Hi Ramon,
FWIW here's what I get when I run code chunk fdfmutex2 from the
OncoSimulR.Rmd vignette on kjohnson (Mac arm64):
> set.seed(1)
> s2fd <- oncoSimulIndiv(afe4,
+ muEF = mtfd,
+ model = "McFL",
+ onlyCancer = FALSE,
+ finalTime = 40,
+ mu = 1e-4,
+ initSize = 5000,
+ keepPhylog = TRUE,
+ seed = NULL,
+ errorHitMaxTries = FALSE,
+ errorHitWallTime = FALSE)
Using old version of fitnessEffects. Transforming fitnessEffects
to last version.
Using old version of fitnessEffects. Transforming fitnessEffects
to last version.
Using old version of fitnessEffects. Transforming fitnessEffects
to last version.
Using old version of fitnessEffects. Transforming fitnessEffects
to last version.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
> plot(s2fd, show = "genotypes")
Error in seq.int(0, 1, length.out = n) :
'length.out' must be a non-negative number
So it looks like the real error actually occurs in oncoSimulIndiv().
This function relies heavily on C++ code.
An orthogonal issue is that oncoSimulIndiv() shouldn't catch the error
like it does right now. Problem with this design is that the function
seems to return normally but the returned object is broken. Would be
better if the error was actually a hard one i.e. if the call to
oncoSimulIndiv() actually failed.
Cheers,
H.
On 04/10/2022 03:45, Ramon Diaz-Uriarte wrote:
Dear Vincent,
On Tue, 04-October-2022, at 11:40:11, Vincent Carey
<st...@channing.harvard.edu> wrote:
We are not running check on ARM platform at this time. If you want to provide
a link
to the
package/error you are having trouble with I will have a look on my machine.
Thanks a lot. This is the link:
https://bioconductor.org/checkResults/3.16/bioc-mac-arm64-LATEST/OncoSimulR/kjohnson-buildsrc.html
To try to figure it out, I split the suspected problematic section of the
vignette where things fail; the newest version of the package (as well as the
former one) passed checks in the other platforms.
Nevertheless, since not passing in this platform will have no consequences, I
would not like to bug you with this. Since there is no rush, I'll use
trial-and-error, preparing new versions as new check results become available.
Best,
R.
If you are
passing
on the other platforms there will be no consequences for remaining in the bioc
ecosystem.
On Tue, Oct 4, 2022 at 5:22 AM Ramon Diaz-Uriarte <rdia...@gmail.com> wrote:
Dear All,
It is unclear to me if the deadline of 28-October-2022 for "packages passing
‘‘R
CMD build’’ and ‘‘R CMD check’’ without errors or warnings"
(https://bioconductor.org/developers/release-schedule/) also applies to this
platform.
Why the question? I am trying to debug an error in this platform of a package
I
maintain but:
a) the snapshot date seems older than the snapshot date in
http://bioconductor.org/checkResults/devel/bioc-LATEST/ (which would
introduce a longer delay in verifying results of code changes)
b) results are not linked from the former page (which, I understand, is the
"canonical" one for checking status).
Thanks,
R.
On Tue, 27-September-2022, at 19:46:01, Jennifer Wokaty
<jennifer.wok...@sph.cuny.edu> wrote:
> Mac ARM64 binaries are now available. You can view the build report at
> https://bioconductor.org/checkResults/3.16/bioc-mac-arm64-LATEST/.
>
> To make use of these binaries
>
> * Install R-4.2.1-arm64.pkg from CRAN at
https://cran.r-project.org/bin/macosx/
> * Install BiocManager as usual
> * Use BiocManager::install() as usual
>
> Note: BiocManager::install() will automatically pick the new arm64 binaries
so
> you should no longer need Xcode.
>
>
> Jennifer Wokaty
> they/them
> Bioconductor Core Team
> CUNY SPH
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-31
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdia...@gmail.com
r.d...@uam.es
https://ligarto.org/rdiaz
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