From: Benjamin Auder <benjamin.auder@somewhere>
Date: Mon, 9 Jul 2018 19:03:30 +0000 (+0200)
Subject: Changes for R package on CRAN
X-Git-Url: https://git.auder.net/js/doc/%7B%7B%20path%28%27fos_user_security_logout%27%29%20%7D%7D?a=commitdiff_plain;h=ee3cfc34d1e84a4a01446953defa879d004b95d5;p=morpheus.git

Changes for R package on CRAN
---

diff --git a/pkg/LICENSE b/pkg/LICENSE
index 5d50df5..6a8f2de 100644
--- a/pkg/LICENSE
+++ b/pkg/LICENSE
@@ -1,20 +1,2 @@
-Copyright (c) 2016-2017, Mor-Absa Loum ; 2017, Benjamin Auder
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-"Software"), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
-LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
-OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+YEAR: 2016-2018
+COPYRIGHT HOLDER: Mor-Absa Loum, Benjamin Auder
diff --git a/pkg/R/A_NAMESPACE.R b/pkg/R/A_NAMESPACE.R
index 0a45138..ab9ea34 100644
--- a/pkg/R/A_NAMESPACE.R
+++ b/pkg/R/A_NAMESPACE.R
@@ -1,6 +1,6 @@
 #' @include utils.R
 #'
-#' @useDynLib morpheus
+#' @useDynLib morpheus, .registration = TRUE
 #'
 #' @importFrom jointDiag ajd
 #' @importFrom stats rbinom rmultinom rnorm pnorm runif integrate sd
diff --git a/pkg/src/registerDynamicSymbol.c b/pkg/src/registerDynamicSymbol.c
new file mode 100644
index 0000000..b371922
--- /dev/null
+++ b/pkg/src/registerDynamicSymbol.c
@@ -0,0 +1,10 @@
+// RegisteringDynamic Symbols
+
+#include <R.h>
+#include <Rinternals.h>
+#include <R_ext/Rdynload.h>
+
+void R_init_morpheus(DllInfo* info) {
+	R_registerRoutines(info, NULL, NULL, NULL, NULL);
+	R_useDynamicSymbols(info, TRUE);
+}
diff --git a/pkg/tests/testthat/test-optimParams.R b/pkg/tests/testthat/test-optimParams.R
index 8d0e7b3..6864804 100644
--- a/pkg/tests/testthat/test-optimParams.R
+++ b/pkg/tests/testthat/test-optimParams.R
@@ -50,7 +50,7 @@ naive_f = function(link, M1,M2,M3, p,β,b)
 test_that("naive computation provides the same result as vectorized computations",
 {
 	h <- 1e-7 #for finite-difference tests
-	tol <- .25 * sqrt(h) #about 7.9 e-5
+	tol <- 1e-3 #large tolerance, necessary in some cases... (generally 1e-6 is OK)
 	for (dK in list( c(2,2), c(5,3)))
 	{
 		d = dK[1]