From cae6c88591d76946fdd42708d71d7959ca8f6f28 Mon Sep 17 00:00:00 2001 From: "George G. Vega Yon" Date: Thu, 7 Sep 2023 10:26:17 -0600 Subject: [PATCH] Error confirmed. MCMC difference is not large enough (so OK) --- docker/Dockerfile.flexiblas | 10 ++++++---- inst/tinytest/test-parameter-estimates-and-formulas.r | 6 +++--- 2 files changed, 9 insertions(+), 7 deletions(-) diff --git a/docker/Dockerfile.flexiblas b/docker/Dockerfile.flexiblas index 8460b7d..c08c327 100644 --- a/docker/Dockerfile.flexiblas +++ b/docker/Dockerfile.flexiblas @@ -6,16 +6,18 @@ RUN dnf install R flexiblas-* -y # Clonning tag v3.3.1 from the repo flexiblas RUN dnf install R-flexiblas -y +RUN flexiblas default ATLAS + RUN echo 'options(repos=c(CRAN="https://cloud.r-project.org"))' >> ~/.Rprofile RUN \ - Rscript -e 'utils::install.packages(c("fmcmc", "MASS", "ape", "coda", "tinytest", "xml2"))' + Rscript -e 'utils::install.packages(c("fmcmc", "MASS", "ape", "coda", "tinytest", "xml2"));' -RUN Rscript -e 'utils::install.packages("lattice")' +RUN Rscript -e 'utils::install.packages("lattice");' -RUN Rscript -e 'utils::install.packages(c("knitr", "rmarkdown"))' +RUN Rscript -e 'utils::install.packages(c("knitr", "rmarkdown"));' -RUN Rscript -e 'utils::install.packages("AUC")' +RUN Rscript -e 'utils::install.packages("AUC");' RUN dnf install R-devtools -y diff --git a/inst/tinytest/test-parameter-estimates-and-formulas.r b/inst/tinytest/test-parameter-estimates-and-formulas.r index 4f9810d..9f78069 100644 --- a/inst/tinytest/test-parameter-estimates-and-formulas.r +++ b/inst/tinytest/test-parameter-estimates-and-formulas.r @@ -1,8 +1,8 @@ if (Sys.getenv("APHYLO_ATLAS_TEST") == "true") { library(flexiblas) - idx <- load_backend("ATLAS") + idx <- flexiblas_load_backend("ATLAS") flexiblas_switch(idx) - message("Using flexiblas with backend: ", flexiblas_backend()) + message("Using flexiblas with backend: ", flexiblas_current_backend()) } suppressMessages(library(coda)) @@ -119,7 +119,7 @@ suppressMessages(library(coda)) do.call( fmcmc::MCMC, c( list( - fun = fun, + fun = fun, initial = aphylo:::APHYLO_PARAM_DEFAULT[-c(7:8)], kernel = fmcmc::kernel_am(ub = .9999, lb = 0.001, freq = 1L) ),