Another attempt at addressing Debian NOTE

Author: graemeleehickey

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 0.4.7
+Date: 2025-01-14 02:18:38 UTC
+SHA: 17a1f29170c6dddf83f8daa57344c5cfc106673a

NAMESPACE

@@ -57,6 +57,7 @@ importFrom(mvtnorm,rmvt)
 importFrom(nlme,fixef)
 importFrom(nlme,getVarCov)
 importFrom(parallel,detectCores)
+importFrom(parallel,makeCluster)
 importFrom(randtoolbox,halton)
 importFrom(randtoolbox,sobol)
 importFrom(stats,sigma)

NEWS.md

@@ -24,7 +24,7 @@
 
 -   Add R-hub workflow to enable checks for platforms not covered already.
 
--   Vignettes now force `Sys.setenv("OMP_THREAD_LIMIT" = 2)` to get around CRAN CMD changes.
+-   Vignettes now force `Sys.setenv("OMP_THREAD_LIMIT" = 1)` and `options(Ncpus = 1)` in a bid to get around CRAN CMD changes.
 
 # joineRML 0.4.6
 

R/bootSE.R

@@ -61,7 +61,7 @@
 #'
 #' @return An object of class \code{bootSE}.
 #' @import foreach
-#' @importFrom parallel detectCores
+#' @importFrom parallel detectCores makeCluster
 #' @importFrom doParallel registerDoParallel
 #' @export
 #'
@@ -177,15 +177,15 @@ bootSE <- function(object, nboot = 100, ci = 0.95, use.mle = TRUE,
         ncores.max))
     }
     # *** Parallel version ***
-    doParallel::registerDoParallel(cores = ncores)
+    cl <- parallel::makeCluster(ncores)
+    doParallel::registerDoParallel(cl)
     out <- foreach(b = 1:nboot, .packages = 'joineRML') %dopar% {
       fit.boot <- bootfun()
       return(list("coefs" = fit.boot$coefficient,
                   "conv" = fit.boot$conv))
     }
     registerDoSEQ()
   } else {
-    doParallel::registerDoParallel(cores = ncores)
     # *** Serial version (incl. progress bar) ***
     out <- list()
     conv.status <- vector(length = nboot)

vignettes/joineRML-tidy.Rmd

@@ -14,7 +14,9 @@ editor_options:
 ```{r load-joineRML, include=FALSE}
 library(joineRML)
 library(knitr)
-Sys.setenv("OMP_THREAD_LIMIT" = 2)
+Sys.setenv("OMP_THREAD_LIMIT" = 1)
+Sys.setenv("OMP_NUM_THREADS" = 1)
+options(Ncpus = 1)
 ```
 
 # Introduction

vignettes/joineRML.Rmd

@@ -22,7 +22,9 @@ if (requireNamespace('joineR', quietly = TRUE)) {
   message("'joineR' not available")
 }
 
-Sys.setenv("OMP_THREAD_LIMIT" = 2)
+Sys.setenv("OMP_THREAD_LIMIT" = 1)
+Sys.setenv("OMP_NUM_THREADS" = 1)
+options(Ncpus = 1)
 ```
 
 # Introduction