From 801e0443416e37de448b5e1a77c50305e21d40fa Mon Sep 17 00:00:00 2001
From: "Matthew L. Fidler" <matthew.fidler@gmail.com>
Date: Thu, 6 Jun 2024 21:49:01 -0500
Subject: [PATCH 1/4] Add cran coments

---
 cran-comments.md | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 cran-comments.md

diff --git a/cran-comments.md b/cran-comments.md
new file mode 100644
index 000000000..e571507d3
--- /dev/null
+++ b/cran-comments.md
@@ -0,0 +1,5 @@
+- This works with the new rxode2 parse
+- This is more pendantic with the no-remap so that no-remap is everywhere :)
+- This moves the ignored steady state indicators to a allocated
+  integer so garbage collection will not cause gcc-USBAN alignment
+  errors

From b74c810e8a6e5b780750542cf9e4730ec0d57464 Mon Sep 17 00:00:00 2001
From: "Matthew L. Fidler" <matthew.fidler@gmail.com>
Date: Thu, 6 Jun 2024 21:49:58 -0500
Subject: [PATCH 2/4] Use dev version

---
 DESCRIPTION | 2 +-
 NEWS.md     | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 7e638a95c..ddf646493 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: rxode2
-Version: 2.1.3
+Version: 2.1.3.9000
 Title: Facilities for Simulating from ODE-Based Models
 Authors@R: c(
    person("Matthew L.","Fidler",
diff --git a/NEWS.md b/NEWS.md
index c8646c1e9..a725a4c8e 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,5 @@
+# rxode2 (development version)
+
 # rxode2 2.1.3
 
 ## Bug fixes

From 35b009e591134ac1159177834ab3754152e1081a Mon Sep 17 00:00:00 2001
From: "Matthew L. Fidler" <matthew.fidler@gmail.com>
Date: Thu, 6 Jun 2024 21:54:17 -0500
Subject: [PATCH 3/4] Add occ testing

---
 tests/testthat/test-occ.R | 65 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 65 insertions(+)

diff --git a/tests/testthat/test-occ.R b/tests/testthat/test-occ.R
index dd96823a2..2039cb0cc 100644
--- a/tests/testthat/test-occ.R
+++ b/tests/testthat/test-occ.R
@@ -289,4 +289,69 @@ rxTest({
 
       .en <- rxExpandNesting(mod, .ni)
   })
+
+  test_that("nesting test from https://github.com/nlmixr2/rxode2random/issues/25", {
+
+    mod <- rxode2({
+      TABS = TV_TABS * exp(eta.TABS + iov.TABS)
+      TR_Fbio = TV_TR_Fbio + eta.TR_Fbio + iov.TR_Fbio
+      CL = TV_CL * exp(eta.CL)
+      V1 = TV_V1 * exp(eta.V1)
+      V2 = TV_V2 * exp(eta.V2)
+      CLD = TV_CLD * exp(eta.CLD)
+      KA = log(2) / (TABS/60)
+      FBIO = 1 / (exp(-TR_Fbio) + 1)
+      DC1 = AMT1/V1
+      DC2 = AMT2/V2
+      d/dt(AMTa) =       -KA * AMTa
+      d/dt(AMT1) = FBIO * KA * AMTa - CLD * DC1 + CLD * DC2 - CL * DC1
+      d/dt(AMT2) =                  + CLD * DC1 - CLD * DC2
+      d/dt(AUC) = DC1
+    })
+
+    n <- 10
+
+    theta <- c("TV_TABS" = 45,
+              "TV_TR_Fbio" = logit(x = 0.85),
+              "TV_CL" = 10,
+              "TV_V1" = 10,
+              "TV_V2" = 65,
+              "TV_CLD" = 25)
+
+
+    omega <- lotri::lotri(
+      lotri::lotri(eta.TABS~0.25,
+                   eta.TR_Fbio~0.20,
+                   eta.CL~0.30,
+                   eta.V1~0.30,
+                   eta.V2~0.45,
+                   eta.CLD~0.15) | id(nu=n),
+      lotri::lotri(iov.TABS~0.15,
+                   iov.TR_Fbio~0.15) | occ(nu=n*2))
+
+    dosing <- et(amt=1000,
+                addl=6,
+                ii=24,
+                evid=1,
+                cmt="AMTa",
+                time=0) %>%
+      et(amt=1000,
+         addl=6,
+         ii=24,
+         evid=4,
+         cmt="AMTa",
+         time = 336) %>%
+      et(seq(0,168,0.5)) %>%
+      et(seq(336,672,0.5)) %>%
+      et(id=seq(1,n))
+
+    dosing <- mutate(dosing, occ = 1) %>%
+      mutate(occ = ifelse(time>=336,2,occ))
+
+    expect_error(rxSolve(object = mod,
+                             theta,
+                             omega=omega,
+                             ev=dosing,
+                             nDisplayProgress=100L), NA)
+  })
 })

From 4b8b7d872e84ec638cedc73b16593bbc77e3f0c8 Mon Sep 17 00:00:00 2001
From: "Matthew L. Fidler" <matthew.fidler@gmail.com>
Date: Thu, 6 Jun 2024 22:03:28 -0500
Subject: [PATCH 4/4] Call out dplyr package in testing

---
 tests/testthat/test-occ.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-occ.R b/tests/testthat/test-occ.R
index 2039cb0cc..b0ed113b4 100644
--- a/tests/testthat/test-occ.R
+++ b/tests/testthat/test-occ.R
@@ -345,8 +345,8 @@ rxTest({
       et(seq(336,672,0.5)) %>%
       et(id=seq(1,n))
 
-    dosing <- mutate(dosing, occ = 1) %>%
-      mutate(occ = ifelse(time>=336,2,occ))
+    dosing <- dplyr::mutate(dosing, occ = 1) %>%
+      dplyr::mutate(occ = ifelse(time>=336,2,occ))
 
     expect_error(rxSolve(object = mod,
                              theta,