Merge pull request #682 from nlmixr2/681-gcc-usban-fixes

681 gcc usban fixes

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

src/rxData.cpp

@@ -1330,6 +1330,7 @@ struct rx_globals {
   int *gsvar;
   int *govar;
   int *gsiV;
+  int *gsi;
   //
   int *slvr_counter;
   int *dadt_counter;
@@ -3448,8 +3449,9 @@ static inline void rxSolve_datSetupHmax(const RObject &obj, const List &rxContro
     CharacterVector dfNames = dataf.names();
     int dfN = dfNames.size();
     IntegerVector evid  = as<IntegerVector>(dataf[rxcEvid]);
+    IntegerVector si = as<IntegerVector>(rxSolveDat->mv[RxMv_state_ignore]);
     if (_globals.gevid != NULL) free(_globals.gevid);
-    _globals.gevid = (int*)calloc(3*evid.size()+dfN, sizeof(int));
+    _globals.gevid = (int*)calloc(3*evid.size()+dfN+si.size(), sizeof(int));
     if (_globals.gevid == NULL){
       rxSolveFree();
       stop(_("can not allocate enough memory to load 'evid'"));
@@ -3458,6 +3460,8 @@ static inline void rxSolve_datSetupHmax(const RObject &obj, const List &rxContro
     _globals.gidose = _globals.gevid + evid.size();
     _globals.gcens = _globals.gidose + evid.size();
     _globals.gpar_cov = _globals.gidose + evid.size();//[dfN];
+    _globals.gsi = _globals.gpar_cov + dfN;//[si.size()];
+    std::copy(si.begin(),si.end(), &_globals.gsi[0]);
 
     int ntot = 1;
 
@@ -4106,8 +4110,7 @@ List rxSolve_df(const RObject &obj,
       doDose = 0;
     }
   }
-  IntegerVector si = rxSolveDat->mv[RxMv_state_ignore];
-  rx->stateIgnore = &si[0];
+  rx->stateIgnore = _globals.gsi;
   int doTBS = (rx->matrix == 3);
   if (doTBS) rx->matrix=2;
   if (rx->matrix == 4 || rx->matrix == 5) rx->matrix=2;