Merge pull request #49 from mrc-ide/r-4.5.0

Update to work with R 4.5.0 new strict naming

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: eppasm
 Title: Age-structured EPP Model for HIV Epidemic Estimates
-Version: 0.8.3
+Version: 0.8.4
 Authors@R: person("Jeff", "Eaton", email = "[email protected]", role = c("aut", "cre"))
 Description: What the package does (one paragraph).
 Depends: R (>= 3.1.0),

NEWS.md

@@ -1,3 +1,8 @@
+## eppasm 0.8.4
+
+* Update to use full names for R internal functions in new 0.8 code e.g. `Rf_allocVector` instead of `allocVector`. Shorthand names are no longer allowed in R v4.5.0. See Nov 10th news https://developer.r-project.org/blosxom.cgi/R-devel
+
+
 ## eppasm 0.8.3
 
 * Implement Spectrum adult ART adjustment by absolute count. This is a user 

src/eppasm.cpp

@@ -349,29 +349,29 @@ extern "C" {
     multi_array_ref<double, 5> aidsdeaths_art(REAL(s_aidsdeaths_art), extents[PROJ_YEARS][NG][hAG][hDS][hTS]);
     memset(REAL(s_aidsdeaths_art), 0, Rf_length(s_aidsdeaths_art)*sizeof(double));
 
-    SEXP s_natdeaths_art = PROTECT(allocVector(REALSXP, hTS * hDS * hAG * NG * PROJ_YEARS));
-    SEXP s_natdeaths_art_dim = PROTECT(allocVector(INTSXP, 5));
+    SEXP s_natdeaths_art = PROTECT(Rf_allocVector(REALSXP, hTS * hDS * hAG * NG * PROJ_YEARS));
+    SEXP s_natdeaths_art_dim = PROTECT(Rf_allocVector(INTSXP, 5));
     INTEGER(s_natdeaths_art_dim)[0] = hTS;
     INTEGER(s_natdeaths_art_dim)[1] = hDS;
     INTEGER(s_natdeaths_art_dim)[2] = hAG;
     INTEGER(s_natdeaths_art_dim)[3] = NG;
     INTEGER(s_natdeaths_art_dim)[4] = PROJ_YEARS;
-    setAttrib(s_natdeaths_art, R_DimSymbol, s_natdeaths_art_dim);
-    setAttrib(s_pop, install("natdeaths_art"), s_natdeaths_art);
+    Rf_setAttrib(s_natdeaths_art, R_DimSymbol, s_natdeaths_art_dim);
+    Rf_setAttrib(s_pop, Rf_install("natdeaths_art"), s_natdeaths_art);
     multi_array_ref<double, 5> natdeaths_art(REAL(s_natdeaths_art), extents[PROJ_YEARS][NG][hAG][hDS][hTS]);
-    memset(REAL(s_natdeaths_art), 0, length(s_natdeaths_art)*sizeof(double));
+    memset(REAL(s_natdeaths_art), 0, Rf_length(s_natdeaths_art)*sizeof(double));
 
-    SEXP s_excessnonaidsdeaths_art = PROTECT(allocVector(REALSXP, hTS * hDS * hAG * NG * PROJ_YEARS));
-    SEXP s_excessnonaidsdeaths_art_dim = PROTECT(allocVector(INTSXP, 5));
+    SEXP s_excessnonaidsdeaths_art = PROTECT(Rf_allocVector(REALSXP, hTS * hDS * hAG * NG * PROJ_YEARS));
+    SEXP s_excessnonaidsdeaths_art_dim = PROTECT(Rf_allocVector(INTSXP, 5));
     INTEGER(s_excessnonaidsdeaths_art_dim)[0] = hTS;
     INTEGER(s_excessnonaidsdeaths_art_dim)[1] = hDS;
     INTEGER(s_excessnonaidsdeaths_art_dim)[2] = hAG;
     INTEGER(s_excessnonaidsdeaths_art_dim)[3] = NG;
     INTEGER(s_excessnonaidsdeaths_art_dim)[4] = PROJ_YEARS;
-    setAttrib(s_excessnonaidsdeaths_art, R_DimSymbol, s_excessnonaidsdeaths_art_dim);
-    setAttrib(s_pop, install("excessnonaidsdeaths_art"), s_excessnonaidsdeaths_art);
+    Rf_setAttrib(s_excessnonaidsdeaths_art, R_DimSymbol, s_excessnonaidsdeaths_art_dim);
+    Rf_setAttrib(s_pop, Rf_install("excessnonaidsdeaths_art"), s_excessnonaidsdeaths_art);
     multi_array_ref<double, 5> excessnonaidsdeaths_art(REAL(s_excessnonaidsdeaths_art), extents[PROJ_YEARS][NG][hAG][hDS][hTS]);
-    memset(REAL(s_excessnonaidsdeaths_art), 0, length(s_excessnonaidsdeaths_art)*sizeof(double));
+    memset(REAL(s_excessnonaidsdeaths_art), 0, Rf_length(s_excessnonaidsdeaths_art)*sizeof(double));
 
     SEXP s_popadjust = PROTECT(Rf_allocVector(REALSXP, pAG * NG * PROJ_YEARS));
     SEXP s_popadjust_dim = PROTECT(Rf_allocVector(INTSXP, 3));