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.

1 files changed, 8 insertions, 4 deletions

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