[Bioc-devel] benchdamic TIMEOUT in merida1 and kunpeng2

[Matteo Calgaro]

Dear Martin and Levi,
I truly appreciate your tips and the time you took to assist me. I'm going
to look further into your suggestions by trying to reduce the computational
time needed to build the vignette. I'll let you know if I manage to fix the
problem.

Matteo

Il giorno lun 17 lug 2023 alle ore 11:45 Levi Waldron <
lwaldron.research using gmail.com> ha scritto:

> It looks to me like benchdamic doesn't actually use the HMP16SData
> package, but a repackaged example dataset placed in the data/ directory. I
> do notice that the vignette takes very long to run, especially the chunks
> below. My guess is that you are seeing differences in speed or number of
> available cores on the build machines, one of which can't build the
> vignette within the 10-minute time limit (e.g. it takes more than 10
> minutes to build on my laptop). Can you reduce the number of rows or
> columns in your example dataset, or reduce permutations, to speed up the
> computation while still demonstrating how the package should be used?
>
> ```{r runMocks}
> bpparam <- BiocParallel::SerialParam()
> # Random grouping each time
> Stool_16S_mockDA <- runMocks(
>     mocks = my_mocks,
>     method_list = my_methods,
>     object = ps_stool_16S,
>     weights = zinbweights,
>     verbose = FALSE,
>     BPPARAM = bpparam)
> ```
>
> ```{r runSplits}
> # Set the parallel framework
> # Remember that ANCOMBC based methods are compatible only with
> SerialParam()
> bpparam <- BiocParallel::SerialParam()
>
> # Make sure the subject ID variable is a factor
> phyloseq::sample_data(ps_plaque_16S)[, "RSID"] <- as.factor(
>     phyloseq::sample_data(ps_plaque_16S)[["RSID"]])
>
> Plaque_16S_splitsDA <- runSplits(
>     split_list = my_splits,
>     method_list = my_methods_noWeights,
>     normalization_list = my_normalizations,
>     object = ps_plaque_16S,
>     min_counts = 0, min_samples = 2,
>     verbose = TRUE,
>     BPPARAM = bpparam)
> ```
>
> (returns lots of "Warning: Computed variance-covariance matrix problem:
> not a positive definite matrix (and positive semidefiniteness is not
> checked); returning NA matrixboundary (singular) fit: see
> help('isSingular')" warnings)
>
>
> --
>
> Levi Waldron
>
> Associate Professor
>
> Department of Epidemiology and Biostatistics
>
> CUNY Graduate School of Public Health and Health Policy
>
> Institute for Implementation Science in Population Health
>
> 55 W 125th St, New York NY 10035
>
> https://waldronlab.io
>
> Book a meeting with me
> <https://outlook.office365.com/owa/calendar/LeviWaldron@CUNY907.onmicrosoft.com/bookings/>
>
> Join the microbiome Virtual International Forum:
> https://microbiome-vif.org
>

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