update Calloc/Free to keep up with R-devel

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: ouch
 Type: Package
 Title: Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses
-Version: 2.17-1
-Date: 2021-08-20
+Version: 2.17-2
+Date: 2022-01-16
 Authors@R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="[email protected]"),
 	  person(given=c("Marguerite","A."),family="Butler",role=c("ctb")))
 Maintainer: Aaron A. King <[email protected]>
@@ -15,7 +15,7 @@ License: GPL-3
 LazyLoad: true
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1.9000
+RoxygenNote: 7.1.2
 BugReports: https://github.com/kingaa/ouch/issues/
 Encoding: UTF-8
 Collate: 

rules.mk

@@ -17,9 +17,9 @@ INSTALL = install
 PKG = $(shell perl -ne 'print $$1 if /Package:\s+((\w+[-\.]?)+)/;' DESCRIPTION)
 VERSION = $(shell perl -ne 'print $$1 if /Version:\s+((\d+[-\.]?)+)/;' DESCRIPTION)
 PKGVERS = $(PKG)_$(VERSION)
-SOURCE=$(wildcard R/*R src/*.c src/*.h data/*)
-CSOURCE=$(wildcard src/*.c)
-TESTS=$(wildcard tests/*R)
+SOURCE=$(sort $(wildcard R/*R src/*.c src/*.h data/*))
+CSOURCE=$(sort $(wildcard src/*.c))
+TESTS=$(sort $(wildcard tests/*R))
 
 default:
 	@echo $(PKGVERS)
@@ -69,7 +69,7 @@ session: install
 revdeps: install
 	mkdir -p library check
 	$(REXE) -e "pkgs <- strsplit('$(REVDEPS)',' ')[[1]]; download.packages(pkgs,destdir='library',repos='https://mirrors.nics.utk.edu/cran/')"
-	$(RCMD) check --library=library -o check library/*.tar.gz
+	$(RCMD) check --as-cran --library=library -o check library/*.tar.gz
 
 roxy: $(SOURCE) headers
 	$(REXE) -e "pkgbuild::compile_dll(); devtools::document(roclets=c('rd','collate','namespace'))"

src/covar-matrix.c

@@ -13,10 +13,10 @@ static void ouch_covar_matrix (int *nchar,
   double tmp;
   int n = *nchar, nt = *nterm;
   int i, j, k, l, r, s;
-  U = Calloc(n*n,double);
-  W = Calloc(n*n,double);
-  elti = Calloc(n,double);
-  eltj = Calloc(n,double);
+  U = R_Calloc(n*n,double);
+  W = R_Calloc(n*n,double);
+  elti = R_Calloc(n,double);
+  eltj = R_Calloc(n,double);
   for (i = 0; i < n; i++) {
     for (j = 0; j < n; j++) {
       U[i+j*n] = 0;
@@ -57,10 +57,10 @@ static void ouch_covar_matrix (int *nchar,
       }
     }
   }
-  Free(U);
-  Free(W);
-  Free(elti);
-  Free(eltj);
+  R_Free(U);
+  R_Free(W);
+  R_Free(elti);
+  R_Free(eltj);
 }
 
 SEXP ouch_covar (SEXP object, SEXP lambda, SEXP S, SEXP sigmasq) {

src/weight-matrix.c

@@ -5,7 +5,7 @@ static void ouch_weight_matrix (int *nchar, int *neps, double *epochs, double *l
   double t;
   int n = *nchar, np = *neps;
   int i, j, k, r;
-  elt = Calloc(np*n,double);
+  elt = R_Calloc(np*n,double);
   for (i = 0; i < np; i++) {
     t = epochs[0]-epochs[i];
     for (j = 0; j < n; j++) 
@@ -24,7 +24,7 @@ static void ouch_weight_matrix (int *nchar, int *neps, double *epochs, double *l
       }
     }
   }
-  Free(elt);
+  R_Free(elt);
 }
 
 SEXP ouch_weights (SEXP object, SEXP lambda, SEXP S, SEXP beta) {
@@ -40,7 +40,7 @@ SEXP ouch_weights (SEXP object, SEXP lambda, SEXP S, SEXP beta) {
   nt = INTEGER(nterm)[0];
   SET_STRING_ELT(nm,0,mkChar("epochs"));
   PROTECT(epochs = GET_SLOT(object,nm)); nprotect++;
-  nreg = Calloc(nchar,int);
+  nreg = R_Calloc(nchar,int);
   totreg = 0;
   for (i = 0; i < nchar; i++) {
     nreg[i] = INTEGER(GET_DIM(VECTOR_ELT(VECTOR_ELT(beta,0),i)))[1];
@@ -50,7 +50,7 @@ SEXP ouch_weights (SEXP object, SEXP lambda, SEXP S, SEXP beta) {
   PROTECT(W = makearray(2,xdim)); nprotect++;
   for (i = 0; i < nt; i++) {
     np = GET_LENGTH(VECTOR_ELT(epochs,i));
-    y = Calloc(nchar*nchar*np,double);
+    y = R_Calloc(nchar*nchar*np,double);
     ouch_weight_matrix(&nchar,&np,REAL(VECTOR_ELT(epochs,i)),REAL(lambda),REAL(S),y);
     for (n = 0, ptr = 0; n < nchar; ptr += nt*nchar*nreg[n++]) {
       wp = &(REAL(W))[ptr];
@@ -64,9 +64,9 @@ SEXP ouch_weights (SEXP object, SEXP lambda, SEXP S, SEXP beta) {
 	}
       }
     }
-    Free(y);
+    R_Free(y);
   }
-  Free(nreg);
+  R_Free(nreg);
   UNPROTECT(nprotect);
   return W;
 }