[Bioc-devel] Mac ARM64 binaries available

[Hervé Pagès]

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 <stvjc using 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 <rdiaz02 using 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.Wokaty using 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 using 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: rdiaz02 using gmail.com
>>          r.diaz using uam.es
>>
>>   https://ligarto.org/rdiaz
>>   _______________________________________________
>>   Bioc-devel using r-project.org mailing list
>>   https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>> The information in this e-mail is intended only for t...{{dropped:13}}