Error running the get started code in the Readme: In mclapply(X, function(...) { : all scheduled cores encountered errors in user code

[pcantalupo]

> scGEM_trained <- minibatchInfer(
+   X,
+   scGEM_init,
+   model_paras = list(b0 = 0.01,
+                      g1 = 5,
+                      g2 = 1,
+                      g3 = 1/3,
+                      g4 = 2/3),
+   max_est = 50,
+   subtree_size = c(1, 20),
+   batch_size = ncol(X),
+   n_epoch = 50,
+   learning_rate = 0.01
+ )
***************************
Epoch: 1/50
 [1/1], Step: 0.01
  |                                                                                                                    |   0%, ETA NA
Error: $ operator is invalid for atomic vectors
In addition: Warning message:
In mclapply(X, function(...) { :
  all scheduled cores encountered errors in user code

I'm running this on Linux (HTC at the University of Pittsburgh)

[hansolo-bioinfo]

Hi Paul, the current version does not support running on HTC (it might be due to one of the parallel packages that are used). I will fix this in next release. For now, it should work fine in MAC and lab server.

If the input number of cells is over than 5000, I suggest change batch_size = ncol(X) to batch_size = 1500 so that you can run in mini-batch mode.