From 543ff09754f18300508d505390f741391f314938 Mon Sep 17 00:00:00 2001
From: Nicholas Tierney <nicholas.tierney@gmail.com>
Date: Tue, 14 Dec 2021 14:56:19 +0800
Subject: [PATCH] attempting to remove the Collate field (it is not successful
 so far)

---
 DESCRIPTION   | 45 ---------------------------------------------
 R/aaa-.R      | 32 ++++++++++++++++++++++++++++++++
 R/inference.R | 10 ----------
 R/utils.R     | 24 ------------------------
 4 files changed, 32 insertions(+), 79 deletions(-)
 create mode 100644 R/aaa-.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 910cbc6e..49b0355c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -37,51 +37,6 @@ SystemRequirements: Python (>= 2.7.0) with header files and shared library;
 Encoding: UTF-8
 Depends:
     R (>= 3.1.0)
-Collate:
-    'package.R'
-    'utils.R'
-    'greta_mcmc_list.R'
-    'tf_functions.R'
-    'overloaded.R'
-    'node_class.R'
-    'node_types.R'
-    'variable.R'
-    'probability_distributions.R'
-    'mixture.R'
-    'joint.R'
-    'unknowns_class.R'
-    'greta_array_class.R'
-    'as_data.R'
-    'distribution.R'
-    'operators.R'
-    'functions.R'
-    'transforms.R'
-    'structures.R'
-    'extract_replace_combine.R'
-    'dag_class.R'
-    'greta_model_class.R'
-    'progress_bar.R'
-    'inference_class.R'
-    'samplers.R'
-    'optimisers.R'
-    'inference.R'
-    'install_tensorflow.R'
-    'calculate.R'
-    'callbacks.R'
-    'simulate.R'
-    'chol2symm.R'
-    'install_greta_deps.R'
-    'conda_greta_env.R'
-    'greta_stash.R'
-    'greta_create_conda_env.R'
-    'greta_install_miniconda.R'
-    'greta_install_python_deps.R'
-    'new_install_process.R'
-    'reinstallers.R'
-    'checkers.R'
-    'test_if_forked_cluster.R'
-    'zzz.R'
-    'internals.R'
 Imports:
     abind,
     callr,
diff --git a/R/aaa-.R b/R/aaa-.R
new file mode 100644
index 00000000..d799fa01
--- /dev/null
+++ b/R/aaa-.R
@@ -0,0 +1,32 @@
+# create an object stash in greta's namespace, to return traces to the user when
+# they abort a run
+greta_stash <- new.env()
+greta_stash$python_has_been_initialised <- FALSE
+greta_stash$numerical_messages <- c(
+  "is not invertible",
+  "Cholesky decomposition was not successful"
+)
+
+# create a named list
+module <- function(..., sort = TRUE) {
+  dots <- list(...)
+  names <- names(dots)
+
+  # guess names from call
+  cl <- match.call()
+  nm <- as.character(as.list(cl)[-1])
+
+  if (is.null(names)) {
+    names(dots) <- nm
+  } else {
+    blank_names <- names == ""
+    names[blank_names] <- nm[blank_names]
+    names(dots) <- names
+  }
+
+  if (sort) {
+    dots <- dots[order(names(dots))]
+  }
+
+  dots
+}
diff --git a/R/inference.R b/R/inference.R
index 39d97a7a..020ca5fb 100644
--- a/R/inference.R
+++ b/R/inference.R
@@ -4,16 +4,6 @@
 #'   MCMC or likelihood/posterior optimisation.
 NULL
 
-
-# create an object stash in greta's namespace, to return traces to the user when
-# they abort a run
-greta_stash <- new.env()
-greta_stash$python_has_been_initialised <- FALSE
-greta_stash$numerical_messages <- c(
-  "is not invertible",
-  "Cholesky decomposition was not successful"
-)
-
 #' @rdname inference
 #' @export
 #' @importFrom stats rnorm runif
diff --git a/R/utils.R b/R/utils.R
index 4d910b1e..2725b3ba 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -1,29 +1,5 @@
 # utility functions
 
-# create a named list
-module <- function(..., sort = TRUE) {
-  dots <- list(...)
-  names <- names(dots)
-
-  # guess names from call
-  cl <- match.call()
-  nm <- as.character(as.list(cl)[-1])
-
-  if (is.null(names)) {
-    names(dots) <- nm
-  } else {
-    blank_names <- names == ""
-    names[blank_names] <- nm[blank_names]
-    names(dots) <- names
-  }
-
-  if (sort) {
-    dots <- dots[order(names(dots))]
-  }
-
-  dots
-}
-
 # find out whether the usr has conda installed and visible
 #' @importFrom reticulate conda_binary
 have_conda <- function() {