Hi George @gvegayon,

I have something funky going on with mclapply function. Please refer to "create_lmer_fits.Rms" vignette file. Starting at line 70, When I apply boots.lmer function to just one bootstrap data set (the 100th bootstrap data out of 5000), I don't get any error. But when I apply boots.lmer to the first 100 bootstrap samples, I get error. The error says: 'Warning in parallel::mclapply(boots.samples.list, function(boots.dat) { :
  all scheduled cores encountered errors in user code'.
Could you please look into it? Thank you!

"UofUEpiBio/PHS7045-advanced-programming#13"

.gitignore

@@ -0,0 +1,4 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

boots.lmer.Rcheck/00_pkg_src/boots.lmer/DESCRIPTION

@@ -12,8 +12,8 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Suggests: knitr, rmarkdown
 VignetteBuilder: knitr
-Imports: data.table
+Depends: data.table, lme4, rlang, parallel, stringr
 NeedsCompilation: no
-Packaged: 2023-03-14 21:35:01 UTC; u1317537
+Packaged: 2023-03-14 22:14:56 UTC; u1317537
 Author: Hyejung Lee [aut, cre] (<https://orcid.org/0000-0002-5293-4134>)
 Maintainer: Hyejung Lee <[email protected]>

boots.lmer.Rcheck/00_pkg_src/boots.lmer/NAMESPACE

@@ -2,4 +2,3 @@
 
 export(boots.lmer)
 export(boots.samples)
-import(data.table)

boots.lmer.Rcheck/00_pkg_src/boots.lmer/R/boots.samples.R

@@ -14,7 +14,6 @@
 #'                         "subjects"=example.subject)
 #' output<-boots.samples(dat=example.dat,sub.id = "subjects",B=4) #create 4 bootstrap samples
 #' output[[1]] #This is the first one!
-#' @import data.table
 #' @export
 boots.samples<-function(dat, sub.id,B){
 
@@ -49,8 +48,10 @@ boots.samples<-function(dat, sub.id,B){
       #bind the index and no.repeat.id. as rows
       temp.dat<-do.call(rbind, lapply(temp, data.table::data.table))
       complete.dat<-data.table::as.data.table(dat[temp.dat$index,])
-      complete.dat[,no.repeat.sub.id:=(temp.dat$no.repeat.id)] # add the new subject ID column, with no repetition
-    }
+      # complete.dat[,no.repeat.sub.id:=(temp.dat$no.repeat.id)] # add the new subject ID column, with no repetition
+      complete.dat[,"no.repeat.sub.id"]<-temp.dat$no.repeat.id
+      return(complete.dat)
+      }
     )
 
   output

boots.lmer.Rcheck/00_pkg_src/boots.lmer/inst/doc/create_bootstrap_samples.html

@@ -149,7 +149,18 @@ <h1 class="title toc-ignore">create_bootstrap_samples</h1>
 
 
 
-<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(boots.lmer)</span></code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(boots.lmer)</span>
+<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Loading required package: data.table</span></span>
+<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Loading required package: lme4</span></span>
+<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Loading required package: Matrix</span></span>
+<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Loading required package: rlang</span></span>
+<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
+<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Attaching package: &#39;rlang&#39;</span></span>
+<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; The following object is masked from &#39;package:data.table&#39;:</span></span>
+<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
+<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     :=</span></span>
+<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Loading required package: parallel</span></span>
+<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Loading required package: stringr</span></span></code></pre></div>
 <p>This vignette contains a walk-through of <code>boots.lmer::boots.samples</code> function.</p>
 <p>The <code>boots.samples</code> function produces a list of bootstrap samples, made especially for longitudinal data. Longitudinal data formatted where multiple observations should be chosen cautiously when sampling for boostrap:</p>
 <ol style="list-style-type: decimal">