title: Stan_glmer object assignment error
body: <p>After waiting a week for three MC chains to run, the object was not
  saved, giving the error "Error: is.atomic(x) is not TRUE".  I have run
  this code or variants thereof many times, so it is probably not my
  syntax, but possibly something about the object size or an internal
  stan_glmer error?  Log is below and thank you for any help (also
  advice on how to save intermediate chains would be useful!)</p>
  
  <pre><code>stan.T.mod &lt;- stan_glmer(form2, iter=5000, warmup=5000, thin=1, 
    family = binomial(link = "logit"), prior = student_t(location=0, df = 1, scale = 2.5), 
    prior_intercept = student_t(location=0, df = 1, scale=2.5),
    prior_covariance = decov(shape = 10, scale = 1), 
    chains = 3, seed = 0305991, data=Tbinary.dt)
  </code></pre>
  
  <blockquote>
    <p>SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 1).</p>
    
    <p>Chain 1, Iteration:    1 / 5000 [  0%]  (Warmup) Chain 1, Iteration: 
    500 / 5000 [ 10%]  (Warmup) Chain 1, Iteration: 1000 / 5000 [ 20%] 
    (Warmup) Chain 1, Iteration: 1500 / 5000 [ 30%]  (Warmup) Chain 1,
    Iteration: 2000 / 5000 [ 40%]  (Warmup) Chain 1, Iteration: 2500 /
    5000 [ 50%]  (Warmup) Chain 1, Iteration: 3000 / 5000 [ 60%]  (Warmup)
    Chain 1, Iteration: 3500 / 5000 [ 70%]  (Warmup) Chain 1, Iteration:
    4000 / 5000 [ 80%]  (Warmup) Chain 1, Iteration: 4500 / 5000 [ 90%] 
    (Warmup) Chain 1, Iteration: 5000 / 5000 [100%]  (Warmup) Elapsed
    Time: 394305 seconds (Warm-up)
                   0 seconds (Sampling)
                   394305 seconds (Total)</p>
    
    <p>SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 2).</p>
    
    <p>Chain 2, Iteration:    1 / 5000 [  0%]  (Warmup) Chain 2, Iteration: 
    500 / 5000 [ 10%]  (Warmup) Chain 2, Iteration: 1000 / 5000 [ 20%] 
    (Warmup) Chain 2, Iteration: 1500 / 5000 [ 30%]  (Warmup) Chain 2,
    Iteration: 2000 / 5000 [ 40%]  (Warmup) Chain 2, Iteration: 2500 /
    5000 [ 50%]  (Warmup) Chain 2, Iteration: 3000 / 5000 [ 60%]  (Warmup)
    Chain 2, Iteration: 3500 / 5000 [ 70%]  (Warmup) Chain 2, Iteration:
    4000 / 5000 [ 80%]  (Warmup) Chain 2, Iteration: 4500 / 5000 [ 90%] 
    (Warmup) Chain 2, Iteration: 5000 / 5000 [100%]  (Warmup) Elapsed
    Time: 434251 seconds (Warm-up)
                   0 seconds (Sampling)
                   434251 seconds (Total)</p>
    
    <p>SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 3).</p>
    
    <p>Chain 3, Iteration:    1 / 5000 [  0%]  (Warmup) Chain 3, Iteration: 
    500 / 5000 [ 10%]  (Warmup) Chain 3, Iteration: 1000 / 5000 [ 20%] 
    (Warmup) Chain 3, Iteration: 1500 / 5000 [ 30%]  (Warmup) Chain 3,
    Iteration: 2000 / 5000 [ 40%]  (Warmup) Chain 3, Iteration: 2500 /
    5000 [ 50%]  (Warmup) Chain 3, Iteration: 3000 / 5000 [ 60%]  (Warmup)
    Chain 3, Iteration: 3500 / 5000 [ 70%]  (Warmup) Chain 3, Iteration:
    4000 / 5000 [ 80%]  (Warmup) Chain 3, Iteration: 4500 / 5000 [ 90%] 
    (Warmup) Chain 3, Iteration: 5000 / 5000 [100%]  (Warmup) Elapsed
    Time: 345070 seconds (Warm-up)
                   0 seconds (Sampling)
                   345070 seconds (Total)</p>
    
    <p>Error: is.atomic(x) is not TRUE</p>
  </blockquote>
  
  <pre><code>save(stan.T.mod, file=paste0(outpath, "stan.GCMfixedmods")); 
  </code></pre>
  
  <blockquote>
    <p>Error in save(stan.T.mod, file = paste0(outpath, "stan.GCMfixedmods")) :<br>
    object ‘stan.T.mod’ not found</p>
    
    <blockquote>
      <p>stan.T.mod Error: object 'stan.T.mod' not found</p>
    </blockquote>
  </blockquote>