From c99a12f1ccb03b46264c536bc9ded5d5de9f85df Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sun, 16 Apr 2023 13:31:14 +0200 Subject: Make the template work on Windows (with RStudio) It seems that we cannot use stored DLLs (for pathway fits) on clusters when using Windows, where we use PSOCK clusters. Although it works on winbuilder in the tests in tests/testthat/test_compiled.R. Maybe it is something RStudio specific. --- .../templates/hierarchical_kinetics/skeleton/skeleton.Rmd | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) (limited to 'inst/rmarkdown/templates/hierarchical_kinetics/skeleton') diff --git a/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd index 71d62677..0baf866a 100644 --- a/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd +++ b/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd @@ -220,9 +220,13 @@ Separate evaluations of all datasets are performed with constant variance and using two-component error. ```{r path-1-sep, dependson = c("path-1-degmod", "ds")} -cl <- start_cluster(n_cores) +cl_path <- NULL +# Uncomment the next line for parallel processing. This does not work on Windows, +# as stored dlls (that we need for caching to work) do not seem to work on +# PSOCK clusters generated on Windows. +# cl_path <- start_cluster(n_cores) sforb_sep_const <- mmkin(list(sforb_path = m_sforb_sfo2), ds, - cluster = cl, quiet = TRUE) + cluster = cl_path, quiet = TRUE) sforb_sep_tc <- update(sforb_sep_const, error_model = "tc") ``` @@ -240,7 +244,7 @@ model that was identified for the parent degradation, are attempted below. path_1 <- mhmkin(list(sforb_sep_const, sforb_sep_tc), no_random_effect = c("lambda_free_0", "log_k_lambda_free_bound"), covariates = covariates, covariate_models = list(log_k_lambda_bound_free ~ pH), - cluster = cl) + cluster = cl_path) ``` ```{r dependson = "path-1"} @@ -294,7 +298,7 @@ endpoints(parent_best_pH_2) ``` ```{r} -stopCluster(cl) +if (!is.null(cl_path)) stopCluster(cl_path) ``` \clearpage -- cgit v1.2.1