clone
$ cd /tmp
$ git clone g...@git.bioconductor.org:packages/trena
$ R -vanilla CMD build --keep-empty-dirs --no-resave-data trena
(the buld system doesn't use vanilla, but I have an ~/.Rprofile and maybe o
I get daily R CMD check failures visible at
https://master.bioconductor.org/checkResults/3.9/bioc-LATEST/trena/malbec2-checksrc.html
The recurring failure, which I cannot replicate on my own systems, is due to
this error:
test_.getScoredMotifs Warning in .seqlengths_TwoBitFile(x) : mustOpen:
Hi Nitesh,
I believe that I completed my email change everywhere where I needed
to including https://git.bioconductor.org/BiocCredentials/profile/
(which I didn't remember about, thanks!).
Best,
Leo
On Mon, May 20, 2019 at 9:15 PM Turaga, Nitesh
wrote:
>
> Hi Leo,
>
> If your old email is regis
I think the problem is that, even if the user were to set.seed(), it will have
different consequences depending on whether DelayedArray is already loaded, or
not yet loaded. DelayedArray gets loaded in some way that is not transparent to
the user, as a dependency-of-a-dependency-of-an annotation
Why don't you let this be under the user's control and not do this at all.
People should know that reproducibility of random numbers requires setting
the seed, but that is best done by the user and not a package author.
On Wed, May 22, 2019 at 9:30 AM Steffi Grote
wrote:
> Hi all,
>
> I tried to
Hi all,
I tried to circumvent the problem by adding an optional seed as parameter like
this:
my_fun = function(..., seed = NULL){
code that might change the RNG
if (!is.null(seed)){
set.seed(seed)
}
code that runs permutations
}
which solves the reproducibi
