in-place update of R extension spatial-7.3-14.tar.gz

[msukhanson]

The R 4.1 extension "spatial-7.3-14.tar.gz" has been changed and needs a new checksum 0c42df479c1a202dfc678f223e924b1adde5822a9902a3d71fd5f2ff36c4b83b applied to R-4.1.0-foss-2021a.eb.

I was able to change a local copy of the .eb, so the installation is ongoing. I have not tested the changes.

Kenny

[Micket]

Unfortunately a bunch of code changes this time, though it seems harmless enough (assuming it still actually builds):

Details

diff -ru spatial/DESCRIPTION spatial_new/DESCRIPTION
--- spatial/DESCRIPTION	2021-05-03 09:03:08.000000000 +0000
+++ spatial_new/DESCRIPTION	2023-01-23 07:10:14.000000000 +0000
@@ -1,7 +1,7 @@
 Package: spatial
 Priority: recommended
 Version: 7.3-14
-Date: 2021-04-17
+Date: 2023-01-23
 Depends: R (>= 3.0.0), graphics, stats, utils
 Suggests: MASS
 Authors@R: c(person("Brian", "Ripley", role = c("aut", "cre", "cph"),
@@ -15,10 +15,10 @@
 License: GPL-2 | GPL-3
 URL: http://www.stats.ox.ac.uk/pub/MASS4/
 NeedsCompilation: yes
-Packaged: 2021-05-03 08:31:23 UTC; ripley
+Packaged: 2023-01-23 06:55:04 UTC; ripley
 Author: Brian Ripley [aut, cre, cph],
   Roger Bivand [ctb],
   William Venables [cph]
 Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
 Repository: CRAN
-Date/Publication: 2021-05-03 09:03:08 UTC
+Date/Publication: 2023-01-23 07:10:14 UTC
diff -ru spatial/MD5 spatial_new/MD5
--- spatial/MD5	2021-05-03 09:03:08.000000000 +0000
+++ spatial_new/MD5	2023-01-23 07:10:14.000000000 +0000
@@ -1,4 +1,4 @@
-d91f6a5f05ebf19140902ba4d9eccc46 *DESCRIPTION
+bae80697c4707f36b0d52666e9a92c88 *DESCRIPTION
 9d3ab186ed88fca8f9806d8bb4a4fd56 *LICENCE.note
 9669a5ba859da001694e764789a4ce73 *NAMESPACE
 e917fff38af0195c39197a553712ebd5 *R/kr.R
@@ -65,7 +65,7 @@
 10c1ade8e7d014160bbf63b5b6793f0b *po/R-pl.po
 014071cd6f6328d8528a29eb7d4a3b6c *po/R-spatial.pot
 3951be1f52409800ec73d9786f1f1c25 *src/init.c
-0d8b51911ae2af1c97850551a14fb8dd *src/krc.c
-cb5dbb445d8c7f8150e6ef4216b18278 *src/pps.c
-df5b3ef820841dc1b4fa04fd07291e84 *src/spatial.h
+1c3d61d8127c14767e3b807448ce6819 *src/krc.c
+7915f2384c1510474cc6b72b7548d859 *src/pps.c
+7418be8b11ecd38cca04ed1424dfbc3a *src/spatial.h
 f756289c2e9a28b1f56db491dadd2f22 *tests/Examples/spatial-Ex.Rout.save
diff -ru spatial/src/krc.c spatial_new/src/krc.c
--- spatial/src/krc.c	2016-04-21 09:07:15.000000000 +0000
+++ spatial_new/src/krc.c	2022-05-29 09:00:47.000000000 +0000
@@ -1,5 +1,5 @@
 /*
- *  spatial/src/krc.c by W. N. Venables and B. D. Ripley  Copyright (C) 1994-2016
+ *  spatial/src/krc.c by W. N. Venables and B. D. Ripley  Copyright (C) 1994-2022
  *
  *  This program is free software; you can redistribute it and/or modify
  *  it under the terms of the GNU General Public License as published by
@@ -29,29 +29,29 @@
 /* defines  gls ls fmat frset alset valn pred prvar correlogram variogram */
 
 static void dscale(double, double, double *, double *);
-static void cholcov(double *, double *, double *, int, Sint *);
+static void cholcov(double *, double *, double *, int, int *);
 static void householder(double *, double *, double *, double *,
-			int, int, Sint *);
-static void chols(int, double *, double *, Sint *);
+			int, int, int *);
+static void chols(int, double *, double *, int *);
 static void solv(double *, double *, int, double *, double *);
 static void fsolv(double *, double *, int, double *);
 static void bsolv(double *, double *, int, double *);
 static void house_rhs(double *, double *, double *, int, int,
 		      double *, double *);
-static double val(double, double, double *, Sint *);
+static double val(double, double, double *, int *);
 
 static double *alph1 = NULL;
 static double xl1, xu1, yl1, yu1;
 
 void
-VR_alset(Sfloat *alph, Sint *nalph)
+VR_alset(double *alph, int *nalph)
 {
     int   i;
 
     if (alph1 != NULL)
-	alph1 = Realloc(alph1, *nalph, double);
+	alph1 = R_Realloc(alph1, *nalph, double);
     else
-	alph1 = Calloc(*nalph, double);
+	alph1 = R_Calloc(*nalph, double);
     for (i = 0; i < *nalph; ++i)
 	alph1[i] = alph[i];
 }
@@ -88,13 +88,13 @@
 }
 
 void
-VR_gls(double *x, double *y, double *z, Sint *n, Sint *np,
-       Sint *npar, double *f, double *l, double *r, double *bz,
-       double *wz, double *yy, double *w, Sint *ifail, double *l1f)
+VR_gls(double *x, double *y, double *z, int *n, int *np,
+       int *npar, double *f, double *l, double *r, double *bz,
+       double *wz, double *yy, double *w, int *ifail, double *l1f)
 {
     double b[28];
-    Sint  i, j;
-    Sint  i1;
+    int  i, j;
+    int  i1;
     double *w1, *w2;
     double *lf, *nu;
 
@@ -116,10 +116,10 @@
    of the covariance matrix */
 
 
-    lf = Calloc(*n * *npar, double);
-    nu = Calloc(*n * *npar, double);
-    w1 = Calloc(*n, double);
-    w2 = Calloc(*n, double);
+    lf = R_Calloc(*n * *npar, double);
+    nu = R_Calloc(*n * *npar, double);
+    w1 = R_Calloc(*n, double);
+    w2 = R_Calloc(*n, double);
     cholcov(x, y, l, *n, ifail);
     if (*ifail > 0)
 	return;
@@ -146,19 +146,19 @@
 	wz[i] = z[i] - val(x[i], y[i], bz, np);
     solv(yy, wz, *n, l, l);
     fsolv(w, wz, *n, l);
-    Free(lf);
-    Free(nu);
-    Free(w1);
-    Free(w2);
+    R_Free(lf);
+    R_Free(nu);
+    R_Free(w1);
+    R_Free(w2);
 }
 
 void
-VR_ls(double *x, double *y, double *z, Sint *n, Sint *np,
-      Sint *npar, double *f, double *r, double *bz, double *wz,
-      Sint *ifail)
+VR_ls(double *x, double *y, double *z, int *n, int *np,
+      int *npar, double *f, double *r, double *bz, double *wz,
+      int *ifail)
 {
     double b[28];
-    Sint  i, j, k;
+    int  i, j, k;
     double *fw, *nu;
 
 /*   Least squares estimation of parameters of spatial regression for
@@ -170,8 +170,8 @@
      i.e. the decomposition of F.
      Copy F matrix to FW for use in householder */
 
-    fw = Calloc(*n * *npar, double);
-    nu = Calloc(*n * *npar, double);
+    fw = R_Calloc(*n * *npar, double);
+    nu = R_Calloc(*n * *npar, double);
     k = 0;
     for (i = 1; i <= *npar; ++i)
 	for (j = 1; j <= *n; ++j) {
@@ -184,13 +184,13 @@
     house_rhs(nu, b, r, *n, *npar, z, bz);
     for (i = 0; i < *n; ++i)
 	wz[i] = z[i] - val(x[i], y[i], bz, np);
-    Free(fw);
-    Free(nu);
+    R_Free(fw);
+    R_Free(nu);
 }
 
 /* -------------------------------------------------------------------- */
 void
-VR_fmat(double *f, double *x, double *y, Sint *n, Sint *np)
+VR_fmat(double *f, double *x, double *y, int *n, int *np)
 {
     int   i, j, k, k1;
     double *xs, *ys;
@@ -198,8 +198,8 @@
 /*  FMAT evaluates the 'regression' matrix F (scaled to [-1,+1]x[-1,+1] to
     avoid excessively large or small values) */
 
-    xs = Calloc(*n, double);
-    ys = Calloc(*n, double);
+    xs = R_Calloc(*n, double);
+    ys = R_Calloc(*n, double);
     for (i = 0; i < *n; ++i)
 	dscale(x[i], y[i], &xs[i], &ys[i]);
     k1 = 0;
@@ -207,12 +207,12 @@
 	for (j = 0; j <= *np - i; ++j)
 	    for (k = 0; k < *n; ++k)
 		f[k1++] = powi(xs[k], j) * powi(ys[k], i);
-    Free(xs);
-    Free(ys);
+    R_Free(xs);
+    R_Free(ys);
 }
 
 static void
-cholcov(double *x, double *y, double *l, int n, Sint *ifail)
+cholcov(double *x, double *y, double *l, int n, int *ifail)
 {
     int   i, j;
     static double *w;
@@ -221,7 +221,7 @@
 
 /*   Finds the Cholesky factor of the covariance matrix */
 
-    w = Calloc(n * (n + 1) / 2, double);
+    w = R_Calloc(n * (n + 1) / 2, double);
     i1 = 0;
     for (i = 0; i < n; ++i)
 	for (j = 0; j <= i; ++j) {
@@ -231,7 +231,7 @@
 	}
     cov(n * (n + 1) / 2, w, 0);
     chols(n, w, l, ifail);
-    Free(w);
+    R_Free(w);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -239,7 +239,7 @@
 
 static void
 householder(double *f, double *nu, double *b, double *r, int n,
-	    int m, Sint *ifail)
+	    int m, int *ifail)
 {
     int   i, j, k;
     double c1, c2;
@@ -305,7 +305,7 @@
     in NU and B the same operations can be performed on any rhs vector Z to
     give least squares estimates beta. */
 
-    w = Calloc(n, double);
+    w = R_Calloc(n, double);
     for (i = 0; i < n; ++i)
 	w[i] = z[i];
     for (k = 0; k < m; ++k) {
@@ -318,11 +318,11 @@
 	    w[i] -= sum * nu[i + k1];
     }
     bsolv(beta, w, m, r);
-    Free(w);
+    R_Free(w);
 }
 
 static void
-chols(int n, double *a, double *l, Sint *ifail)
+chols(int n, double *a, double *l, int *ifail)
 {
     double eps = 1e-9;
 
@@ -435,14 +435,14 @@
 
 /*   Solves Ax = y where A = LU  */
 
-    w = Calloc(n, double);
+    w = R_Calloc(n, double);
     fsolv(w, y, n, l);
     bsolv(x, w, n, u);
-    Free(w);
+    R_Free(w);
 }
 
 void
-VR_frset(Sfloat *xl, Sfloat *xu, Sfloat *yl, Sfloat *yu)
+VR_frset(double *xl, double *xu, double *yl, double *yu)
 {
     xl1 = *xl;
     yl1 = *yl;
@@ -467,7 +467,7 @@
 /*   VARIANCE/COVARIANCE,PREDICTION AND STANDARD ERROR ROUTINES */
 
 static double
-val(double xp, double yp, double *beta, Sint *np)
+val(double xp, double yp, double *beta, int *np)
 {
     int   i, j, i1;
     double xs, ys, sum;
@@ -484,7 +484,7 @@
 }
 
 void
-VR_valn(double *z, double *x, double *y, Sint *n, double *beta, Sint *np)
+VR_valn(double *z, double *x, double *y, int *n, double *beta, int *np)
 {
     int   i, j, i1;
     int   it;
@@ -507,7 +507,7 @@
 
 void
 VR_krpred(double *z, double *xs, double *ys, double *x, double *y,
-	  Sint *npt, Sint *n, double *yy)
+	  int *npt, int *n, double *yy)
 {
     double *d;
     int   i;
@@ -518,7 +518,7 @@
 
 /*   Gives value of interpolator at the point (XP,YP) */
 
-    d = Calloc(*n, double);
+    d = R_Calloc(*n, double);
     for (it = 0; it < *npt; ++it) {
 	xp = xs[it];
 	yp = ys[it];
@@ -534,13 +534,13 @@
 	}
 	z[it] = sum;
     }
-    Free(d);
+    R_Free(d);
 }
 
 void
-VR_prvar(double *z, double *xp, double *yp, Sint *npt,
-	 double *x, double *y, double *l, double *r, Sint *n,
-	 Sint *np, Sint *npar, double *l1f)
+VR_prvar(double *z, double *xp, double *yp, int *npt,
+	 double *x, double *y, double *l, double *r, int *n,
+	 int *np, int *npar, double *l1f)
 {
     int   i, j, k, i1, k1, it;
 
@@ -550,8 +550,8 @@
 
 /*   Evaluates prediction variance at (XP,YP) */
 
-    w1 = Calloc(*n, double);
-    w2 = Calloc(*n, double);
+    w1 = R_Calloc(*n, double);
+    w2 = R_Calloc(*n, double);
     for (it = 0; it < *npt; ++it) {
 	for (i = 0; i < *n; ++i) {
 	    xd = x[i] - xp[it];
@@ -580,8 +580,8 @@
 	    sum += w2[i] * w2[i];
 	z[it] = sum1 + sum;
     }
-    Free(w1);
-    Free(w2);
+    R_Free(w1);
+    R_Free(w2);
 }
 
 
@@ -589,8 +589,8 @@
 /*  CORRELOGRAM AND VARIOGRAM ROUTINES */
 
 void
-VR_correlogram(Sfloat *xp, Sfloat *yp, Sint *nint, double *x,
-	       double *y, double *z, Sint *n, Sint *cnt)
+VR_correlogram(double *xp, double *yp, int *nint, double *x,
+	       double *y, double *z, int *n, int *cnt)
 {
     double xd, yd, d, sc, zb, xm, var, sum;
     int   i, j, i1, ibin;
@@ -602,8 +602,8 @@
    for the NINT intervals based on the NCP observations in each interval.
    XM defines the upper limit on the x axis. */
 
-    cp = Calloc(*nint + 1, double);
-    ncp = Calloc(*nint + 1, int);
+    cp = R_Calloc(*nint + 1, double);
+    ncp = R_Calloc(*nint + 1, int);
     zb = 0.0;
     for (i = 0; i < *n; ++i) {
 	zb += z[i];
@@ -650,13 +650,13 @@
 	}
     }
     *nint = i1;
-    Free(cp);
-    Free(ncp);
+    R_Free(cp);
+    R_Free(ncp);
 }
 
 void
-VR_variogram(Sfloat *xp, Sfloat *yp, Sint *nint, double *x,
-	     double *y, double *z, Sint *n, Sint *cnt)
+VR_variogram(double *xp, double  *yp, int *nint, double *x,
+	     double *y, double *z, int *n, int *cnt)
 {
     double xd, yd, d, sc, xm;
 
@@ -669,8 +669,8 @@
     in each interval.
  */
 
-    sv = Calloc(*nint + 1, double);
-    nsv = Calloc(*nint + 1, int);
+    sv = R_Calloc(*nint + 1, double);
+    nsv = R_Calloc(*nint + 1, int);
     for (i = 0; i < *nint; ++i) {
 	nsv[i] = 0;
 	sv[i] = 0.0;
@@ -706,6 +706,6 @@
 	}
     }
     *nint = i1;
-    Free(sv);
-    Free(nsv);
+    R_Free(sv);
+    R_Free(nsv);
 }
diff -ru spatial/src/pps.c spatial_new/src/pps.c
--- spatial/src/pps.c	2016-04-21 09:07:15.000000000 +0000
+++ spatial_new/src/pps.c	2022-05-29 09:00:35.000000000 +0000
@@ -32,7 +32,7 @@
 #  define min(a,b) ((a) < (b) ? (a) : (b))
 #endif
 
-static Sfloat xl0, yl0, xu0, yu0;
+static double xl0, yl0, xu0, yu0;
 
 
 static void
@@ -44,7 +44,7 @@
 
 
 void
-VR_ppset(Sfloat *area)
+VR_ppset(double *area)
 {
     xl0 = *area++;
     xu0 = *area++;
@@ -54,9 +54,9 @@
 }
 
 void
-VR_ppget(Sfloat *xx)
+VR_ppget(double *xx)
 {
-    Sfloat *z = xx;
+    double *z = xx;
 
     testinit();
     *z++ = xl0;
@@ -65,10 +65,10 @@
     *z++ = yu0;
 }
 
-static Sfloat
-edge(Sfloat x, Sfloat y, Sfloat a)
+static double
+edge(double x, double y, double a)
 {
-    Sfloat b, c, c1, c2, r[6], w;
+    double b, c, c1, c2, r[6], w;
     int   i;
 
     w = x - xl0;
@@ -99,11 +99,11 @@
 }
 
 void
-VR_sp_pp2(Sfloat *x, Sfloat *y, Sint *npt, Sint *k,
-	  Sfloat *h, Sfloat *dmin, Sfloat *lm, Sfloat *fs)
+VR_sp_pp2(double *x, double *y, int *npt, int *k,
+	  double *h, double *dmin, double *lm, double *fs)
 {
     int   n = *npt, kk = *k, k1, i, j, ib;
-    Sfloat ax, ay, xi, yi, sarea, g, dm, alm;
+    double ax, ay, xi, yi, sarea, g, dm, alm;
     double a, x1, y1, rr, fss = *fs, fs1, s1;
 
     testinit();
@@ -147,10 +147,10 @@
 }
 
 void
-VR_pdata(Sint *npt, Sfloat *x, Sfloat *y)
+VR_pdata(int *npt, double *x, double *y)
 {
     int   i;
-    Sfloat ax, ay;
+    double ax, ay;
 
     testinit();
     ax = xu0 - xl0;
@@ -165,11 +165,11 @@
 
 
 void
-VR_simpat(Sint *npt, Sfloat *x, Sfloat *y, Sfloat *c,
-	  Sfloat *r, Sint *init)
+VR_simpat(int *npt, double *x, double *y, double *c,
+	  double *r, int *init)
 {
     int   i, attempts = 0, id, j, mm, n = *npt;
-    Sfloat cc, rr, ax, ay, d, x1, y1, u;
+    double cc, rr, ax, ay, d, x1, y1, u;
 
     testinit();
     cc = *c;
@@ -209,10 +209,10 @@
 }
 
 void
-VR_simmat(Sint *npt, Sfloat *x, Sfloat *y, Sfloat *r)
+VR_simmat(int *npt, double *x, double *y, double *r)
 {
     int   i, icnt, attempts = 0, j, n = *npt;
-    Sfloat x1, y1, rr, ax, ay;
+    double x1, y1, rr, ax, ay;
 
     testinit();
     RANDIN;
@@ -242,10 +242,10 @@
 }
 
 void
-VR_plike(Sfloat *x, Sfloat *y, Sint *npt, Sfloat *c,
-	 Sfloat *r, Sint *ng, Sfloat *target, Sfloat *res)
+VR_plike(double *x, double *y, int *npt, double *c,
+	 double *r, int *ng, double *target, double *res)
 {
-    Sfloat ar, rr, suma = 0, sumb = 0, xi, yi, x1, y1, c1, cc = *c;
+    double ar, rr, suma = 0, sumb = 0, xi, yi, x1, y1, c1, cc = *c;
     int   ic, i1, i2, j, n = *npt, g = *ng;
 
     testinit();
diff -ru spatial/src/spatial.h spatial_new/src/spatial.h
--- spatial/src/spatial.h	2012-05-15 23:17:49.000000000 +0000
+++ spatial_new/src/spatial.h	2022-05-29 09:01:49.000000000 +0000
@@ -1,63 +1,63 @@
 void
-VR_alset(Sfloat *alph, Sint *nalph);
+VR_alset(double *alph, int *nalph);
 
 void
-VR_gls(double *x, double *y, double *z, Sint *n, Sint *np,
-       Sint *npar, double *f, double *l, double *r, double *bz,
-       double *wz, double *yy, double *w, Sint *ifail, double *l1f);
+VR_gls(double *x, double *y, double *z, int *n, int *np,
+       int *npar, double *f, double *l, double *r, double *bz,
+       double *wz, double *yy, double *w, int *ifail, double *l1f);
 
 void
-VR_ls(double *x, double *y, double *z, Sint *n, Sint *np,
-      Sint *npar, double *f, double *r, double *bz, double *wz,
-      Sint *ifail);
+VR_ls(double *x, double *y, double *z, int *n, int *np,
+      int *npar, double *f, double *r, double *bz, double *wz,
+      int *ifail);
 
 void
-VR_fmat(double *f, double *x, double *y, Sint *n, Sint *np);
+VR_fmat(double *f, double *x, double *y, int *n, int *np);
 
 void
-VR_frset(Sfloat *xl, Sfloat *xu, Sfloat *yl, Sfloat *yu);
+VR_frset(double *xl, double *xu, double *yl, double *yu);
 
 void
-VR_valn(double *z, double *x, double *y, Sint *n, double *beta, Sint *np);
+VR_valn(double *z, double *x, double *y, int *n, double *beta, int *np);
 
 void
 VR_krpred(double *z, double *xs, double *ys, double *x, double *y,
-	  Sint *npt, Sint *n, double *yy);
+	  int *npt, int *n, double *yy);
 
 void
-VR_prvar(double *z, double *xp, double *yp, Sint *npt,
-	 double *x, double *y, double *l, double *r, Sint *n,
-	 Sint *np, Sint *npar, double *l1f);
+VR_prvar(double *z, double *xp, double *yp, int *npt,
+	 double *x, double *y, double *l, double *r, int *n,
+	 int *np, int *npar, double *l1f);
 
 void
-VR_correlogram(Sfloat *xp, Sfloat *yp, Sint *nint, double *x,
-	       double *y, double *z, Sint *n, Sint *cnt);
+VR_correlogram(double *xp, double *yp, int *nint, double *x,
+	       double *y, double *z, int *n, int *cnt);
 
 void
-VR_variogram(Sfloat *xp, Sfloat *yp, Sint *nint, double *x,
-	     double *y, double *z, Sint *n, Sint *cnt);
+VR_variogram(double *xp, double *yp, int *nint, double *x,
+	     double *y, double *z, int *n, int *cnt);
 
 void
-VR_ppset(Sfloat *area);
+VR_ppset(double *area);
 
 void
-VR_ppget(Sfloat *xx);
+VR_ppget(double *xx);
 
 void
-VR_sp_pp2(Sfloat *x, Sfloat *y, Sint *npt, Sint *k,
-	  Sfloat *h, Sfloat *dmin, Sfloat *lm, Sfloat *fs);
+VR_sp_pp2(double *x, double *y, int *npt, int *k,
+	  double *h, double *dmin, double *lm, double *fs);
 
 void
-VR_pdata(Sint *npt, Sfloat *x, Sfloat *y);
+VR_pdata(int *npt, double *x, double *y);
 
 void
-VR_simpat(Sint *npt, Sfloat *x, Sfloat *y, Sfloat *c,
-	  Sfloat *r, Sint *init);
+VR_simpat(int *npt, double *x, double *y, double *c,
+	  double *r, int *init);
 
 void
-VR_simmat(Sint *npt, Sfloat *x, Sfloat *y, Sfloat *r);
+VR_simmat(int *npt, double *x, double *y, double *r);
 
 void
-VR_plike(Sfloat *x, Sfloat *y, Sint *npt, Sfloat *c,
-	 Sfloat *r, Sint *ng, Sfloat *target, Sfloat *res);
+VR_plike(double *x, double *y, int *npt, double *c,
+	 double *r, int *ng, double *target, double *res);
 

[boegel]

Since there's actual code changes, there's not much we can do other than fixing the checksum?

We should also reach out to the package authors and ask them WTF is going on here though, to at least point out to them that this is bad practice...

[boegel]

Although there are actual code changes, they actually look benign, basically just replacing the use of Sint with int, Sfloat with double, Realloc with R_Realloc, Calloc with R_Calloc, Free with R_Free, etc.
There are no functional changes from what I can tell.
So, we can just add an alternative checksum in this case...

[boegel]

While checking this, I noticed that the source tarball for spatial 7.3-13 and 7.3-15 was not changed, so this only affects spatial 7.3-14 included in R-4.1.0-foss-2021a.eb and R-4.1.2-foss-2021b.eb