Error confirmed. MCMC difference is not large enough (so OK)

USCbiostats · Sep 7, 2023 · cae6c88 · cae6c88
1 parent 86ee0ed
commit cae6c88
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diff --git 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
@@ -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)
           ),