Merge pull request #543 from aloctavodia/test

Fix tests: set conditional parallel

Author: aloctavodia

vignettes/latent.Rmd

@@ -555,7 +555,12 @@ The message concerning `latent_ilink` can be safely ignored here (the internal d
 
 Run `cv_varsel()`:
 ```{r weibull_cvvs}
-doParallel::registerDoParallel(ncores)
+# For running projpred's CV in parallel (see cv_varsel()'s argument `parallel`):
+# Note: Parallel processing is disabled during package building to avoid issues
+use_parallel <- FALSE  # Set to TRUE for actual parallel processing
+if (use_parallel) {
+  doParallel::registerDoParallel(ncores)
+}
 cvvs_weib <- cv_varsel(
   refm_weib,
   ### Only for the sake of speed (not recommended in general):
@@ -564,13 +569,16 @@ cvvs_weib <- cv_varsel(
   nterms_max = 11,
   nclusters_pred = 20,
   ###
-  parallel = TRUE,
+  parallel = use_parallel,
   ### In interactive use, we recommend not to deactivate the verbose mode:
   verbose = 0
   ###
 )
-doParallel::stopImplicitCluster()
-foreach::registerDoSEQ()
+# Tear down the CV parallelization setup:
+if (use_parallel) {
+  doParallel::stopImplicitCluster()
+  foreach::registerDoSEQ()
+}
 ```
 In this case, we will ignore the warnings about high Pareto-$\hat{k}$ values because we chose quite rough settings (e.g., only 2 MCMC chains) in this vignette (for technical reasons).
 We will also ignore the warning that SIS is used (instead of PSIS) because this is due to `nclusters_pred = 20` which we used only to speed up the building of the vignette.
@@ -688,7 +696,12 @@ The message concerning `latent_ilink` can be safely ignored here (the internal d
 
 Run `cv_varsel()`:
 ```{r lognormal_cvvs}
-doParallel::registerDoParallel(ncores)
+# For running projpred's CV in parallel (see cv_varsel()'s argument `parallel`):
+# Note: Parallel processing is disabled during package building to avoid issues
+use_parallel <- FALSE  # Set to TRUE for actual parallel processing
+if (use_parallel) {
+  doParallel::registerDoParallel(ncores)
+}
 cvvs_lnorm <- cv_varsel(
   refm_lnorm,
   ### Only for the sake of speed (not recommended in general):
@@ -697,13 +710,16 @@ cvvs_lnorm <- cv_varsel(
   nterms_max = 11,
   nclusters_pred = 20,
   ###
-  parallel = TRUE,
+  parallel = use_parallel,
   ### In interactive use, we recommend not to deactivate the verbose mode:
   verbose = 0
   ###
 )
-doParallel::stopImplicitCluster()
-foreach::registerDoSEQ()
+# Tear down the CV parallelization setup:
+if (use_parallel) {
+  doParallel::stopImplicitCluster()
+  foreach::registerDoSEQ()
+}
 ```
 In this case, we will ignore the warnings about high Pareto-$\hat{k}$ values because we chose quite rough settings (e.g., only 2 MCMC chains) in this vignette (for technical reasons).
 We will also ignore the warning that SIS is used (instead of PSIS) because this is due to `nclusters_pred = 20` which we used only to speed up the building of the vignette.